BANGLINE	CASE_MATCH	ENTITY_NAME	FULL_TEXT	GPL	GPL_NAME	GSE	GSE_NAME	GSM	GSM_NAME	PMID	REPO_FILE	SET	SORT	SOURCE	SOURCE_TEXT_CTRL	SRR	TERM_ID	TERM_NAME	TERM_TYPE	MAP
growth_protocol	MOPS rich medium		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770989	Ribosome profiling at 37°C in WT cells_1	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001737	MCO000003160	MOPS medium	Medium	True
growth_protocol	MOPS rich medium		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770991	Ribosome profiling 30 min after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001739	MCO000003160	MOPS medium	Medium	True
growth_protocol	MOPS rich medium		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770994	Ribosome profiling 4 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001742	MCO000003160	MOPS medium	Medium	True
growth_protocol	MOPS rich medium		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770995	Ribosome profiling 6 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001743	MCO000003160	MOPS medium	Medium	True
growth_protocol	MOPS rich medium		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770996	Ribosome profiling 5 min after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001744	MCO000003160	MOPS medium	Medium	True
growth_protocol	MOPS rich medium		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770997	Ribosome profiling 10 min after shift to 10°C in WT cells_2	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001745	MCO000003160	MOPS medium	Medium	True
growth_protocol	MOPS rich medium		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770998	Ribosome profiling 15 min after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001746	MCO000003160	MOPS medium	Medium	True
growth_protocol	MOPS rich medium		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770999	Ribosome profiling 8 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001747SRR6001748	MCO000003160	MOPS medium	Medium	True
growth_protocol	MOPS rich medium		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771000	Ribosome profiling 8 hr after shift to 10°C in ∆cspABEG cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001749SRR6001750	MCO000003160	MOPS medium	Medium	True
growth_protocol	MOPS rich medium		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771001	Ribosome profiling at 37°C in WT cells_2	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001751	MCO000003160	MOPS medium	Medium	True
growth_protocol	MOPS rich medium		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771002	Ribosome profiling at 37°C in ∆cspABCEG cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001752	MCO000003160	MOPS medium	Medium	True
growth_protocol	MOPS rich medium		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771008	mRNA-seq 4 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001758	MCO000003160	MOPS medium	Medium	True
growth_protocol	MOPS rich medium		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771010	mRNA-seq 8 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001760SRR6001761	MCO000003160	MOPS medium	Medium	True
growth_protocol	MOPS rich medium		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771011	mRNA-seq 8 hr after shift to 10°C in ∆cspABEG cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001762SRR6001763	MCO000003160	MOPS medium	Medium	True
growth_protocol	MOPS rich medium		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771014	DMS-seq 30 min after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001766	MCO000003160	MOPS medium	Medium	True
growth_protocol	MOPS rich medium		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771015	DMS-seq 6 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001769	MCO000003160	MOPS medium	Medium	True
growth_protocol	MOPS rich medium		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771016	DMS-seq 8 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001772	MCO000003160	MOPS medium	Medium	True
growth_protocol	MOPS rich medium		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771017	DMS-seq 8 hr after shift to 10°C in ∆cspABEG cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001773	MCO000003160	MOPS medium	Medium	True
growth_protocol	MOPS rich medium		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771018	DMS-seq 8 hr after shift to 10°C in ∆cspBG cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001774	MCO000003160	MOPS medium	Medium	True
growth_protocol	MOPS rich medium		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771019	Total RNA-seq 20 min after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001775	MCO000003160	MOPS medium	Medium	True
growth_protocol	MOPS rich medium		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771020	Total RNA-seq 4 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001776	MCO000003160	MOPS medium	Medium	True
growth_protocol	MOPS rich medium		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771021	Total RNA-seq 8 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001777	MCO000003160	MOPS medium	Medium	True
growth_protocol	MOPS rich medium		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771022	Total RNA-seq 20 min after shift to 10°C in ∆rnr cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001778	MCO000003160	MOPS medium	Medium	True
growth_protocol	MOPS rich medium		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771023	Total RNA-seq 4 hr after shift to 10°C in ∆rnr cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001779	MCO000003160	MOPS medium	Medium	True
growth_protocol	MOPS rich medium		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771024	Total RNA-seq 8 hr after shift to 10°C in ∆rnr cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001780	MCO000003160	MOPS medium	Medium	True
growth_protocol	MOPS rich medium		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771025	Total RNA-seq before rifampicin treatment -- 2 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001781	MCO000003160	MOPS medium	Medium	True
growth_protocol	MOPS rich medium		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771026	Total RNA-seq after rifampicin treatment -- 4 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001782	MCO000003160	MOPS medium	Medium	True
growth_protocol	MOPS rich medium		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771027	Total RNA-seq before rifampicin treatment -- 2 hr after shift to 10°C in ∆rnr cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001783	MCO000003160	MOPS medium	Medium	True
growth_protocol	MOPS rich medium		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771028	Total RNA-seq after rifampicin treatment -- 4 hr after shift to 10°C in ∆rnr cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001784	MCO000003160	MOPS medium	Medium	True
growth_protocol	glucose 0.2%		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770989	Ribosome profiling at 37°C in WT cells_1	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001737	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770991	Ribosome profiling 30 min after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001739	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770994	Ribosome profiling 4 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001742	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770995	Ribosome profiling 6 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001743	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770996	Ribosome profiling 5 min after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001744	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770997	Ribosome profiling 10 min after shift to 10°C in WT cells_2	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001745	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770998	Ribosome profiling 15 min after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001746	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770999	Ribosome profiling 8 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001747SRR6001748	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771000	Ribosome profiling 8 hr after shift to 10°C in ∆cspABEG cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001749SRR6001750	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771001	Ribosome profiling at 37°C in WT cells_2	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001751	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771002	Ribosome profiling at 37°C in ∆cspABCEG cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001752	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771008	mRNA-seq 4 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001758	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771010	mRNA-seq 8 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001760SRR6001761	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771011	mRNA-seq 8 hr after shift to 10°C in ∆cspABEG cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001762SRR6001763	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771014	DMS-seq 30 min after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001766	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771015	DMS-seq 6 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001769	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771016	DMS-seq 8 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001772	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771017	DMS-seq 8 hr after shift to 10°C in ∆cspABEG cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001773	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771018	DMS-seq 8 hr after shift to 10°C in ∆cspBG cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001774	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771019	Total RNA-seq 20 min after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001775	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771020	Total RNA-seq 4 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001776	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771021	Total RNA-seq 8 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001777	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771022	Total RNA-seq 20 min after shift to 10°C in ∆rnr cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001778	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771023	Total RNA-seq 4 hr after shift to 10°C in ∆rnr cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001779	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771024	Total RNA-seq 8 hr after shift to 10°C in ∆rnr cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001780	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771025	Total RNA-seq before rifampicin treatment -- 2 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001781	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771026	Total RNA-seq after rifampicin treatment -- 4 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001782	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771027	Total RNA-seq before rifampicin treatment -- 2 hr after shift to 10°C in ∆rnr cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001783	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771028	Total RNA-seq after rifampicin treatment -- 4 hr after shift to 10°C in ∆rnr cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001784	MCO000002770	0.2 % glucose	Medium supplement	True
characteristics	glucose 0.2%		media : <Med> M9 minimal media </Med> w / <Supp> 0.2 % glucose </Supp> and 10mM glutamate 	GPL17024-GPL17439-GPL18995-GPL25769	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	GSE122211	Expression profiling of E. coli K-12 MG1655	GSM3461164	MG_glu_1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 0.2% glucose and 10mM glutamate PGCGROWTHCONDITIONS	SRR8164484	MCO000002770	0.2 % glucose	Medium supplement	True
characteristics	glucose 0.2%		media : <Med> M9 minimal media </Med> w / <Supp> 0.2 % glucose </Supp> and 10mM glutamate 	GPL17024-GPL17439-GPL18995-GPL25769	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	GSE122211	Expression profiling of E. coli K-12 MG1655	GSM3461165	MG_glu_2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 0.2% glucose and 10mM glutamate PGCGROWTHCONDITIONS	SRR8164485	MCO000002770	0.2 % glucose	Medium supplement	True
characteristics	glucose 0.2%		media : <Med> M9 minimal media </Med> w / <Supp> 0.2 % glucose </Supp> 	GPL17024-GPL17439-GPL18995-GPL25769	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	GSE122211	Expression profiling of E. coli K-12 MG1655	GSM3461166	MG_glc	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 0.2% glucose PGCGROWTHCONDITIONS	SRR8164486	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K12 MG1655 was grown to <Phase> mid-log phase </Phase> ( <OD> O.D. 600nm 0.5 </OD> ) or to stationary phase ( <OD> O.D. 600nm 1.5 </OD> ) <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> or <Med> W2 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> and 0.2 % glutamine . For heatshock conditions , cells were grown to mid-log phase and incubated at 42oC for 10 min . 	GPL17137	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	GSE46737	Genome-scale reconstruction of the sigma factor network in E. coli	GSM1137316	E. coli stationary 1	24461193	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE46737/GSE46737.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 MG1655 was grown to mid-log phase (O.D.600nm 0.5) or to stationary phase (O.D.600nm 1.5) aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose or W2 minimal media supplemented with 0.2% glucose and 0.2% glutamine. For heatshock conditions, cells were grown to mid-log phase and incubated at 42oC for 10 min. PGCGROWTHCONDITIONS	SRR847728	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K12 MG1655 was grown to <Phase> mid-log phase </Phase> ( <OD> O.D. 600nm 0.5 </OD> ) or to stationary phase ( <OD> O.D. 600nm 1.5 </OD> ) <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> or <Med> W2 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> and 0.2 % glutamine . For heatshock conditions , cells were grown to mid-log phase and incubated at 42oC for 10 min . 	GPL17137	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	GSE46737	Genome-scale reconstruction of the sigma factor network in E. coli	GSM1137318	E. coli glutamine 1	24461193	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE46737/GSE46737.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 MG1655 was grown to mid-log phase (O.D.600nm 0.5) or to stationary phase (O.D.600nm 1.5) aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose or W2 minimal media supplemented with 0.2% glucose and 0.2% glutamine. For heatshock conditions, cells were grown to mid-log phase and incubated at 42oC for 10 min. PGCGROWTHCONDITIONS	SRR847730	MCO000002770	0.2 % glucose	Medium supplement	True
source_name	glucose 0.2%		Cells at mid-log phase ( OD600nm 0.5 ) in W2 media supplemented with <Supp> 0.2 % glucose </Supp> and <Supp> 0.2 % glutamine </Supp> 	GPL17137	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	GSE46737	Genome-scale reconstruction of the sigma factor network in E. coli	GSM1137318	E. coli glutamine 1	24461193	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE46737/GSE46737.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells at mid-log phase (OD600nm 0.5) in W2 media supplemented with 0.2% glucose and 0.2% glutamine PGCGROWTHCONDITIONS	SRR847730	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K12 MG1655 was grown to <Phase> mid-log phase </Phase> ( <OD> O.D. 600nm 0.5 </OD> ) or to stationary phase ( <OD> O.D. 600nm 1.5 </OD> ) <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> or <Med> W2 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> and 0.2 % glutamine . For heatshock conditions , cells were grown to mid-log phase and incubated at 42oC for 10 min . 	GPL17137	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	GSE46737	Genome-scale reconstruction of the sigma factor network in E. coli	GSM1137319	E. coli glutamine 2	24461193	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE46737/GSE46737.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 MG1655 was grown to mid-log phase (O.D.600nm 0.5) or to stationary phase (O.D.600nm 1.5) aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose or W2 minimal media supplemented with 0.2% glucose and 0.2% glutamine. For heatshock conditions, cells were grown to mid-log phase and incubated at 42oC for 10 min. PGCGROWTHCONDITIONS	SRR847731	MCO000002770	0.2 % glucose	Medium supplement	True
source_name	glucose 0.2%		Cells at mid-log phase ( OD600nm 0.5 ) in W2 media supplemented with <Supp> 0.2 % glucose </Supp> and <Supp> 0.2 % glutamine </Supp> 	GPL17137	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	GSE46737	Genome-scale reconstruction of the sigma factor network in E. coli	GSM1137319	E. coli glutamine 2	24461193	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE46737/GSE46737.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells at mid-log phase (OD600nm 0.5) in W2 media supplemented with 0.2% glucose and 0.2% glutamine PGCGROWTHCONDITIONS	SRR847731	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K12 MG1655 was grown to <Phase> mid-log phase </Phase> ( <OD> O.D. 600nm 0.5 </OD> ) or to stationary phase ( <OD> O.D. 600nm 1.5 </OD> ) <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> or <Med> W2 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> and 0.2 % glutamine . For heatshock conditions , cells were grown to mid-log phase and incubated at 42oC for 10 min . 	GPL17137	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	GSE46737	Genome-scale reconstruction of the sigma factor network in E. coli	GSM1137320	E. coli heatshock 1	24461193	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE46737/GSE46737.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 MG1655 was grown to mid-log phase (O.D.600nm 0.5) or to stationary phase (O.D.600nm 1.5) aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose or W2 minimal media supplemented with 0.2% glucose and 0.2% glutamine. For heatshock conditions, cells were grown to mid-log phase and incubated at 42oC for 10 min. PGCGROWTHCONDITIONS	SRR847732	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K12 MG1655 was grown to <Phase> mid-log phase </Phase> ( <OD> O.D. 600nm 0.5 </OD> ) or to stationary phase ( <OD> O.D. 600nm 1.5 </OD> ) <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> or <Med> W2 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> and 0.2 % glutamine . For heatshock conditions , cells were grown to mid-log phase and incubated at 42oC for 10 min . 	GPL17137	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	GSE46737	Genome-scale reconstruction of the sigma factor network in E. coli	GSM1137321	E. coli heatshock 2	24461193	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE46737/GSE46737.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 MG1655 was grown to mid-log phase (O.D.600nm 0.5) or to stationary phase (O.D.600nm 1.5) aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose or W2 minimal media supplemented with 0.2% glucose and 0.2% glutamine. For heatshock conditions, cells were grown to mid-log phase and incubated at 42oC for 10 min. PGCGROWTHCONDITIONS	SRR847733	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		All cultures were based on MOPS media with <Supp> 0.2 % glucose </Supp> ( Teknova ) , with either full supplement ( Neidhardt et al. , 1974 ) . An overnight liquid culture was diluted 400-fold into 200 ml <Med> fresh media </Med> . The culture was kept in a 2.8-liter flask at 37C with aeration ( 180 rpm ) until OD600 reached 0.3 . 	GPL14548-GPL18133	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE53767	Absolute quantification of protein production reveals principles underlying protein synthesis rates	GSM1300282	mRNA-seq in rich defined media	24766808	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE53767/GSE53767.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All cultures were based on MOPS media with 0.2% glucose (Teknova), with either full supplement (Neidhardt et al., 1974). An overnight liquid culture was diluted 400-fold into 200 ml fresh media. The culture was kept in a 2.8-liter flask at 37C with aeration (180 rpm) until OD600 reached 0.3. PGCGROWTHCONDITIONS	SRR1067773SRR1067774	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT and Δfur were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . For iron treated cells , 0.1 mM of FeCl2 were treated from the beginning of culture , and for DPD treated cells , <Supp> 0.2 mM of DPD </Supp> were added at early-log phase and continued to culture for additional <Supp> 2h </Supp> . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE54900	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GSM1326347	WT with Fe 1 (RNA-seq)	25222563	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT and Δfur were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. PGCGROWTHCONDITIONS	SRR1168133	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT and Δfur were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . For iron treated cells , 0.1 mM of FeCl2 were treated from the beginning of culture , and for DPD treated cells , <Supp> 0.2 mM of DPD </Supp> were added at early-log phase and continued to culture for additional <Supp> 2h </Supp> . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE54900	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GSM1326348	WT with Fe 2 (RNA-seq)	25222563	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT and Δfur were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. PGCGROWTHCONDITIONS	SRR1168134	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT and Δfur were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . For iron treated cells , 0.1 mM of FeCl2 were treated from the beginning of culture , and for DPD treated cells , <Supp> 0.2 mM of DPD </Supp> were added at early-log phase and continued to culture for additional <Supp> 2h </Supp> . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE54900	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GSM1326349	WT with DPD 1 (RNA-seq)	25222563	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT and Δfur were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. PGCGROWTHCONDITIONS	SRR1168135	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT and Δfur were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . For iron treated cells , 0.1 mM of FeCl2 were treated from the beginning of culture , and for DPD treated cells , <Supp> 0.2 mM of DPD </Supp> were added at early-log phase and continued to culture for additional <Supp> 2h </Supp> . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE54900	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GSM1326350	WT with DPD 2 (RNA-seq)	25222563	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT and Δfur were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. PGCGROWTHCONDITIONS	SRR1168136	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT and Δfur were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . For iron treated cells , 0.1 mM of FeCl2 were treated from the beginning of culture , and for DPD treated cells , <Supp> 0.2 mM of DPD </Supp> were added at early-log phase and continued to culture for additional <Supp> 2h </Supp> . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE54900	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GSM1326351	Δfur with Fe 1 (RNA-seq)	25222563	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT and Δfur were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. PGCGROWTHCONDITIONS	SRR1168137	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT and Δfur were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . For iron treated cells , 0.1 mM of FeCl2 were treated from the beginning of culture , and for DPD treated cells , <Supp> 0.2 mM of DPD </Supp> were added at early-log phase and continued to culture for additional <Supp> 2h </Supp> . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE54900	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GSM1326352	Δfur with Fe 2 (RNA-seq)	25222563	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT and Δfur were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. PGCGROWTHCONDITIONS	SRR1168138	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT and Δfur were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . For iron treated cells , 0.1 mM of FeCl2 were treated from the beginning of culture , and for DPD treated cells , <Supp> 0.2 mM of DPD </Supp> were added at early-log phase and continued to culture for additional <Supp> 2h </Supp> . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE54900	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GSM1326353	Δfur with DPD 1 (RNA-seq)	25222563	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT and Δfur were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. PGCGROWTHCONDITIONS	SRR1168139	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT and Δfur were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . For iron treated cells , 0.1 mM of FeCl2 were treated from the beginning of culture , and for DPD treated cells , <Supp> 0.2 mM of DPD </Supp> were added at early-log phase and continued to culture for additional <Supp> 2h </Supp> . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE54900	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GSM1326354	Δfur with DPD 2 (RNA-seq)	25222563	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT and Δfur were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. PGCGROWTHCONDITIONS	SRR1168140	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		<Gtype> Wild type </Gtype> E. coli K-12 ( strain BW38038 ) and BW39452 ( ΔrpoS ) cultures were grown on <Med> MOPS glucose minimal medium </Med> with <Supp> 0.2 % glucose </Supp> as sole carbon source at <Temp> 37 °C </Temp> , pH was initially 7.4 , and the agitation speed was 500 rpm . Culture samples were harvested during logarithmic growth and following entry into stationary phase for the WT and rpoS mutant . OD600 measurements were made on a Beckman Coulter DU 800 spectrophotometer . Samples were harvested directly into ice-cold RNAlater at a 1:1 dilution to protect RNA from degradation and cells then were pelleted by centrifugation at 8000rpm for 10 minutes . Cell pellets were stored at -80 °C in an equal volume of RNAlater prior to RNA extraction . 	GPL18814	GPL18814: Illumina HiSeq 2000 (Escherichia coli BW38028)	GSE58556	RNA sequencing based analysis of the bacterial transcriptome	GSM1413874	WT_glucose_log	25483350	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE58556/GSE58556.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Wild type E. coli K-12 (strain BW38038) and BW39452(ΔrpoS) cultures were grown on MOPS glucose minimal medium with 0.2% glucose as sole carbon source at 37°C, pH was initially 7.4,  and the agitation speed was 500 rpm. Culture samples were harvested during logarithmic growth and  following entry into stationary phase for the WT and rpoS mutant. OD600 measurements were made on a Beckman Coulter DU 800 spectrophotometer. Samples were harvested directly into ice-cold RNAlater at a 1:1 dilution to protect RNA from degradation and cells then were pelleted by centrifugation at 8000rpm for 10 minutes. Cell pellets were stored at -80°C in an equal volume of RNAlater prior to RNA extraction. PGCGROWTHCONDITIONS	SRR1411272	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT , and Δcra were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> , fructose and acetate . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602347	WT glucose 1	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, and Δcra were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS	SRR1787590	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT , and Δcra were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> , fructose and acetate . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602348	WT glucose 2	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, and Δcra were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS	SRR1787591	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT , and Δcra were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> , fructose and acetate . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602349	WT fructose 1	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, and Δcra were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS	SRR1787592	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT , and Δcra were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> , fructose and acetate . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602350	WT fructose 2	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, and Δcra were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS	SRR1787593	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT , and Δcra were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> , fructose and acetate . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602351	WT acetate 1	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, and Δcra were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS	SRR1787594	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT , and Δcra were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> , fructose and acetate . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602352	WT acetate 2	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, and Δcra were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS	SRR1787595	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT , and Δcra were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> , fructose and acetate . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602353	Δcra glucose 1	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, and Δcra were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS	SRR1787596	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT , and Δcra were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> , fructose and acetate . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602354	Δcra glucose 2	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, and Δcra were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS	SRR1787597	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT , and Δcra were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> , fructose and acetate . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602355	Δcra fructose 1	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, and Δcra were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS	SRR1787598	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT , and Δcra were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> , fructose and acetate . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602356	Δcra fructose 2	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, and Δcra were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS	SRR1787599	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT , and Δcra were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> , fructose and acetate . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602357	Δcra acetate 1	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, and Δcra were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS	SRR1787600	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT , and Δcra were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> , fructose and acetate . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602358	Δcra acetate 2	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, and Δcra were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS	SRR1787601	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT , ΔoxyR , ΔsoxR , and ΔsoxS were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65711	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GSM1603386	WT PQ 1	26279566	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, ΔoxyR, ΔsoxR, and ΔsoxS were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation. PGCGROWTHCONDITIONS	SRR1796598	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT , ΔoxyR , ΔsoxR , and ΔsoxS were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65711	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GSM1603387	WT PQ 2	26279566	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, ΔoxyR, ΔsoxR, and ΔsoxS were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation. PGCGROWTHCONDITIONS	SRR1796599	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT , ΔoxyR , ΔsoxR , and ΔsoxS were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65711	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GSM1603388	ΔoxyR PQ 1	26279566	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, ΔoxyR, ΔsoxR, and ΔsoxS were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation. PGCGROWTHCONDITIONS	SRR1796600	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT , ΔoxyR , ΔsoxR , and ΔsoxS were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65711	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GSM1603389	ΔoxyR PQ 2	26279566	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, ΔoxyR, ΔsoxR, and ΔsoxS were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation. PGCGROWTHCONDITIONS	SRR1796601	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT , ΔoxyR , ΔsoxR , and ΔsoxS were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65711	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GSM1603391	ΔsoxR PQ 2	26279566	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, ΔoxyR, ΔsoxR, and ΔsoxS were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation. PGCGROWTHCONDITIONS	SRR1796603	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT , ΔoxyR , ΔsoxR , and ΔsoxS were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65711	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GSM1603392	ΔsoxS PQ 1	26279566	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, ΔoxyR, ΔsoxR, and ΔsoxS were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation. PGCGROWTHCONDITIONS	SRR1796604	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT , ΔoxyR , ΔsoxR , and ΔsoxS were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65711	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GSM1603393	ΔsoxS PQ 2	26279566	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, ΔoxyR, ΔsoxR, and ΔsoxS were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation. PGCGROWTHCONDITIONS	SRR1796605	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT , gadE , gadW and gadX mutant cells were grown to <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) <Air> aerobically </Air> ( <Agit> 250 rpm </Agit> ) at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> at <pH> pH 5.5 </pH> . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623160	WT pH5.5 1	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5. PGCGROWTHCONDITIONS	SRR1824557	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT , gadE , gadW and gadX mutant cells were grown to <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) <Air> aerobically </Air> ( <Agit> 250 rpm </Agit> ) at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> at <pH> pH 5.5 </pH> . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623161	WT pH5.5 2	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5. PGCGROWTHCONDITIONS	SRR1824558	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT , gadE , gadW and gadX mutant cells were grown to <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) <Air> aerobically </Air> ( <Agit> 250 rpm </Agit> ) at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> at <pH> pH 5.5 </pH> . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623162	ΔgadE pH5.5 1	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5. PGCGROWTHCONDITIONS	SRR1824559	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT , gadE , gadW and gadX mutant cells were grown to <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) <Air> aerobically </Air> ( <Agit> 250 rpm </Agit> ) at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> at <pH> pH 5.5 </pH> . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623163	ΔgadE pH5.5 2	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5. PGCGROWTHCONDITIONS	SRR1824560	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT , gadE , gadW and gadX mutant cells were grown to <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) <Air> aerobically </Air> ( <Agit> 250 rpm </Agit> ) at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> at <pH> pH 5.5 </pH> . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623164	ΔgadW pH5.5 1	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5. PGCGROWTHCONDITIONS	SRR1824561	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT , gadE , gadW and gadX mutant cells were grown to <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) <Air> aerobically </Air> ( <Agit> 250 rpm </Agit> ) at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> at <pH> pH 5.5 </pH> . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623165	ΔgadW pH5.5 2	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5. PGCGROWTHCONDITIONS	SRR1824562	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT , gadE , gadW and gadX mutant cells were grown to <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) <Air> aerobically </Air> ( <Agit> 250 rpm </Agit> ) at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> at <pH> pH 5.5 </pH> . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623166	ΔgadX pH5.5 1	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5. PGCGROWTHCONDITIONS	SRR1824563	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT , gadE , gadW and gadX mutant cells were grown to <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) <Air> aerobically </Air> ( <Agit> 250 rpm </Agit> ) at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> at <pH> pH 5.5 </pH> . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623167	ΔgadX pH5.5 2	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5. PGCGROWTHCONDITIONS	SRR1824564	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		All cultures were based on MOPS media with <Supp> 0.2 % glucose </Supp> ( Teknova ) , with full supplement ( Neidhardt et al. , 1974 ) minus methionine . An overnight liquid culture was diluted 400-fold into 200 ml <Med> fresh media </Med> . The culture was kept in a 1 liter flask at <Temp> 37 °C </Temp> with aeration until OD420 reached 0.4 . 	GPL14548-GPL21433	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE77617	Operon mRNAs are organized into ORF-centric structures that predict translation efficiency	GSM2462936	mRNA-seq 37°C in WT with control plasmid	28139975	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE77617/GSE77617.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All cultures were based on MOPS media with 0.2% glucose (Teknova), with full supplement (Neidhardt et al., 1974) minus methionine. An overnight liquid culture was diluted 400-fold into 200 ml fresh media. The culture was kept in a 1 liter flask at 37°C with aeration until OD420 reached 0.4. PGCGROWTHCONDITIONS	SRR5186139	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		All cultures were based on MOPS media with <Supp> 0.2 % glucose </Supp> ( Teknova ) , with full supplement ( Neidhardt et al. , 1974 ) minus methionine . An overnight liquid culture was diluted 400-fold into 200 ml <Med> fresh media </Med> . The culture was kept in a 1 liter flask at <Temp> 37 °C </Temp> with aeration until OD420 reached 0.4 . 	GPL14548-GPL21433	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE77617	Operon mRNAs are organized into ORF-centric structures that predict translation efficiency	GSM2462937	mRNA-seq 37°C in WT with plasmid expressing mini-ORF CUA	28139975	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE77617/GSE77617.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All cultures were based on MOPS media with 0.2% glucose (Teknova), with full supplement (Neidhardt et al., 1974) minus methionine. An overnight liquid culture was diluted 400-fold into 200 ml fresh media. The culture was kept in a 1 liter flask at 37°C with aeration until OD420 reached 0.4. PGCGROWTHCONDITIONS	SRR5186140	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		All cultures were based on MOPS media with <Supp> 0.2 % glucose </Supp> ( Teknova ) , with full supplement ( Neidhardt et al. , 1974 ) minus methionine . An overnight liquid culture was diluted 400-fold into 200 ml <Med> fresh media </Med> . The culture was kept in a 1 liter flask at <Temp> 37 °C </Temp> with aeration until OD420 reached 0.4 . 	GPL14548-GPL21433	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE77617	Operon mRNAs are organized into ORF-centric structures that predict translation efficiency	GSM2462938	mRNA-seq 37°C in WT with plasmid expressing mini-ORF CUG	28139975	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE77617/GSE77617.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All cultures were based on MOPS media with 0.2% glucose (Teknova), with full supplement (Neidhardt et al., 1974) minus methionine. An overnight liquid culture was diluted 400-fold into 200 ml fresh media. The culture was kept in a 1 liter flask at 37°C with aeration until OD420 reached 0.4. PGCGROWTHCONDITIONS	SRR5186141	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT and ΔompR were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . Then cells were treated with <Supp> 0.3 M of NaCl </Supp> at mid-log pahse for <Supp> 30 min </Supp> with agitation . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE88980	Revealing the genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles and unexpected importance of narU under osmotic stress in Escherichia coli K-12 MG1655 [RNA-seq]	GSM2356687	WT NaCl 1	28526842	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88980/GSE88980.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT and ΔompR were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 0.3 M of NaCl at mid-log pahse for 30 min with agitation. PGCGROWTHCONDITIONS	SRR4435464	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT and ΔompR were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . Then cells were treated with <Supp> 0.3 M of NaCl </Supp> at mid-log pahse for <Supp> 30 min </Supp> with agitation . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE88980	Revealing the genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles and unexpected importance of narU under osmotic stress in Escherichia coli K-12 MG1655 [RNA-seq]	GSM2356688	WT NaCl 2	28526842	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88980/GSE88980.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT and ΔompR were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 0.3 M of NaCl at mid-log pahse for 30 min with agitation. PGCGROWTHCONDITIONS	SRR4435465	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT and ΔompR were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . Then cells were treated with <Supp> 0.3 M of NaCl </Supp> at mid-log pahse for <Supp> 30 min </Supp> with agitation . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE88980	Revealing the genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles and unexpected importance of narU under osmotic stress in Escherichia coli K-12 MG1655 [RNA-seq]	GSM2356689	ΔompR NaCl 1	28526842	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88980/GSE88980.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT and ΔompR were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 0.3 M of NaCl at mid-log pahse for 30 min with agitation. PGCGROWTHCONDITIONS	SRR4435466	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		E. coli K-12 MG1655 WT and ΔompR were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . Then cells were treated with <Supp> 0.3 M of NaCl </Supp> at mid-log pahse for <Supp> 30 min </Supp> with agitation . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE88980	Revealing the genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles and unexpected importance of narU under osmotic stress in Escherichia coli K-12 MG1655 [RNA-seq]	GSM2356690	ΔompR NaCl 2	28526842	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88980/GSE88980.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT and ΔompR were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 0.3 M of NaCl at mid-log pahse for 30 min with agitation. PGCGROWTHCONDITIONS	SRR4435467	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		Duplicate O/N cultures in LB with 15 mg/L chloramphenicol each of strains pCA24N,-gfp / DA4201 , Svi3-3 comp . ( recoded Svi3-3 ) / DA4201 and pORF1/DA4201 were diluted 1:100 into two , four and four cultures of 20 mL M9 + <Supp> 0.2 % glucose </Supp> with 5 μg/mL chloramphenicol . The pCA24N,-gfp / DA4201 cultures and two cultures each of Svi3-3 comp . ( recoded Svi3-3 ) / DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG . The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics . 	GPL18956	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	GSE92601	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GSM2433290	ORF1_1_IPTG	29807996	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Duplicate O/N cultures in LB with 15 mg/L chloramphenicol each of strains pCA24N,-gfp/DA4201, Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were diluted 1:100 into two, four and four cultures of 20 mL M9 + 0.2% glucose with 5 μg/mL chloramphenicol.  The pCA24N,-gfp/DA4201 cultures and two cultures each of Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG. The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics. PGCGROWTHCONDITIONS	SRR5121109	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		Duplicate O/N cultures in LB with 15 mg/L chloramphenicol each of strains pCA24N,-gfp / DA4201 , Svi3-3 comp . ( recoded Svi3-3 ) / DA4201 and pORF1/DA4201 were diluted 1:100 into two , four and four cultures of 20 mL M9 + <Supp> 0.2 % glucose </Supp> with 5 μg/mL chloramphenicol . The pCA24N,-gfp / DA4201 cultures and two cultures each of Svi3-3 comp . ( recoded Svi3-3 ) / DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG . The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics . 	GPL18956	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	GSE92601	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GSM2433291	ORF1_1	29807996	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Duplicate O/N cultures in LB with 15 mg/L chloramphenicol each of strains pCA24N,-gfp/DA4201, Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were diluted 1:100 into two, four and four cultures of 20 mL M9 + 0.2% glucose with 5 μg/mL chloramphenicol.  The pCA24N,-gfp/DA4201 cultures and two cultures each of Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG. The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics. PGCGROWTHCONDITIONS	SRR5121110	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		Duplicate O/N cultures in LB with 15 mg/L chloramphenicol each of strains pCA24N,-gfp / DA4201 , Svi3-3 comp . ( recoded Svi3-3 ) / DA4201 and pORF1/DA4201 were diluted 1:100 into two , four and four cultures of 20 mL M9 + <Supp> 0.2 % glucose </Supp> with 5 μg/mL chloramphenicol . The pCA24N,-gfp / DA4201 cultures and two cultures each of Svi3-3 comp . ( recoded Svi3-3 ) / DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG . The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics . 	GPL18956	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	GSE92601	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GSM2433292	ORF1_2_IPTG	29807996	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Duplicate O/N cultures in LB with 15 mg/L chloramphenicol each of strains pCA24N,-gfp/DA4201, Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were diluted 1:100 into two, four and four cultures of 20 mL M9 + 0.2% glucose with 5 μg/mL chloramphenicol.  The pCA24N,-gfp/DA4201 cultures and two cultures each of Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG. The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics. PGCGROWTHCONDITIONS	SRR5121111	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		Duplicate O/N cultures in LB with 15 mg/L chloramphenicol each of strains pCA24N,-gfp / DA4201 , Svi3-3 comp . ( recoded Svi3-3 ) / DA4201 and pORF1/DA4201 were diluted 1:100 into two , four and four cultures of 20 mL M9 + <Supp> 0.2 % glucose </Supp> with 5 μg/mL chloramphenicol . The pCA24N,-gfp / DA4201 cultures and two cultures each of Svi3-3 comp . ( recoded Svi3-3 ) / DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG . The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics . 	GPL18956	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	GSE92601	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GSM2433293	ORF1_2	29807996	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Duplicate O/N cultures in LB with 15 mg/L chloramphenicol each of strains pCA24N,-gfp/DA4201, Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were diluted 1:100 into two, four and four cultures of 20 mL M9 + 0.2% glucose with 5 μg/mL chloramphenicol.  The pCA24N,-gfp/DA4201 cultures and two cultures each of Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG. The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics. PGCGROWTHCONDITIONS	SRR5121112	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		Duplicate O/N cultures in LB with 15 mg/L chloramphenicol each of strains pCA24N,-gfp / DA4201 , Svi3-3 comp . ( recoded Svi3-3 ) / DA4201 and pORF1/DA4201 were diluted 1:100 into two , four and four cultures of 20 mL M9 + <Supp> 0.2 % glucose </Supp> with 5 μg/mL chloramphenicol . The pCA24N,-gfp / DA4201 cultures and two cultures each of Svi3-3 comp . ( recoded Svi3-3 ) / DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG . The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics . 	GPL18956	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	GSE92601	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GSM2433294	Svi3_3_1_IPTG	29807996	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Duplicate O/N cultures in LB with 15 mg/L chloramphenicol each of strains pCA24N,-gfp/DA4201, Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were diluted 1:100 into two, four and four cultures of 20 mL M9 + 0.2% glucose with 5 μg/mL chloramphenicol.  The pCA24N,-gfp/DA4201 cultures and two cultures each of Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG. The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics. PGCGROWTHCONDITIONS	SRR5121113	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		Duplicate O/N cultures in LB with 15 mg/L chloramphenicol each of strains pCA24N,-gfp / DA4201 , Svi3-3 comp . ( recoded Svi3-3 ) / DA4201 and pORF1/DA4201 were diluted 1:100 into two , four and four cultures of 20 mL M9 + <Supp> 0.2 % glucose </Supp> with 5 μg/mL chloramphenicol . The pCA24N,-gfp / DA4201 cultures and two cultures each of Svi3-3 comp . ( recoded Svi3-3 ) / DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG . The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics . 	GPL18956	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	GSE92601	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GSM2433295	Svi3_3_1	29807996	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Duplicate O/N cultures in LB with 15 mg/L chloramphenicol each of strains pCA24N,-gfp/DA4201, Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were diluted 1:100 into two, four and four cultures of 20 mL M9 + 0.2% glucose with 5 μg/mL chloramphenicol.  The pCA24N,-gfp/DA4201 cultures and two cultures each of Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG. The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics. PGCGROWTHCONDITIONS	SRR5121114	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		Duplicate O/N cultures in LB with 15 mg/L chloramphenicol each of strains pCA24N,-gfp / DA4201 , Svi3-3 comp . ( recoded Svi3-3 ) / DA4201 and pORF1/DA4201 were diluted 1:100 into two , four and four cultures of 20 mL M9 + <Supp> 0.2 % glucose </Supp> with 5 μg/mL chloramphenicol . The pCA24N,-gfp / DA4201 cultures and two cultures each of Svi3-3 comp . ( recoded Svi3-3 ) / DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG . The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics . 	GPL18956	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	GSE92601	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GSM2433296	Svi3_3_2_IPTG	29807996	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Duplicate O/N cultures in LB with 15 mg/L chloramphenicol each of strains pCA24N,-gfp/DA4201, Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were diluted 1:100 into two, four and four cultures of 20 mL M9 + 0.2% glucose with 5 μg/mL chloramphenicol.  The pCA24N,-gfp/DA4201 cultures and two cultures each of Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG. The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics. PGCGROWTHCONDITIONS	SRR5121115	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		Duplicate O/N cultures in LB with 15 mg/L chloramphenicol each of strains pCA24N,-gfp / DA4201 , Svi3-3 comp . ( recoded Svi3-3 ) / DA4201 and pORF1/DA4201 were diluted 1:100 into two , four and four cultures of 20 mL M9 + <Supp> 0.2 % glucose </Supp> with 5 μg/mL chloramphenicol . The pCA24N,-gfp / DA4201 cultures and two cultures each of Svi3-3 comp . ( recoded Svi3-3 ) / DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG . The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics . 	GPL18956	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	GSE92601	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GSM2433297	Svi3_3_2	29807996	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Duplicate O/N cultures in LB with 15 mg/L chloramphenicol each of strains pCA24N,-gfp/DA4201, Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were diluted 1:100 into two, four and four cultures of 20 mL M9 + 0.2% glucose with 5 μg/mL chloramphenicol.  The pCA24N,-gfp/DA4201 cultures and two cultures each of Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG. The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics. PGCGROWTHCONDITIONS	SRR5121116	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		Duplicate O/N cultures in LB with 15 mg/L chloramphenicol each of strains pCA24N,-gfp / DA4201 , Svi3-3 comp . ( recoded Svi3-3 ) / DA4201 and pORF1/DA4201 were diluted 1:100 into two , four and four cultures of 20 mL M9 + <Supp> 0.2 % glucose </Supp> with 5 μg/mL chloramphenicol . The pCA24N,-gfp / DA4201 cultures and two cultures each of Svi3-3 comp . ( recoded Svi3-3 ) / DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG . The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics . 	GPL18956	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	GSE92601	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GSM2433298	WT1_IPTG	29807996	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Duplicate O/N cultures in LB with 15 mg/L chloramphenicol each of strains pCA24N,-gfp/DA4201, Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were diluted 1:100 into two, four and four cultures of 20 mL M9 + 0.2% glucose with 5 μg/mL chloramphenicol.  The pCA24N,-gfp/DA4201 cultures and two cultures each of Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG. The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics. PGCGROWTHCONDITIONS	SRR5121117	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	glucose 0.2%		Duplicate O/N cultures in LB with 15 mg/L chloramphenicol each of strains pCA24N,-gfp / DA4201 , Svi3-3 comp . ( recoded Svi3-3 ) / DA4201 and pORF1/DA4201 were diluted 1:100 into two , four and four cultures of 20 mL M9 + <Supp> 0.2 % glucose </Supp> with 5 μg/mL chloramphenicol . The pCA24N,-gfp / DA4201 cultures and two cultures each of Svi3-3 comp . ( recoded Svi3-3 ) / DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG . The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics . 	GPL18956	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	GSE92601	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GSM2433299	WT2_IPTG	29807996	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Duplicate O/N cultures in LB with 15 mg/L chloramphenicol each of strains pCA24N,-gfp/DA4201, Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were diluted 1:100 into two, four and four cultures of 20 mL M9 + 0.2% glucose with 5 μg/mL chloramphenicol.  The pCA24N,-gfp/DA4201 cultures and two cultures each of Svi3-3 comp. (recoded Svi3-3)/DA4201 and pORF1/DA4201 were supplemented by 50 μM IPTG. The cells were grown to OD 0.15-0.2 and cells were withdrawn for RNA extraction and whole cell proteomics. PGCGROWTHCONDITIONS	SRR5121118	MCO000002770	0.2 % glucose	Medium supplement	True
growth_protocol	35.7 C		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770989	Ribosome profiling at 37°C in WT cells_1	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001737	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		For in vivo DMS modification , 15 mL of E. coli culture was incubated with 750 µL DMS . Incubation was performed for 2 min at <Temp> 37 °C </Temp> or for 45 min at 10 °C . DMS was quenched by adding 30 mL 0 °C stop solution ( 30 % β-mercaptoethanol , 25 % isoamyl alcohol ) , after which cells were quickly put on ice , collected by centrifugation at 8000 x g , 4 °C for 2 min , and washed with 8 mL 30 % BME solution . Cells were then resuspended in 450 µL total RNA lysis buffer ( 10 mM EDTA , 50 mM sodium acetate pH 5.5 ) , and total RNA was purified with hot acid phenol ( Ambion ) . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770989	Ribosome profiling at 37°C in WT cells_1	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS	SRR6001737	MCO000003199	37 °C	Temperature	True
characteristics	35.7 C		temperature : <Temp> 37 °C </Temp> 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770989	Ribosome profiling at 37°C in WT cells_1	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	temperature: 37°C PGCGROWTHCONDITIONS	SRR6001737	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770991	Ribosome profiling 30 min after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001739	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		For in vivo DMS modification , 15 mL of E. coli culture was incubated with 750 µL DMS . Incubation was performed for 2 min at <Temp> 37 °C </Temp> or for 45 min at 10 °C . DMS was quenched by adding 30 mL 0 °C stop solution ( 30 % β-mercaptoethanol , 25 % isoamyl alcohol ) , after which cells were quickly put on ice , collected by centrifugation at 8000 x g , 4 °C for 2 min , and washed with 8 mL 30 % BME solution . Cells were then resuspended in 450 µL total RNA lysis buffer ( 10 mM EDTA , 50 mM sodium acetate pH 5.5 ) , and total RNA was purified with hot acid phenol ( Ambion ) . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770991	Ribosome profiling 30 min after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS	SRR6001739	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770994	Ribosome profiling 4 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001742	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		For in vivo DMS modification , 15 mL of E. coli culture was incubated with 750 µL DMS . Incubation was performed for 2 min at <Temp> 37 °C </Temp> or for 45 min at 10 °C . DMS was quenched by adding 30 mL 0 °C stop solution ( 30 % β-mercaptoethanol , 25 % isoamyl alcohol ) , after which cells were quickly put on ice , collected by centrifugation at 8000 x g , 4 °C for 2 min , and washed with 8 mL 30 % BME solution . Cells were then resuspended in 450 µL total RNA lysis buffer ( 10 mM EDTA , 50 mM sodium acetate pH 5.5 ) , and total RNA was purified with hot acid phenol ( Ambion ) . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770994	Ribosome profiling 4 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS	SRR6001742	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770995	Ribosome profiling 6 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001743	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		For in vivo DMS modification , 15 mL of E. coli culture was incubated with 750 µL DMS . Incubation was performed for 2 min at <Temp> 37 °C </Temp> or for 45 min at 10 °C . DMS was quenched by adding 30 mL 0 °C stop solution ( 30 % β-mercaptoethanol , 25 % isoamyl alcohol ) , after which cells were quickly put on ice , collected by centrifugation at 8000 x g , 4 °C for 2 min , and washed with 8 mL 30 % BME solution . Cells were then resuspended in 450 µL total RNA lysis buffer ( 10 mM EDTA , 50 mM sodium acetate pH 5.5 ) , and total RNA was purified with hot acid phenol ( Ambion ) . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770995	Ribosome profiling 6 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS	SRR6001743	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770996	Ribosome profiling 5 min after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001744	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		For in vivo DMS modification , 15 mL of E. coli culture was incubated with 750 µL DMS . Incubation was performed for 2 min at <Temp> 37 °C </Temp> or for 45 min at 10 °C . DMS was quenched by adding 30 mL 0 °C stop solution ( 30 % β-mercaptoethanol , 25 % isoamyl alcohol ) , after which cells were quickly put on ice , collected by centrifugation at 8000 x g , 4 °C for 2 min , and washed with 8 mL 30 % BME solution . Cells were then resuspended in 450 µL total RNA lysis buffer ( 10 mM EDTA , 50 mM sodium acetate pH 5.5 ) , and total RNA was purified with hot acid phenol ( Ambion ) . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770996	Ribosome profiling 5 min after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS	SRR6001744	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770997	Ribosome profiling 10 min after shift to 10°C in WT cells_2	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001745	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		For in vivo DMS modification , 15 mL of E. coli culture was incubated with 750 µL DMS . Incubation was performed for 2 min at <Temp> 37 °C </Temp> or for 45 min at 10 °C . DMS was quenched by adding 30 mL 0 °C stop solution ( 30 % β-mercaptoethanol , 25 % isoamyl alcohol ) , after which cells were quickly put on ice , collected by centrifugation at 8000 x g , 4 °C for 2 min , and washed with 8 mL 30 % BME solution . Cells were then resuspended in 450 µL total RNA lysis buffer ( 10 mM EDTA , 50 mM sodium acetate pH 5.5 ) , and total RNA was purified with hot acid phenol ( Ambion ) . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770997	Ribosome profiling 10 min after shift to 10°C in WT cells_2	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS	SRR6001745	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770998	Ribosome profiling 15 min after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001746	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		For in vivo DMS modification , 15 mL of E. coli culture was incubated with 750 µL DMS . Incubation was performed for 2 min at <Temp> 37 °C </Temp> or for 45 min at 10 °C . DMS was quenched by adding 30 mL 0 °C stop solution ( 30 % β-mercaptoethanol , 25 % isoamyl alcohol ) , after which cells were quickly put on ice , collected by centrifugation at 8000 x g , 4 °C for 2 min , and washed with 8 mL 30 % BME solution . Cells were then resuspended in 450 µL total RNA lysis buffer ( 10 mM EDTA , 50 mM sodium acetate pH 5.5 ) , and total RNA was purified with hot acid phenol ( Ambion ) . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770998	Ribosome profiling 15 min after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS	SRR6001746	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770999	Ribosome profiling 8 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001747SRR6001748	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		For in vivo DMS modification , 15 mL of E. coli culture was incubated with 750 µL DMS . Incubation was performed for 2 min at <Temp> 37 °C </Temp> or for 45 min at 10 °C . DMS was quenched by adding 30 mL 0 °C stop solution ( 30 % β-mercaptoethanol , 25 % isoamyl alcohol ) , after which cells were quickly put on ice , collected by centrifugation at 8000 x g , 4 °C for 2 min , and washed with 8 mL 30 % BME solution . Cells were then resuspended in 450 µL total RNA lysis buffer ( 10 mM EDTA , 50 mM sodium acetate pH 5.5 ) , and total RNA was purified with hot acid phenol ( Ambion ) . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770999	Ribosome profiling 8 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS	SRR6001747SRR6001748	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771000	Ribosome profiling 8 hr after shift to 10°C in ∆cspABEG cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001749SRR6001750	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		For in vivo DMS modification , 15 mL of E. coli culture was incubated with 750 µL DMS . Incubation was performed for 2 min at <Temp> 37 °C </Temp> or for 45 min at 10 °C . DMS was quenched by adding 30 mL 0 °C stop solution ( 30 % β-mercaptoethanol , 25 % isoamyl alcohol ) , after which cells were quickly put on ice , collected by centrifugation at 8000 x g , 4 °C for 2 min , and washed with 8 mL 30 % BME solution . Cells were then resuspended in 450 µL total RNA lysis buffer ( 10 mM EDTA , 50 mM sodium acetate pH 5.5 ) , and total RNA was purified with hot acid phenol ( Ambion ) . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771000	Ribosome profiling 8 hr after shift to 10°C in ∆cspABEG cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS	SRR6001749SRR6001750	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771001	Ribosome profiling at 37°C in WT cells_2	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001751	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		For in vivo DMS modification , 15 mL of E. coli culture was incubated with 750 µL DMS . Incubation was performed for 2 min at <Temp> 37 °C </Temp> or for 45 min at 10 °C . DMS was quenched by adding 30 mL 0 °C stop solution ( 30 % β-mercaptoethanol , 25 % isoamyl alcohol ) , after which cells were quickly put on ice , collected by centrifugation at 8000 x g , 4 °C for 2 min , and washed with 8 mL 30 % BME solution . Cells were then resuspended in 450 µL total RNA lysis buffer ( 10 mM EDTA , 50 mM sodium acetate pH 5.5 ) , and total RNA was purified with hot acid phenol ( Ambion ) . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771001	Ribosome profiling at 37°C in WT cells_2	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS	SRR6001751	MCO000003199	37 °C	Temperature	True
characteristics	35.7 C		temperature : <Temp> 37 °C </Temp> 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771001	Ribosome profiling at 37°C in WT cells_2	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	temperature: 37°C PGCGROWTHCONDITIONS	SRR6001751	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771002	Ribosome profiling at 37°C in ∆cspABCEG cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001752	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		For in vivo DMS modification , 15 mL of E. coli culture was incubated with 750 µL DMS . Incubation was performed for 2 min at <Temp> 37 °C </Temp> or for 45 min at 10 °C . DMS was quenched by adding 30 mL 0 °C stop solution ( 30 % β-mercaptoethanol , 25 % isoamyl alcohol ) , after which cells were quickly put on ice , collected by centrifugation at 8000 x g , 4 °C for 2 min , and washed with 8 mL 30 % BME solution . Cells were then resuspended in 450 µL total RNA lysis buffer ( 10 mM EDTA , 50 mM sodium acetate pH 5.5 ) , and total RNA was purified with hot acid phenol ( Ambion ) . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771002	Ribosome profiling at 37°C in ∆cspABCEG cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS	SRR6001752	MCO000003199	37 °C	Temperature	True
characteristics	35.7 C		temperature : <Temp> 37 °C </Temp> 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771002	Ribosome profiling at 37°C in ∆cspABCEG cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	temperature: 37°C PGCGROWTHCONDITIONS	SRR6001752	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771008	mRNA-seq 4 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001758	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		For in vivo DMS modification , 15 mL of E. coli culture was incubated with 750 µL DMS . Incubation was performed for 2 min at <Temp> 37 °C </Temp> or for 45 min at 10 °C . DMS was quenched by adding 30 mL 0 °C stop solution ( 30 % β-mercaptoethanol , 25 % isoamyl alcohol ) , after which cells were quickly put on ice , collected by centrifugation at 8000 x g , 4 °C for 2 min , and washed with 8 mL 30 % BME solution . Cells were then resuspended in 450 µL total RNA lysis buffer ( 10 mM EDTA , 50 mM sodium acetate pH 5.5 ) , and total RNA was purified with hot acid phenol ( Ambion ) . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771008	mRNA-seq 4 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS	SRR6001758	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771010	mRNA-seq 8 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001760SRR6001761	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		For in vivo DMS modification , 15 mL of E. coli culture was incubated with 750 µL DMS . Incubation was performed for 2 min at <Temp> 37 °C </Temp> or for 45 min at 10 °C . DMS was quenched by adding 30 mL 0 °C stop solution ( 30 % β-mercaptoethanol , 25 % isoamyl alcohol ) , after which cells were quickly put on ice , collected by centrifugation at 8000 x g , 4 °C for 2 min , and washed with 8 mL 30 % BME solution . Cells were then resuspended in 450 µL total RNA lysis buffer ( 10 mM EDTA , 50 mM sodium acetate pH 5.5 ) , and total RNA was purified with hot acid phenol ( Ambion ) . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771010	mRNA-seq 8 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS	SRR6001760SRR6001761	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771011	mRNA-seq 8 hr after shift to 10°C in ∆cspABEG cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001762SRR6001763	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		For in vivo DMS modification , 15 mL of E. coli culture was incubated with 750 µL DMS . Incubation was performed for 2 min at <Temp> 37 °C </Temp> or for 45 min at 10 °C . DMS was quenched by adding 30 mL 0 °C stop solution ( 30 % β-mercaptoethanol , 25 % isoamyl alcohol ) , after which cells were quickly put on ice , collected by centrifugation at 8000 x g , 4 °C for 2 min , and washed with 8 mL 30 % BME solution . Cells were then resuspended in 450 µL total RNA lysis buffer ( 10 mM EDTA , 50 mM sodium acetate pH 5.5 ) , and total RNA was purified with hot acid phenol ( Ambion ) . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771011	mRNA-seq 8 hr after shift to 10°C in ∆cspABEG cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS	SRR6001762SRR6001763	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771014	DMS-seq 30 min after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001766	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		For in vivo DMS modification , 15 mL of E. coli culture was incubated with 750 µL DMS . Incubation was performed for 2 min at <Temp> 37 °C </Temp> or for 45 min at 10 °C . DMS was quenched by adding 30 mL 0 °C stop solution ( 30 % β-mercaptoethanol , 25 % isoamyl alcohol ) , after which cells were quickly put on ice , collected by centrifugation at 8000 x g , 4 °C for 2 min , and washed with 8 mL 30 % BME solution . Cells were then resuspended in 450 µL total RNA lysis buffer ( 10 mM EDTA , 50 mM sodium acetate pH 5.5 ) , and total RNA was purified with hot acid phenol ( Ambion ) . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771014	DMS-seq 30 min after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS	SRR6001766	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771015	DMS-seq 6 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001769	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		For in vivo DMS modification , 15 mL of E. coli culture was incubated with 750 µL DMS . Incubation was performed for 2 min at <Temp> 37 °C </Temp> or for 45 min at 10 °C . DMS was quenched by adding 30 mL 0 °C stop solution ( 30 % β-mercaptoethanol , 25 % isoamyl alcohol ) , after which cells were quickly put on ice , collected by centrifugation at 8000 x g , 4 °C for 2 min , and washed with 8 mL 30 % BME solution . Cells were then resuspended in 450 µL total RNA lysis buffer ( 10 mM EDTA , 50 mM sodium acetate pH 5.5 ) , and total RNA was purified with hot acid phenol ( Ambion ) . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771015	DMS-seq 6 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS	SRR6001769	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771016	DMS-seq 8 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001772	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		For in vivo DMS modification , 15 mL of E. coli culture was incubated with 750 µL DMS . Incubation was performed for 2 min at <Temp> 37 °C </Temp> or for 45 min at 10 °C . DMS was quenched by adding 30 mL 0 °C stop solution ( 30 % β-mercaptoethanol , 25 % isoamyl alcohol ) , after which cells were quickly put on ice , collected by centrifugation at 8000 x g , 4 °C for 2 min , and washed with 8 mL 30 % BME solution . Cells were then resuspended in 450 µL total RNA lysis buffer ( 10 mM EDTA , 50 mM sodium acetate pH 5.5 ) , and total RNA was purified with hot acid phenol ( Ambion ) . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771016	DMS-seq 8 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS	SRR6001772	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771017	DMS-seq 8 hr after shift to 10°C in ∆cspABEG cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001773	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		For in vivo DMS modification , 15 mL of E. coli culture was incubated with 750 µL DMS . Incubation was performed for 2 min at <Temp> 37 °C </Temp> or for 45 min at 10 °C . DMS was quenched by adding 30 mL 0 °C stop solution ( 30 % β-mercaptoethanol , 25 % isoamyl alcohol ) , after which cells were quickly put on ice , collected by centrifugation at 8000 x g , 4 °C for 2 min , and washed with 8 mL 30 % BME solution . Cells were then resuspended in 450 µL total RNA lysis buffer ( 10 mM EDTA , 50 mM sodium acetate pH 5.5 ) , and total RNA was purified with hot acid phenol ( Ambion ) . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771017	DMS-seq 8 hr after shift to 10°C in ∆cspABEG cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS	SRR6001773	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771018	DMS-seq 8 hr after shift to 10°C in ∆cspBG cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001774	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		For in vivo DMS modification , 15 mL of E. coli culture was incubated with 750 µL DMS . Incubation was performed for 2 min at <Temp> 37 °C </Temp> or for 45 min at 10 °C . DMS was quenched by adding 30 mL 0 °C stop solution ( 30 % β-mercaptoethanol , 25 % isoamyl alcohol ) , after which cells were quickly put on ice , collected by centrifugation at 8000 x g , 4 °C for 2 min , and washed with 8 mL 30 % BME solution . Cells were then resuspended in 450 µL total RNA lysis buffer ( 10 mM EDTA , 50 mM sodium acetate pH 5.5 ) , and total RNA was purified with hot acid phenol ( Ambion ) . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771018	DMS-seq 8 hr after shift to 10°C in ∆cspBG cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS	SRR6001774	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771019	Total RNA-seq 20 min after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001775	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		For in vivo DMS modification , 15 mL of E. coli culture was incubated with 750 µL DMS . Incubation was performed for 2 min at <Temp> 37 °C </Temp> or for 45 min at 10 °C . DMS was quenched by adding 30 mL 0 °C stop solution ( 30 % β-mercaptoethanol , 25 % isoamyl alcohol ) , after which cells were quickly put on ice , collected by centrifugation at 8000 x g , 4 °C for 2 min , and washed with 8 mL 30 % BME solution . Cells were then resuspended in 450 µL total RNA lysis buffer ( 10 mM EDTA , 50 mM sodium acetate pH 5.5 ) , and total RNA was purified with hot acid phenol ( Ambion ) . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771019	Total RNA-seq 20 min after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS	SRR6001775	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771020	Total RNA-seq 4 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001776	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		For in vivo DMS modification , 15 mL of E. coli culture was incubated with 750 µL DMS . Incubation was performed for 2 min at <Temp> 37 °C </Temp> or for 45 min at 10 °C . DMS was quenched by adding 30 mL 0 °C stop solution ( 30 % β-mercaptoethanol , 25 % isoamyl alcohol ) , after which cells were quickly put on ice , collected by centrifugation at 8000 x g , 4 °C for 2 min , and washed with 8 mL 30 % BME solution . Cells were then resuspended in 450 µL total RNA lysis buffer ( 10 mM EDTA , 50 mM sodium acetate pH 5.5 ) , and total RNA was purified with hot acid phenol ( Ambion ) . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771020	Total RNA-seq 4 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS	SRR6001776	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771021	Total RNA-seq 8 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001777	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		For in vivo DMS modification , 15 mL of E. coli culture was incubated with 750 µL DMS . Incubation was performed for 2 min at <Temp> 37 °C </Temp> or for 45 min at 10 °C . DMS was quenched by adding 30 mL 0 °C stop solution ( 30 % β-mercaptoethanol , 25 % isoamyl alcohol ) , after which cells were quickly put on ice , collected by centrifugation at 8000 x g , 4 °C for 2 min , and washed with 8 mL 30 % BME solution . Cells were then resuspended in 450 µL total RNA lysis buffer ( 10 mM EDTA , 50 mM sodium acetate pH 5.5 ) , and total RNA was purified with hot acid phenol ( Ambion ) . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771021	Total RNA-seq 8 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS	SRR6001777	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771022	Total RNA-seq 20 min after shift to 10°C in ∆rnr cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001778	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		For in vivo DMS modification , 15 mL of E. coli culture was incubated with 750 µL DMS . Incubation was performed for 2 min at <Temp> 37 °C </Temp> or for 45 min at 10 °C . DMS was quenched by adding 30 mL 0 °C stop solution ( 30 % β-mercaptoethanol , 25 % isoamyl alcohol ) , after which cells were quickly put on ice , collected by centrifugation at 8000 x g , 4 °C for 2 min , and washed with 8 mL 30 % BME solution . Cells were then resuspended in 450 µL total RNA lysis buffer ( 10 mM EDTA , 50 mM sodium acetate pH 5.5 ) , and total RNA was purified with hot acid phenol ( Ambion ) . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771022	Total RNA-seq 20 min after shift to 10°C in ∆rnr cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS	SRR6001778	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771023	Total RNA-seq 4 hr after shift to 10°C in ∆rnr cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001779	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		For in vivo DMS modification , 15 mL of E. coli culture was incubated with 750 µL DMS . Incubation was performed for 2 min at <Temp> 37 °C </Temp> or for 45 min at 10 °C . DMS was quenched by adding 30 mL 0 °C stop solution ( 30 % β-mercaptoethanol , 25 % isoamyl alcohol ) , after which cells were quickly put on ice , collected by centrifugation at 8000 x g , 4 °C for 2 min , and washed with 8 mL 30 % BME solution . Cells were then resuspended in 450 µL total RNA lysis buffer ( 10 mM EDTA , 50 mM sodium acetate pH 5.5 ) , and total RNA was purified with hot acid phenol ( Ambion ) . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771023	Total RNA-seq 4 hr after shift to 10°C in ∆rnr cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS	SRR6001779	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771024	Total RNA-seq 8 hr after shift to 10°C in ∆rnr cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001780	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		For in vivo DMS modification , 15 mL of E. coli culture was incubated with 750 µL DMS . Incubation was performed for 2 min at <Temp> 37 °C </Temp> or for 45 min at 10 °C . DMS was quenched by adding 30 mL 0 °C stop solution ( 30 % β-mercaptoethanol , 25 % isoamyl alcohol ) , after which cells were quickly put on ice , collected by centrifugation at 8000 x g , 4 °C for 2 min , and washed with 8 mL 30 % BME solution . Cells were then resuspended in 450 µL total RNA lysis buffer ( 10 mM EDTA , 50 mM sodium acetate pH 5.5 ) , and total RNA was purified with hot acid phenol ( Ambion ) . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771024	Total RNA-seq 8 hr after shift to 10°C in ∆rnr cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS	SRR6001780	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771025	Total RNA-seq before rifampicin treatment -- 2 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001781	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		For in vivo DMS modification , 15 mL of E. coli culture was incubated with 750 µL DMS . Incubation was performed for 2 min at <Temp> 37 °C </Temp> or for 45 min at 10 °C . DMS was quenched by adding 30 mL 0 °C stop solution ( 30 % β-mercaptoethanol , 25 % isoamyl alcohol ) , after which cells were quickly put on ice , collected by centrifugation at 8000 x g , 4 °C for 2 min , and washed with 8 mL 30 % BME solution . Cells were then resuspended in 450 µL total RNA lysis buffer ( 10 mM EDTA , 50 mM sodium acetate pH 5.5 ) , and total RNA was purified with hot acid phenol ( Ambion ) . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771025	Total RNA-seq before rifampicin treatment -- 2 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS	SRR6001781	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771026	Total RNA-seq after rifampicin treatment -- 4 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001782	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		For in vivo DMS modification , 15 mL of E. coli culture was incubated with 750 µL DMS . Incubation was performed for 2 min at <Temp> 37 °C </Temp> or for 45 min at 10 °C . DMS was quenched by adding 30 mL 0 °C stop solution ( 30 % β-mercaptoethanol , 25 % isoamyl alcohol ) , after which cells were quickly put on ice , collected by centrifugation at 8000 x g , 4 °C for 2 min , and washed with 8 mL 30 % BME solution . Cells were then resuspended in 450 µL total RNA lysis buffer ( 10 mM EDTA , 50 mM sodium acetate pH 5.5 ) , and total RNA was purified with hot acid phenol ( Ambion ) . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771026	Total RNA-seq after rifampicin treatment -- 4 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS	SRR6001782	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771027	Total RNA-seq before rifampicin treatment -- 2 hr after shift to 10°C in ∆rnr cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001783	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		For in vivo DMS modification , 15 mL of E. coli culture was incubated with 750 µL DMS . Incubation was performed for 2 min at <Temp> 37 °C </Temp> or for 45 min at 10 °C . DMS was quenched by adding 30 mL 0 °C stop solution ( 30 % β-mercaptoethanol , 25 % isoamyl alcohol ) , after which cells were quickly put on ice , collected by centrifugation at 8000 x g , 4 °C for 2 min , and washed with 8 mL 30 % BME solution . Cells were then resuspended in 450 µL total RNA lysis buffer ( 10 mM EDTA , 50 mM sodium acetate pH 5.5 ) , and total RNA was purified with hot acid phenol ( Ambion ) . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771027	Total RNA-seq before rifampicin treatment -- 2 hr after shift to 10°C in ∆rnr cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS	SRR6001783	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All culture experiments were performed in <Med> MOPS medium </Med> supplemented with <Supp> 0.2 % glucose </Supp> , 19 amino acids ( without methionine ) , vitamins , bases and micronutrients ( MOPS rich defined medium minus methionine , Teknova ) . Cells were grown in an overnight liquid culture at <Temp> 37 °C </Temp> , diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected . For 10 °C samples , cultures were grown to OD420 = 1.1 at <Temp> 37 °C </Temp> and cold shock was performed by mixing 70mL of <Temp> 37 °C </Temp> culture with 130mL of 0 °C media pre-chilled in ice-water slurry , with continued growth of the culture in a 10 °C shaker . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771028	Total RNA-seq after rifampicin treatment -- 4 hr after shift to 10°C in ∆rnr cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All culture experiments were performed in MOPS medium supplemented with 0.2% glucose, 19 amino acids (without methionine), vitamins, bases and micronutrients (MOPS rich defined medium minus methionine, Teknova). Cells were grown in an overnight liquid culture at 37°C, diluted to an OD420 = .001 in fresh medium and grown until OD420 reached 0.4 where samples were collected.  For 10°C samples, cultures were grown to OD420 = 1.1 at 37°C and cold shock was performed by mixing 70mL of 37°C culture with 130mL of 0°C media pre-chilled in ice-water slurry, with continued growth of the culture in a 10°C shaker. PGCGROWTHCONDITIONS	SRR6001784	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		For in vivo DMS modification , 15 mL of E. coli culture was incubated with 750 µL DMS . Incubation was performed for 2 min at <Temp> 37 °C </Temp> or for 45 min at 10 °C . DMS was quenched by adding 30 mL 0 °C stop solution ( 30 % β-mercaptoethanol , 25 % isoamyl alcohol ) , after which cells were quickly put on ice , collected by centrifugation at 8000 x g , 4 °C for 2 min , and washed with 8 mL 30 % BME solution . Cells were then resuspended in 450 µL total RNA lysis buffer ( 10 mM EDTA , 50 mM sodium acetate pH 5.5 ) , and total RNA was purified with hot acid phenol ( Ambion ) . 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771028	Total RNA-seq after rifampicin treatment -- 4 hr after shift to 10°C in ∆rnr cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For in vivo DMS modification, 15 mL of E. coli culture was incubated with 750 µL DMS. Incubation was performed for 2 min at 37°C or for 45 min at 10°C. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol), after which cells were quickly put on ice, collected by centrifugation at 8000 x g, 4 °C for 2 min, and washed with 8 mL 30% BME solution. Cells were then resuspended in 450 µL total RNA lysis buffer (10 mM EDTA, 50 mM sodium acetate pH 5.5), and total RNA was purified with hot acid phenol (Ambion). PGCGROWTHCONDITIONS	SRR6001784	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cells with construct and control plasmids were grown at <Temp> 37 °C </Temp> overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic . In the morning , 60 μl of each sample were diluted into 3 ml <Med> of fresh medium </Med> and grown at <Temp> 37 °C </Temp> with shaking for another hour ( outgrowth ) . 200 μl of each sample were then transferred in 8 wells of a 96-well plate ( Costar ) at approximately 0.1 OD ( 600 nm ) . The samples were placed in a Synergy HT Microplate Reader ( BioTek ) and incubated at <Temp> 37 °C </Temp> with orbital shaking at 1,000 rpm for 1 h , performing measurements of GFP ( excitation ( ex . ) , 485 nm ; emission ( em . ) , 528 nm ) and OD ( 600 nm ) every 15 minutes . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE107093	Burden- driven feedback control of gene expression	GSM2861128	R2 DH10BGFP_pLys_M1_1	29578536	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS	SRR6305247	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cells with construct and control plasmids were grown at <Temp> 37 °C </Temp> overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic . In the morning , 60 μl of each sample were diluted into 3 ml <Med> of fresh medium </Med> and grown at <Temp> 37 °C </Temp> with shaking for another hour ( outgrowth ) . 200 μl of each sample were then transferred in 8 wells of a 96-well plate ( Costar ) at approximately 0.1 OD ( 600 nm ) . The samples were placed in a Synergy HT Microplate Reader ( BioTek ) and incubated at <Temp> 37 °C </Temp> with orbital shaking at 1,000 rpm for 1 h , performing measurements of GFP ( excitation ( ex . ) , 485 nm ; emission ( em . ) , 528 nm ) and OD ( 600 nm ) every 15 minutes . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE107093	Burden- driven feedback control of gene expression	GSM2861129	R3 DH10BGFP_pSB1C3_1	29578536	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS	SRR6305248	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cells with construct and control plasmids were grown at <Temp> 37 °C </Temp> overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic . In the morning , 60 μl of each sample were diluted into 3 ml <Med> of fresh medium </Med> and grown at <Temp> 37 °C </Temp> with shaking for another hour ( outgrowth ) . 200 μl of each sample were then transferred in 8 wells of a 96-well plate ( Costar ) at approximately 0.1 OD ( 600 nm ) . The samples were placed in a Synergy HT Microplate Reader ( BioTek ) and incubated at <Temp> 37 °C </Temp> with orbital shaking at 1,000 rpm for 1 h , performing measurements of GFP ( excitation ( ex . ) , 485 nm ; emission ( em . ) , 528 nm ) and OD ( 600 nm ) every 15 minutes . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE107093	Burden- driven feedback control of gene expression	GSM2861132	R6 DH10BGFP_pD864_LacZ_1	29578536	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS	SRR6305251	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cells with construct and control plasmids were grown at <Temp> 37 °C </Temp> overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic . In the morning , 60 μl of each sample were diluted into 3 ml <Med> of fresh medium </Med> and grown at <Temp> 37 °C </Temp> with shaking for another hour ( outgrowth ) . 200 μl of each sample were then transferred in 8 wells of a 96-well plate ( Costar ) at approximately 0.1 OD ( 600 nm ) . The samples were placed in a Synergy HT Microplate Reader ( BioTek ) and incubated at <Temp> 37 °C </Temp> with orbital shaking at 1,000 rpm for 1 h , performing measurements of GFP ( excitation ( ex . ) , 485 nm ; emission ( em . ) , 528 nm ) and OD ( 600 nm ) every 15 minutes . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE107093	Burden- driven feedback control of gene expression	GSM2861137	R11 DH10BGFP_pLys_1	29578536	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS	SRR6305256	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cells with construct and control plasmids were grown at <Temp> 37 °C </Temp> overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic . In the morning , 60 μl of each sample were diluted into 3 ml <Med> of fresh medium </Med> and grown at <Temp> 37 °C </Temp> with shaking for another hour ( outgrowth ) . 200 μl of each sample were then transferred in 8 wells of a 96-well plate ( Costar ) at approximately 0.1 OD ( 600 nm ) . The samples were placed in a Synergy HT Microplate Reader ( BioTek ) and incubated at <Temp> 37 °C </Temp> with orbital shaking at 1,000 rpm for 1 h , performing measurements of GFP ( excitation ( ex . ) , 485 nm ; emission ( em . ) , 528 nm ) and OD ( 600 nm ) every 15 minutes . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE107093	Burden- driven feedback control of gene expression	GSM2861142	R16 MG1655GFP_pLys_M1_1	29578536	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS	SRR6305261	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cells with construct and control plasmids were grown at <Temp> 37 °C </Temp> overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic . In the morning , 60 μl of each sample were diluted into 3 ml <Med> of fresh medium </Med> and grown at <Temp> 37 °C </Temp> with shaking for another hour ( outgrowth ) . 200 μl of each sample were then transferred in 8 wells of a 96-well plate ( Costar ) at approximately 0.1 OD ( 600 nm ) . The samples were placed in a Synergy HT Microplate Reader ( BioTek ) and incubated at <Temp> 37 °C </Temp> with orbital shaking at 1,000 rpm for 1 h , performing measurements of GFP ( excitation ( ex . ) , 485 nm ; emission ( em . ) , 528 nm ) and OD ( 600 nm ) every 15 minutes . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE107093	Burden- driven feedback control of gene expression	GSM2861145	R19 MG1655GFP_Lux_1	29578536	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS	SRR6305264	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cells with construct and control plasmids were grown at <Temp> 37 °C </Temp> overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic . In the morning , 60 μl of each sample were diluted into 3 ml <Med> of fresh medium </Med> and grown at <Temp> 37 °C </Temp> with shaking for another hour ( outgrowth ) . 200 μl of each sample were then transferred in 8 wells of a 96-well plate ( Costar ) at approximately 0.1 OD ( 600 nm ) . The samples were placed in a Synergy HT Microplate Reader ( BioTek ) and incubated at <Temp> 37 °C </Temp> with orbital shaking at 1,000 rpm for 1 h , performing measurements of GFP ( excitation ( ex . ) , 485 nm ; emission ( em . ) , 528 nm ) and OD ( 600 nm ) every 15 minutes . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE107093	Burden- driven feedback control of gene expression	GSM2861152	R26 MG1655GFP_Lux_1	29578536	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS	SRR6305271	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cells with construct and control plasmids were grown at <Temp> 37 °C </Temp> overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic . In the morning , 60 μl of each sample were diluted into 3 ml <Med> of fresh medium </Med> and grown at <Temp> 37 °C </Temp> with shaking for another hour ( outgrowth ) . 200 μl of each sample were then transferred in 8 wells of a 96-well plate ( Costar ) at approximately 0.1 OD ( 600 nm ) . The samples were placed in a Synergy HT Microplate Reader ( BioTek ) and incubated at <Temp> 37 °C </Temp> with orbital shaking at 1,000 rpm for 1 h , performing measurements of GFP ( excitation ( ex . ) , 485 nm ; emission ( em . ) , 528 nm ) and OD ( 600 nm ) every 15 minutes . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE107093	Burden- driven feedback control of gene expression	GSM2861153	R27 MG1655GFP_pD864_LacZ_1	29578536	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS	SRR6305272	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cells with construct and control plasmids were grown at <Temp> 37 °C </Temp> overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic . In the morning , 60 μl of each sample were diluted into 3 ml <Med> of fresh medium </Med> and grown at <Temp> 37 °C </Temp> with shaking for another hour ( outgrowth ) . 200 μl of each sample were then transferred in 8 wells of a 96-well plate ( Costar ) at approximately 0.1 OD ( 600 nm ) . The samples were placed in a Synergy HT Microplate Reader ( BioTek ) and incubated at <Temp> 37 °C </Temp> with orbital shaking at 1,000 rpm for 1 h , performing measurements of GFP ( excitation ( ex . ) , 485 nm ; emission ( em . ) , 528 nm ) and OD ( 600 nm ) every 15 minutes . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE107093	Burden- driven feedback control of gene expression	GSM2861155	R29 DH10BGFP_None_1	29578536	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS	SRR6305274	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cells with construct and control plasmids were grown at <Temp> 37 °C </Temp> overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic . In the morning , 60 μl of each sample were diluted into 3 ml <Med> of fresh medium </Med> and grown at <Temp> 37 °C </Temp> with shaking for another hour ( outgrowth ) . 200 μl of each sample were then transferred in 8 wells of a 96-well plate ( Costar ) at approximately 0.1 OD ( 600 nm ) . The samples were placed in a Synergy HT Microplate Reader ( BioTek ) and incubated at <Temp> 37 °C </Temp> with orbital shaking at 1,000 rpm for 1 h , performing measurements of GFP ( excitation ( ex . ) , 485 nm ; emission ( em . ) , 528 nm ) and OD ( 600 nm ) every 15 minutes . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE107093	Burden- driven feedback control of gene expression	GSM2861159	B3 DH10BGFP_pSB1C3_2	29578536	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS	SRR6305278	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cells with construct and control plasmids were grown at <Temp> 37 °C </Temp> overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic . In the morning , 60 μl of each sample were diluted into 3 ml <Med> of fresh medium </Med> and grown at <Temp> 37 °C </Temp> with shaking for another hour ( outgrowth ) . 200 μl of each sample were then transferred in 8 wells of a 96-well plate ( Costar ) at approximately 0.1 OD ( 600 nm ) . The samples were placed in a Synergy HT Microplate Reader ( BioTek ) and incubated at <Temp> 37 °C </Temp> with orbital shaking at 1,000 rpm for 1 h , performing measurements of GFP ( excitation ( ex . ) , 485 nm ; emission ( em . ) , 528 nm ) and OD ( 600 nm ) every 15 minutes . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE107093	Burden- driven feedback control of gene expression	GSM2861160	B4 DH10BGFP_pLys_2	29578536	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS	SRR6305279	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cells with construct and control plasmids were grown at <Temp> 37 °C </Temp> overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic . In the morning , 60 μl of each sample were diluted into 3 ml <Med> of fresh medium </Med> and grown at <Temp> 37 °C </Temp> with shaking for another hour ( outgrowth ) . 200 μl of each sample were then transferred in 8 wells of a 96-well plate ( Costar ) at approximately 0.1 OD ( 600 nm ) . The samples were placed in a Synergy HT Microplate Reader ( BioTek ) and incubated at <Temp> 37 °C </Temp> with orbital shaking at 1,000 rpm for 1 h , performing measurements of GFP ( excitation ( ex . ) , 485 nm ; emission ( em . ) , 528 nm ) and OD ( 600 nm ) every 15 minutes . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE107093	Burden- driven feedback control of gene expression	GSM2861163	B7 DH10BGFP_pD864_2	29578536	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS	SRR6305282	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cells with construct and control plasmids were grown at <Temp> 37 °C </Temp> overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic . In the morning , 60 μl of each sample were diluted into 3 ml <Med> of fresh medium </Med> and grown at <Temp> 37 °C </Temp> with shaking for another hour ( outgrowth ) . 200 μl of each sample were then transferred in 8 wells of a 96-well plate ( Costar ) at approximately 0.1 OD ( 600 nm ) . The samples were placed in a Synergy HT Microplate Reader ( BioTek ) and incubated at <Temp> 37 °C </Temp> with orbital shaking at 1,000 rpm for 1 h , performing measurements of GFP ( excitation ( ex . ) , 485 nm ; emission ( em . ) , 528 nm ) and OD ( 600 nm ) every 15 minutes . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE107093	Burden- driven feedback control of gene expression	GSM2861165	B9 DH10BGFP_pLys_M1_2	29578536	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS	SRR6305284	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cells with construct and control plasmids were grown at <Temp> 37 °C </Temp> overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic . In the morning , 60 μl of each sample were diluted into 3 ml <Med> of fresh medium </Med> and grown at <Temp> 37 °C </Temp> with shaking for another hour ( outgrowth ) . 200 μl of each sample were then transferred in 8 wells of a 96-well plate ( Costar ) at approximately 0.1 OD ( 600 nm ) . The samples were placed in a Synergy HT Microplate Reader ( BioTek ) and incubated at <Temp> 37 °C </Temp> with orbital shaking at 1,000 rpm for 1 h , performing measurements of GFP ( excitation ( ex . ) , 485 nm ; emission ( em . ) , 528 nm ) and OD ( 600 nm ) every 15 minutes . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE107093	Burden- driven feedback control of gene expression	GSM2861166	B10 DH10BGFP_pSB1C3_2	29578536	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS	SRR6305285	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cells with construct and control plasmids were grown at <Temp> 37 °C </Temp> overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic . In the morning , 60 μl of each sample were diluted into 3 ml <Med> of fresh medium </Med> and grown at <Temp> 37 °C </Temp> with shaking for another hour ( outgrowth ) . 200 μl of each sample were then transferred in 8 wells of a 96-well plate ( Costar ) at approximately 0.1 OD ( 600 nm ) . The samples were placed in a Synergy HT Microplate Reader ( BioTek ) and incubated at <Temp> 37 °C </Temp> with orbital shaking at 1,000 rpm for 1 h , performing measurements of GFP ( excitation ( ex . ) , 485 nm ; emission ( em . ) , 528 nm ) and OD ( 600 nm ) every 15 minutes . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE107093	Burden- driven feedback control of gene expression	GSM2861173	B17 MG1655GFP_pSB1C3_2	29578536	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS	SRR6305292	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cells with construct and control plasmids were grown at <Temp> 37 °C </Temp> overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic . In the morning , 60 μl of each sample were diluted into 3 ml <Med> of fresh medium </Med> and grown at <Temp> 37 °C </Temp> with shaking for another hour ( outgrowth ) . 200 μl of each sample were then transferred in 8 wells of a 96-well plate ( Costar ) at approximately 0.1 OD ( 600 nm ) . The samples were placed in a Synergy HT Microplate Reader ( BioTek ) and incubated at <Temp> 37 °C </Temp> with orbital shaking at 1,000 rpm for 1 h , performing measurements of GFP ( excitation ( ex . ) , 485 nm ; emission ( em . ) , 528 nm ) and OD ( 600 nm ) every 15 minutes . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE107093	Burden- driven feedback control of gene expression	GSM2861178	B22 MG1655GFP_pSB1C3_H3_2	29578536	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS	SRR6305297	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cells with construct and control plasmids were grown at <Temp> 37 °C </Temp> overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic . In the morning , 60 μl of each sample were diluted into 3 ml <Med> of fresh medium </Med> and grown at <Temp> 37 °C </Temp> with shaking for another hour ( outgrowth ) . 200 μl of each sample were then transferred in 8 wells of a 96-well plate ( Costar ) at approximately 0.1 OD ( 600 nm ) . The samples were placed in a Synergy HT Microplate Reader ( BioTek ) and incubated at <Temp> 37 °C </Temp> with orbital shaking at 1,000 rpm for 1 h , performing measurements of GFP ( excitation ( ex . ) , 485 nm ; emission ( em . ) , 528 nm ) and OD ( 600 nm ) every 15 minutes . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE107093	Burden- driven feedback control of gene expression	GSM2861182	B26 MG1655GFP_Lux_2	29578536	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS	SRR6305301	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cells with construct and control plasmids were grown at <Temp> 37 °C </Temp> overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic . In the morning , 60 μl of each sample were diluted into 3 ml <Med> of fresh medium </Med> and grown at <Temp> 37 °C </Temp> with shaking for another hour ( outgrowth ) . 200 μl of each sample were then transferred in 8 wells of a 96-well plate ( Costar ) at approximately 0.1 OD ( 600 nm ) . The samples were placed in a Synergy HT Microplate Reader ( BioTek ) and incubated at <Temp> 37 °C </Temp> with orbital shaking at 1,000 rpm for 1 h , performing measurements of GFP ( excitation ( ex . ) , 485 nm ; emission ( em . ) , 528 nm ) and OD ( 600 nm ) every 15 minutes . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE107093	Burden- driven feedback control of gene expression	GSM2861191	G5 DH10BGFP_Lux_3	29578536	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS	SRR6305310	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cells with construct and control plasmids were grown at <Temp> 37 °C </Temp> overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic . In the morning , 60 μl of each sample were diluted into 3 ml <Med> of fresh medium </Med> and grown at <Temp> 37 °C </Temp> with shaking for another hour ( outgrowth ) . 200 μl of each sample were then transferred in 8 wells of a 96-well plate ( Costar ) at approximately 0.1 OD ( 600 nm ) . The samples were placed in a Synergy HT Microplate Reader ( BioTek ) and incubated at <Temp> 37 °C </Temp> with orbital shaking at 1,000 rpm for 1 h , performing measurements of GFP ( excitation ( ex . ) , 485 nm ; emission ( em . ) , 528 nm ) and OD ( 600 nm ) every 15 minutes . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE107093	Burden- driven feedback control of gene expression	GSM2861192	G6 DH10BGFP_pD864_LacZ_3	29578536	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS	SRR6305311	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cells with construct and control plasmids were grown at <Temp> 37 °C </Temp> overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic . In the morning , 60 μl of each sample were diluted into 3 ml <Med> of fresh medium </Med> and grown at <Temp> 37 °C </Temp> with shaking for another hour ( outgrowth ) . 200 μl of each sample were then transferred in 8 wells of a 96-well plate ( Costar ) at approximately 0.1 OD ( 600 nm ) . The samples were placed in a Synergy HT Microplate Reader ( BioTek ) and incubated at <Temp> 37 °C </Temp> with orbital shaking at 1,000 rpm for 1 h , performing measurements of GFP ( excitation ( ex . ) , 485 nm ; emission ( em . ) , 528 nm ) and OD ( 600 nm ) every 15 minutes . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE107093	Burden- driven feedback control of gene expression	GSM2861207	G21 MG1655GFP_pD864_3	29578536	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS	SRR6305326	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cells with construct and control plasmids were grown at <Temp> 37 °C </Temp> overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic . In the morning , 60 μl of each sample were diluted into 3 ml <Med> of fresh medium </Med> and grown at <Temp> 37 °C </Temp> with shaking for another hour ( outgrowth ) . 200 μl of each sample were then transferred in 8 wells of a 96-well plate ( Costar ) at approximately 0.1 OD ( 600 nm ) . The samples were placed in a Synergy HT Microplate Reader ( BioTek ) and incubated at <Temp> 37 °C </Temp> with orbital shaking at 1,000 rpm for 1 h , performing measurements of GFP ( excitation ( ex . ) , 485 nm ; emission ( em . ) , 528 nm ) and OD ( 600 nm ) every 15 minutes . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE107093	Burden- driven feedback control of gene expression	GSM2861209	G23 MG1655GFP_pLys_M1_3	29578536	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS	SRR6305328	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cells with construct and control plasmids were grown at <Temp> 37 °C </Temp> overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic . In the morning , 60 μl of each sample were diluted into 3 ml <Med> of fresh medium </Med> and grown at <Temp> 37 °C </Temp> with shaking for another hour ( outgrowth ) . 200 μl of each sample were then transferred in 8 wells of a 96-well plate ( Costar ) at approximately 0.1 OD ( 600 nm ) . The samples were placed in a Synergy HT Microplate Reader ( BioTek ) and incubated at <Temp> 37 °C </Temp> with orbital shaking at 1,000 rpm for 1 h , performing measurements of GFP ( excitation ( ex . ) , 485 nm ; emission ( em . ) , 528 nm ) and OD ( 600 nm ) every 15 minutes . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE107093	Burden- driven feedback control of gene expression	GSM2861214	G28 MG1655GFP_pD864_3	29578536	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS	SRR6305333	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cells with construct and control plasmids were grown at <Temp> 37 °C </Temp> overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic . In the morning , 60 μl of each sample were diluted into 3 ml <Med> of fresh medium </Med> and grown at <Temp> 37 °C </Temp> with shaking for another hour ( outgrowth ) . 200 μl of each sample were then transferred in 8 wells of a 96-well plate ( Costar ) at approximately 0.1 OD ( 600 nm ) . The samples were placed in a Synergy HT Microplate Reader ( BioTek ) and incubated at <Temp> 37 °C </Temp> with orbital shaking at 1,000 rpm for 1 h , performing measurements of GFP ( excitation ( ex . ) , 485 nm ; emission ( em . ) , 528 nm ) and OD ( 600 nm ) every 15 minutes . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE107093	Burden- driven feedback control of gene expression	GSM2861215	G29 DH10BGFP_None_3	29578536	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cells with construct and control plasmids were grown at 37°C overnight with aeration in a shaking incubator in 5 ml of defined supplemented M9 medium with the appropriate antibiotic. In the morning, 60 μl of each sample were diluted into 3 ml of fresh medium and grown at 37°C with shaking for another hour (outgrowth). 200 μl of each sample were then transferred in 8 wells of a 96-well plate (Costar) at approximately 0.1 OD (600 nm). The samples were placed in a Synergy HT Microplate Reader (BioTek) and incubated at 37°C with orbital shaking at 1,000 rpm for 1 h, performing measurements of GFP (excitation (ex.), 485 nm; emission (em.), 528 nm) and OD (600 nm) every 15 minutes. PGCGROWTHCONDITIONS	SRR6305334	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		For 3C-seq : ≈ 1-2 x 109 crosslinked cells ( 7 % formaldehyde , unless otherwise stated ) are suspended in 600 μl Tris 10 mM EDTA 0.5 mM ( TE ) ( pH 8 ) with 4 μl of lysozyme ( 35 U/μl ; Tebu Bio ) , and incubated at RT for 20 minutes . SDS is added to the mix ( final concentration 0.5 % ) and the cells are incubated for 10 minutes at RT. 50μl of lysed cells are then transferred in 8 tubes containing 450μL of digestion mix ( 1X NEB 1 buffer , 1 % triton X-100 , and 100U HpaII enzyme ) . DNA is digested for 3 hours at <Temp> 37 °C </Temp> , split in 4 aliquots , and diluted in 8 ml ligation buffer ( 1X ligation buffer NEB without ATP , 1 mM ATP , 0.1 mg/ml BSA , 125 Units of T4 DNA ligase 5 U/μl ) . Ligation is then performed at 16 °C for 4 hours , followed by incubation overnight ( ON ) at 65 °C in presence of 250 μg/ml proteinase K and 5 mM EDTA . Precipitation of DNA is performed using an equal volume of 3 M Na-Acetate ( pH 5.2 ) and two volumes of iso-propanol . After one hour at -80 °C , DNA is pelleted , suspended in 500μl 1X TE buffer , and incubated for 30 minutes at <Temp> 37 °C </Temp> in presence of RNAse A ( 0.03 mg/ml ) . DNA is then transferred into 2 ml centrifuge tubes , extracted twice with 500 μl phenol-chloroform pH 8.0 , precipitated , washed with 1 ml cold ethanol 70 % and diluted in 30 μl 1X TE buffer . All tubes are pooled and the resulting 3C library is quantified on gel using Quantity One software ( BioRad ) . 	GPL15010-GPL21117	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21117: Illumina NextSeq 500 (Escherichia coli str. K-12 substr. MG1655)	GSE107301	Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins	GSM2870440	RNA-seq of E. coli wt cells in stationary phase 30°C (30h)	29358050	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107301/GSE107301.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For 3C-seq: ≈ 1-2 x 109 crosslinked cells (7% formaldehyde, unless otherwise stated ) are suspended in 600 μl Tris 10 mM EDTA 0.5 mM (TE) (pH 8) with 4 μl of lysozyme (35 U/μl; Tebu Bio), and incubated at RT for 20 minutes. SDS is added to the mix (final concentration 0.5%) and the cells are incubated for 10 minutes at RT. 50μl of lysed cells are then transferred in 8 tubes containing 450μL of digestion mix (1X NEB 1 buffer, 1% triton X-100, and 100U HpaII enzyme). DNA is digested for 3 hours at 37°C, split in 4 aliquots, and diluted in 8 ml ligation buffer (1X ligation buffer NEB without ATP, 1 mM ATP, 0.1 mg/ml BSA, 125 Units of T4 DNA ligase 5 U/μl). Ligation is then performed at 16°C for 4 hours, followed by incubation overnight (ON) at 65°C in presence of 250 μg/ml proteinase K and 5 mM EDTA. Precipitation of DNA is performed using an equal volume of 3 M Na-Acetate (pH 5.2) and two volumes of iso-propanol. After one hour at -80°C, DNA is pelleted, suspended in 500μl 1X TE buffer, and incubated for 30 minutes at 37°C in presence of RNAse A (0.03 mg/ml). DNA is then transferred into 2 ml centrifuge tubes, extracted twice with 500 μl phenol-chloroform pH 8.0, precipitated, washed with 1 ml cold ethanol 70% and diluted in 30 μl 1X TE buffer. All tubes are pooled and the resulting 3C library is quantified on gel using Quantity One software (BioRad). PGCGROWTHCONDITIONS	SRR6354578	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cells were grown at 22 °C , 30 °C and <Temp> 37 °C </Temp> in either Lennox Broth ( LB ) or liquid minimal medium A supplemented with 0.12 % casamino acids and 0.4 % glucose . The cultures were grown to OD600 = 0.2 ( early exponential ) or 2 ( stationary phase ) . 	GPL15010-GPL21117	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21117: Illumina NextSeq 500 (Escherichia coli str. K-12 substr. MG1655)	GSE107301	Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins	GSM2870440	RNA-seq of E. coli wt cells in stationary phase 30°C (30h)	29358050	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107301/GSE107301.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cells were grown at 22°C, 30°C and 37°C in either Lennox Broth (LB) or liquid minimal medium A supplemented with 0.12% casamino acids and 0.4% glucose. The cultures were grown to OD600 = 0.2 (early exponential) or 2 (stationary phase). PGCGROWTHCONDITIONS	SRR6354578	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		For 3C-seq : ≈ 1-2 x 109 crosslinked cells ( 7 % formaldehyde , unless otherwise stated ) are suspended in 600 μl Tris 10 mM EDTA 0.5 mM ( TE ) ( pH 8 ) with 4 μl of lysozyme ( 35 U/μl ; Tebu Bio ) , and incubated at RT for 20 minutes . SDS is added to the mix ( final concentration 0.5 % ) and the cells are incubated for 10 minutes at RT. 50μl of lysed cells are then transferred in 8 tubes containing 450μL of digestion mix ( 1X NEB 1 buffer , 1 % triton X-100 , and 100U HpaII enzyme ) . DNA is digested for 3 hours at <Temp> 37 °C </Temp> , split in 4 aliquots , and diluted in 8 ml ligation buffer ( 1X ligation buffer NEB without ATP , 1 mM ATP , 0.1 mg/ml BSA , 125 Units of T4 DNA ligase 5 U/μl ) . Ligation is then performed at 16 °C for 4 hours , followed by incubation overnight ( ON ) at 65 °C in presence of 250 μg/ml proteinase K and 5 mM EDTA . Precipitation of DNA is performed using an equal volume of 3 M Na-Acetate ( pH 5.2 ) and two volumes of iso-propanol . After one hour at -80 °C , DNA is pelleted , suspended in 500μl 1X TE buffer , and incubated for 30 minutes at <Temp> 37 °C </Temp> in presence of RNAse A ( 0.03 mg/ml ) . DNA is then transferred into 2 ml centrifuge tubes , extracted twice with 500 μl phenol-chloroform pH 8.0 , precipitated , washed with 1 ml cold ethanol 70 % and diluted in 30 μl 1X TE buffer . All tubes are pooled and the resulting 3C library is quantified on gel using Quantity One software ( BioRad ) . 	GPL15010-GPL21117	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21117: Illumina NextSeq 500 (Escherichia coli str. K-12 substr. MG1655)	GSE107301	Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins	GSM2870441	RNA-seq of E. coli wt cells in stationary phase 30°C (30h) -Replicate 1	29358050	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107301/GSE107301.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For 3C-seq: ≈ 1-2 x 109 crosslinked cells (7% formaldehyde, unless otherwise stated ) are suspended in 600 μl Tris 10 mM EDTA 0.5 mM (TE) (pH 8) with 4 μl of lysozyme (35 U/μl; Tebu Bio), and incubated at RT for 20 minutes. SDS is added to the mix (final concentration 0.5%) and the cells are incubated for 10 minutes at RT. 50μl of lysed cells are then transferred in 8 tubes containing 450μL of digestion mix (1X NEB 1 buffer, 1% triton X-100, and 100U HpaII enzyme). DNA is digested for 3 hours at 37°C, split in 4 aliquots, and diluted in 8 ml ligation buffer (1X ligation buffer NEB without ATP, 1 mM ATP, 0.1 mg/ml BSA, 125 Units of T4 DNA ligase 5 U/μl). Ligation is then performed at 16°C for 4 hours, followed by incubation overnight (ON) at 65°C in presence of 250 μg/ml proteinase K and 5 mM EDTA. Precipitation of DNA is performed using an equal volume of 3 M Na-Acetate (pH 5.2) and two volumes of iso-propanol. After one hour at -80°C, DNA is pelleted, suspended in 500μl 1X TE buffer, and incubated for 30 minutes at 37°C in presence of RNAse A (0.03 mg/ml). DNA is then transferred into 2 ml centrifuge tubes, extracted twice with 500 μl phenol-chloroform pH 8.0, precipitated, washed with 1 ml cold ethanol 70% and diluted in 30 μl 1X TE buffer. All tubes are pooled and the resulting 3C library is quantified on gel using Quantity One software (BioRad). PGCGROWTHCONDITIONS	SRR6354579	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cells were grown at 22 °C , 30 °C and <Temp> 37 °C </Temp> in either Lennox Broth ( LB ) or liquid minimal medium A supplemented with 0.12 % casamino acids and 0.4 % glucose . The cultures were grown to OD600 = 0.2 ( early exponential ) or 2 ( stationary phase ) . 	GPL15010-GPL21117	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21117: Illumina NextSeq 500 (Escherichia coli str. K-12 substr. MG1655)	GSE107301	Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins	GSM2870441	RNA-seq of E. coli wt cells in stationary phase 30°C (30h) -Replicate 1	29358050	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107301/GSE107301.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cells were grown at 22°C, 30°C and 37°C in either Lennox Broth (LB) or liquid minimal medium A supplemented with 0.12% casamino acids and 0.4% glucose. The cultures were grown to OD600 = 0.2 (early exponential) or 2 (stationary phase). PGCGROWTHCONDITIONS	SRR6354579	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Separate E. coli colonies were picked from LB agar plates for each replicate . Overnight cultures ( 12-16 hrs ) were grown at <Temp> 37 °C </Temp> in M9 media supplemented with 0.1 % casamino acids , 0.4 % glycerol , 0.4 % glucose , 2 mM MgSO4 , and 0.1 mM CaCl2 . Overnight cultures were back diluted into fresh <Med> media </Med> and grown 3-4 hours to an <OD> OD600 of ~ 0.35 </OD> at <Temp> 37 °C </Temp> in an orbital shaker at 200 RPM . Cultures were centrifuged , washed , and back diluted into media lacking glucose . After at least 30 minutes of recovery Para was induced by adding arabinose to 0.2 % . Cells were harvested by centrifuging 1 mL of culture for 1 minute at maximum speed on a benchtop centrifuge . Pellets were immediately flash frozen in lN2 . 	GPL21222	GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE107327	E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis [RNA-seq]	GSM2864853	emptyvec_mRNA_5m_rep1	29861158	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107327/GSE107327.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Separate E. coli colonies were picked from LB agar plates for each replicate. Overnight cultures (12-16 hrs) were grown at 37°C in M9 media supplemented with 0.1% casamino acids, 0.4% glycerol, 0.4% glucose, 2 mM MgSO4, and 0.1 mM CaCl2. Overnight cultures were back diluted into fresh media and grown 3-4 hours to an OD600 of ~0.35 at 37°C in an orbital shaker at 200 RPM. Cultures were centrifuged, washed, and back diluted into media lacking glucose. After at least 30 minutes of recovery Para was induced by adding arabinose to 0.2%. Cells were harvested by centrifuging 1 mL of culture for 1 minute at maximum speed on a benchtop centrifuge. Pellets were immediately flash frozen in lN2. PGCGROWTHCONDITIONS	SRR6322033	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Separate E. coli colonies were picked from LB agar plates for each replicate . Overnight cultures ( 12-16 hrs ) were grown at <Temp> 37 °C </Temp> in M9 media supplemented with 0.1 % casamino acids , 0.4 % glycerol , 0.4 % glucose , 2 mM MgSO4 , and 0.1 mM CaCl2 . Overnight cultures were back diluted into fresh <Med> media </Med> and grown 3-4 hours to an <OD> OD600 of ~ 0.35 </OD> at <Temp> 37 °C </Temp> in an orbital shaker at 200 RPM . Cultures were centrifuged , washed , and back diluted into media lacking glucose . After at least 30 minutes of recovery Para was induced by adding arabinose to 0.2 % . Cells were harvested by centrifuging 1 mL of culture for 1 minute at maximum speed on a benchtop centrifuge . Pellets were immediately flash frozen in lN2 . 	GPL21222	GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE107327	E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis [RNA-seq]	GSM2864854	emptyvec_mRNA_5m_rep2	29861158	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107327/GSE107327.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Separate E. coli colonies were picked from LB agar plates for each replicate. Overnight cultures (12-16 hrs) were grown at 37°C in M9 media supplemented with 0.1% casamino acids, 0.4% glycerol, 0.4% glucose, 2 mM MgSO4, and 0.1 mM CaCl2. Overnight cultures were back diluted into fresh media and grown 3-4 hours to an OD600 of ~0.35 at 37°C in an orbital shaker at 200 RPM. Cultures were centrifuged, washed, and back diluted into media lacking glucose. After at least 30 minutes of recovery Para was induced by adding arabinose to 0.2%. Cells were harvested by centrifuging 1 mL of culture for 1 minute at maximum speed on a benchtop centrifuge. Pellets were immediately flash frozen in lN2. PGCGROWTHCONDITIONS	SRR6322034	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Separate E. coli colonies were picked from LB agar plates for each replicate . Overnight cultures ( 12-16 hrs ) were grown at <Temp> 37 °C </Temp> in M9 media supplemented with 0.1 % casamino acids , 0.4 % glycerol , 0.4 % glucose , 2 mM MgSO4 , and 0.1 mM CaCl2 . Overnight cultures were back diluted into fresh <Med> media </Med> and grown 3-4 hours to an <OD> OD600 of ~ 0.35 </OD> at <Temp> 37 °C </Temp> in an orbital shaker at 200 RPM . Cultures were centrifuged , washed , and back diluted into media lacking glucose . After at least 30 minutes of recovery Para was induced by adding arabinose to 0.2 % . Cells were harvested by centrifuging 1 mL of culture for 1 minute at maximum speed on a benchtop centrifuge . Pellets were immediately flash frozen in lN2 . 	GPL21222	GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE107327	E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis [RNA-seq]	GSM2864855	MazF_mRNA_5m_rep1	29861158	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107327/GSE107327.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Separate E. coli colonies were picked from LB agar plates for each replicate. Overnight cultures (12-16 hrs) were grown at 37°C in M9 media supplemented with 0.1% casamino acids, 0.4% glycerol, 0.4% glucose, 2 mM MgSO4, and 0.1 mM CaCl2. Overnight cultures were back diluted into fresh media and grown 3-4 hours to an OD600 of ~0.35 at 37°C in an orbital shaker at 200 RPM. Cultures were centrifuged, washed, and back diluted into media lacking glucose. After at least 30 minutes of recovery Para was induced by adding arabinose to 0.2%. Cells were harvested by centrifuging 1 mL of culture for 1 minute at maximum speed on a benchtop centrifuge. Pellets were immediately flash frozen in lN2. PGCGROWTHCONDITIONS	SRR6322035	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Separate E. coli colonies were picked from LB agar plates for each replicate . Overnight cultures ( 12-16 hrs ) were grown at <Temp> 37 °C </Temp> in M9 media supplemented with 0.1 % casamino acids , 0.4 % glycerol , 0.4 % glucose , 2 mM MgSO4 , and 0.1 mM CaCl2 . Overnight cultures were back diluted into fresh <Med> media </Med> and grown 3-4 hours to an <OD> OD600 of ~ 0.35 </OD> at <Temp> 37 °C </Temp> in an orbital shaker at 200 RPM . Cultures were centrifuged , washed , and back diluted into media lacking glucose . After at least 30 minutes of recovery Para was induced by adding arabinose to 0.2 % . Cells were harvested by centrifuging 1 mL of culture for 1 minute at maximum speed on a benchtop centrifuge . Pellets were immediately flash frozen in lN2 . 	GPL21222	GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE107327	E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis [RNA-seq]	GSM2864856	MazF_mRNA_5m_rep2	29861158	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107327/GSE107327.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Separate E. coli colonies were picked from LB agar plates for each replicate. Overnight cultures (12-16 hrs) were grown at 37°C in M9 media supplemented with 0.1% casamino acids, 0.4% glycerol, 0.4% glucose, 2 mM MgSO4, and 0.1 mM CaCl2. Overnight cultures were back diluted into fresh media and grown 3-4 hours to an OD600 of ~0.35 at 37°C in an orbital shaker at 200 RPM. Cultures were centrifuged, washed, and back diluted into media lacking glucose. After at least 30 minutes of recovery Para was induced by adding arabinose to 0.2%. Cells were harvested by centrifuging 1 mL of culture for 1 minute at maximum speed on a benchtop centrifuge. Pellets were immediately flash frozen in lN2. PGCGROWTHCONDITIONS	SRR6322036	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		RNA was extracted using Trizol and chloroform in conjunction with Qiagen 's RNeasy Mini kit ( Qiagen , Valencia , CA ) following the A. Untergasser protocol ( http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm ) with one modification : <Gtype> Phase Lock Gel </Gtype> tubes ( Eppendorf , Westbury , NY ) were used to better separate organic and aqueous phases after the addition of chloroform . DNA was digested with Ambion rDNAse I ( Life Technologies , Carlsbad , CA ) for <Supp> 30 min </Supp> at <Temp> 37 °C </Temp> . Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 ( Agilent Technologies , Santa Clara , CA ) . Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit ( Life Technologies , Carlsbad , CA ) and were used for library construction . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914313	CF104.3.3_y2	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	RNA was extracted using Trizol and chloroform in conjunction with Qiagen’s RNeasy Mini kit (Qiagen, Valencia, CA) following the A. Untergasser protocol (http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm) with one modification: Phase Lock Gel tubes (Eppendorf, Westbury, NY) were used to better separate organic and aqueous phases after the addition of chloroform. DNA was digested with Ambion rDNAse I (Life Technologies, Carlsbad, CA) for 30 min at 37°C. Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 (Agilent Technologies, Santa Clara, CA). Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit (Life Technologies, Carlsbad, CA) and were used for library construction. PGCGROWTHCONDITIONS	SRR6449107	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Experiments were performed at <Temp> 37 °C </Temp> and followed three steps : seed culture , pre-culture and experimental culture . In the seed culture the cells were grown overnight in Luria Broth , then diluted 1:100 in either <Med> M9 minimal media </Med> with glycerol or glucose for the pre-cultures . Finally , the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm ( OD600 ) of 0.05 . Cultures were harvested at mid-exponential phase , cells were immediately spun down and cell pellets stored at -80 °C until processed . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914313	CF104.3.3_y2	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS	SRR6449107	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		RNA was extracted using Trizol and chloroform in conjunction with Qiagen 's RNeasy Mini kit ( Qiagen , Valencia , CA ) following the A. Untergasser protocol ( http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm ) with one modification : <Gtype> Phase Lock Gel </Gtype> tubes ( Eppendorf , Westbury , NY ) were used to better separate organic and aqueous phases after the addition of chloroform . DNA was digested with Ambion rDNAse I ( Life Technologies , Carlsbad , CA ) for <Supp> 30 min </Supp> at <Temp> 37 °C </Temp> . Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 ( Agilent Technologies , Santa Clara , CA ) . Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit ( Life Technologies , Carlsbad , CA ) and were used for library construction . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914315	CF108.4B_y3	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	RNA was extracted using Trizol and chloroform in conjunction with Qiagen’s RNeasy Mini kit (Qiagen, Valencia, CA) following the A. Untergasser protocol (http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm) with one modification: Phase Lock Gel tubes (Eppendorf, Westbury, NY) were used to better separate organic and aqueous phases after the addition of chloroform. DNA was digested with Ambion rDNAse I (Life Technologies, Carlsbad, CA) for 30 min at 37°C. Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 (Agilent Technologies, Santa Clara, CA). Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit (Life Technologies, Carlsbad, CA) and were used for library construction. PGCGROWTHCONDITIONS	SRR6449109	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Experiments were performed at <Temp> 37 °C </Temp> and followed three steps : seed culture , pre-culture and experimental culture . In the seed culture the cells were grown overnight in Luria Broth , then diluted 1:100 in either <Med> M9 minimal media </Med> with glycerol or glucose for the pre-cultures . Finally , the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm ( OD600 ) of 0.05 . Cultures were harvested at mid-exponential phase , cells were immediately spun down and cell pellets stored at -80 °C until processed . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914315	CF108.4B_y3	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS	SRR6449109	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		RNA was extracted using Trizol and chloroform in conjunction with Qiagen 's RNeasy Mini kit ( Qiagen , Valencia , CA ) following the A. Untergasser protocol ( http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm ) with one modification : <Gtype> Phase Lock Gel </Gtype> tubes ( Eppendorf , Westbury , NY ) were used to better separate organic and aqueous phases after the addition of chloroform . DNA was digested with Ambion rDNAse I ( Life Technologies , Carlsbad , CA ) for <Supp> 30 min </Supp> at <Temp> 37 °C </Temp> . Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 ( Agilent Technologies , Santa Clara , CA ) . Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit ( Life Technologies , Carlsbad , CA ) and were used for library construction . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914317	CON206.3A_y1	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	RNA was extracted using Trizol and chloroform in conjunction with Qiagen’s RNeasy Mini kit (Qiagen, Valencia, CA) following the A. Untergasser protocol (http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm) with one modification: Phase Lock Gel tubes (Eppendorf, Westbury, NY) were used to better separate organic and aqueous phases after the addition of chloroform. DNA was digested with Ambion rDNAse I (Life Technologies, Carlsbad, CA) for 30 min at 37°C. Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 (Agilent Technologies, Santa Clara, CA). Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit (Life Technologies, Carlsbad, CA) and were used for library construction. PGCGROWTHCONDITIONS	SRR6449111	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Experiments were performed at <Temp> 37 °C </Temp> and followed three steps : seed culture , pre-culture and experimental culture . In the seed culture the cells were grown overnight in Luria Broth , then diluted 1:100 in either <Med> M9 minimal media </Med> with glycerol or glucose for the pre-cultures . Finally , the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm ( OD600 ) of 0.05 . Cultures were harvested at mid-exponential phase , cells were immediately spun down and cell pellets stored at -80 °C until processed . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914317	CON206.3A_y1	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS	SRR6449111	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		RNA was extracted using Trizol and chloroform in conjunction with Qiagen 's RNeasy Mini kit ( Qiagen , Valencia , CA ) following the A. Untergasser protocol ( http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm ) with one modification : <Gtype> Phase Lock Gel </Gtype> tubes ( Eppendorf , Westbury , NY ) were used to better separate organic and aqueous phases after the addition of chloroform . DNA was digested with Ambion rDNAse I ( Life Technologies , Carlsbad , CA ) for <Supp> 30 min </Supp> at <Temp> 37 °C </Temp> . Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 ( Agilent Technologies , Santa Clara , CA ) . Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit ( Life Technologies , Carlsbad , CA ) and were used for library construction . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914318	CON206.3A_y2	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	RNA was extracted using Trizol and chloroform in conjunction with Qiagen’s RNeasy Mini kit (Qiagen, Valencia, CA) following the A. Untergasser protocol (http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm) with one modification: Phase Lock Gel tubes (Eppendorf, Westbury, NY) were used to better separate organic and aqueous phases after the addition of chloroform. DNA was digested with Ambion rDNAse I (Life Technologies, Carlsbad, CA) for 30 min at 37°C. Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 (Agilent Technologies, Santa Clara, CA). Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit (Life Technologies, Carlsbad, CA) and were used for library construction. PGCGROWTHCONDITIONS	SRR6449112	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Experiments were performed at <Temp> 37 °C </Temp> and followed three steps : seed culture , pre-culture and experimental culture . In the seed culture the cells were grown overnight in Luria Broth , then diluted 1:100 in either <Med> M9 minimal media </Med> with glycerol or glucose for the pre-cultures . Finally , the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm ( OD600 ) of 0.05 . Cultures were harvested at mid-exponential phase , cells were immediately spun down and cell pellets stored at -80 °C until processed . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914318	CON206.3A_y2	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS	SRR6449112	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		RNA was extracted using Trizol and chloroform in conjunction with Qiagen 's RNeasy Mini kit ( Qiagen , Valencia , CA ) following the A. Untergasser protocol ( http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm ) with one modification : <Gtype> Phase Lock Gel </Gtype> tubes ( Eppendorf , Westbury , NY ) were used to better separate organic and aqueous phases after the addition of chloroform . DNA was digested with Ambion rDNAse I ( Life Technologies , Carlsbad , CA ) for <Supp> 30 min </Supp> at <Temp> 37 °C </Temp> . Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 ( Agilent Technologies , Santa Clara , CA ) . Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit ( Life Technologies , Carlsbad , CA ) and were used for library construction . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914319	CON208.3A_y2	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	RNA was extracted using Trizol and chloroform in conjunction with Qiagen’s RNeasy Mini kit (Qiagen, Valencia, CA) following the A. Untergasser protocol (http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm) with one modification: Phase Lock Gel tubes (Eppendorf, Westbury, NY) were used to better separate organic and aqueous phases after the addition of chloroform. DNA was digested with Ambion rDNAse I (Life Technologies, Carlsbad, CA) for 30 min at 37°C. Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 (Agilent Technologies, Santa Clara, CA). Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit (Life Technologies, Carlsbad, CA) and were used for library construction. PGCGROWTHCONDITIONS	SRR6449113	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Experiments were performed at <Temp> 37 °C </Temp> and followed three steps : seed culture , pre-culture and experimental culture . In the seed culture the cells were grown overnight in Luria Broth , then diluted 1:100 in either <Med> M9 minimal media </Med> with glycerol or glucose for the pre-cultures . Finally , the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm ( OD600 ) of 0.05 . Cultures were harvested at mid-exponential phase , cells were immediately spun down and cell pellets stored at -80 °C until processed . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914319	CON208.3A_y2	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS	SRR6449113	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		RNA was extracted using Trizol and chloroform in conjunction with Qiagen 's RNeasy Mini kit ( Qiagen , Valencia , CA ) following the A. Untergasser protocol ( http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm ) with one modification : <Gtype> Phase Lock Gel </Gtype> tubes ( Eppendorf , Westbury , NY ) were used to better separate organic and aqueous phases after the addition of chloroform . DNA was digested with Ambion rDNAse I ( Life Technologies , Carlsbad , CA ) for <Supp> 30 min </Supp> at <Temp> 37 °C </Temp> . Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 ( Agilent Technologies , Santa Clara , CA ) . Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit ( Life Technologies , Carlsbad , CA ) and were used for library construction . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914320	CON208.3A_y6	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	RNA was extracted using Trizol and chloroform in conjunction with Qiagen’s RNeasy Mini kit (Qiagen, Valencia, CA) following the A. Untergasser protocol (http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm) with one modification: Phase Lock Gel tubes (Eppendorf, Westbury, NY) were used to better separate organic and aqueous phases after the addition of chloroform. DNA was digested with Ambion rDNAse I (Life Technologies, Carlsbad, CA) for 30 min at 37°C. Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 (Agilent Technologies, Santa Clara, CA). Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit (Life Technologies, Carlsbad, CA) and were used for library construction. PGCGROWTHCONDITIONS	SRR6449114	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Experiments were performed at <Temp> 37 °C </Temp> and followed three steps : seed culture , pre-culture and experimental culture . In the seed culture the cells were grown overnight in Luria Broth , then diluted 1:100 in either <Med> M9 minimal media </Med> with glycerol or glucose for the pre-cultures . Finally , the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm ( OD600 ) of 0.05 . Cultures were harvested at mid-exponential phase , cells were immediately spun down and cell pellets stored at -80 °C until processed . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914320	CON208.3A_y6	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS	SRR6449114	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		RNA was extracted using Trizol and chloroform in conjunction with Qiagen 's RNeasy Mini kit ( Qiagen , Valencia , CA ) following the A. Untergasser protocol ( http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm ) with one modification : <Gtype> Phase Lock Gel </Gtype> tubes ( Eppendorf , Westbury , NY ) were used to better separate organic and aqueous phases after the addition of chloroform . DNA was digested with Ambion rDNAse I ( Life Technologies , Carlsbad , CA ) for <Supp> 30 min </Supp> at <Temp> 37 °C </Temp> . Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 ( Agilent Technologies , Santa Clara , CA ) . Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit ( Life Technologies , Carlsbad , CA ) and were used for library construction . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914321	CF104.3.3_u1	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	RNA was extracted using Trizol and chloroform in conjunction with Qiagen’s RNeasy Mini kit (Qiagen, Valencia, CA) following the A. Untergasser protocol (http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm) with one modification: Phase Lock Gel tubes (Eppendorf, Westbury, NY) were used to better separate organic and aqueous phases after the addition of chloroform. DNA was digested with Ambion rDNAse I (Life Technologies, Carlsbad, CA) for 30 min at 37°C. Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 (Agilent Technologies, Santa Clara, CA). Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit (Life Technologies, Carlsbad, CA) and were used for library construction. PGCGROWTHCONDITIONS	SRR6449115	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Experiments were performed at <Temp> 37 °C </Temp> and followed three steps : seed culture , pre-culture and experimental culture . In the seed culture the cells were grown overnight in Luria Broth , then diluted 1:100 in either <Med> M9 minimal media </Med> with glycerol or glucose for the pre-cultures . Finally , the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm ( OD600 ) of 0.05 . Cultures were harvested at mid-exponential phase , cells were immediately spun down and cell pellets stored at -80 °C until processed . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914321	CF104.3.3_u1	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS	SRR6449115	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		RNA was extracted using Trizol and chloroform in conjunction with Qiagen 's RNeasy Mini kit ( Qiagen , Valencia , CA ) following the A. Untergasser protocol ( http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm ) with one modification : <Gtype> Phase Lock Gel </Gtype> tubes ( Eppendorf , Westbury , NY ) were used to better separate organic and aqueous phases after the addition of chloroform . DNA was digested with Ambion rDNAse I ( Life Technologies , Carlsbad , CA ) for <Supp> 30 min </Supp> at <Temp> 37 °C </Temp> . Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 ( Agilent Technologies , Santa Clara , CA ) . Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit ( Life Technologies , Carlsbad , CA ) and were used for library construction . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914322	CF104.3.3_u7	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	RNA was extracted using Trizol and chloroform in conjunction with Qiagen’s RNeasy Mini kit (Qiagen, Valencia, CA) following the A. Untergasser protocol (http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm) with one modification: Phase Lock Gel tubes (Eppendorf, Westbury, NY) were used to better separate organic and aqueous phases after the addition of chloroform. DNA was digested with Ambion rDNAse I (Life Technologies, Carlsbad, CA) for 30 min at 37°C. Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 (Agilent Technologies, Santa Clara, CA). Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit (Life Technologies, Carlsbad, CA) and were used for library construction. PGCGROWTHCONDITIONS	SRR6449116	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Experiments were performed at <Temp> 37 °C </Temp> and followed three steps : seed culture , pre-culture and experimental culture . In the seed culture the cells were grown overnight in Luria Broth , then diluted 1:100 in either <Med> M9 minimal media </Med> with glycerol or glucose for the pre-cultures . Finally , the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm ( OD600 ) of 0.05 . Cultures were harvested at mid-exponential phase , cells were immediately spun down and cell pellets stored at -80 °C until processed . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914322	CF104.3.3_u7	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS	SRR6449116	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		RNA was extracted using Trizol and chloroform in conjunction with Qiagen 's RNeasy Mini kit ( Qiagen , Valencia , CA ) following the A. Untergasser protocol ( http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm ) with one modification : <Gtype> Phase Lock Gel </Gtype> tubes ( Eppendorf , Westbury , NY ) were used to better separate organic and aqueous phases after the addition of chloroform . DNA was digested with Ambion rDNAse I ( Life Technologies , Carlsbad , CA ) for <Supp> 30 min </Supp> at <Temp> 37 °C </Temp> . Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 ( Agilent Technologies , Santa Clara , CA ) . Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit ( Life Technologies , Carlsbad , CA ) and were used for library construction . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914323	CF108.4B_u1	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	RNA was extracted using Trizol and chloroform in conjunction with Qiagen’s RNeasy Mini kit (Qiagen, Valencia, CA) following the A. Untergasser protocol (http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm) with one modification: Phase Lock Gel tubes (Eppendorf, Westbury, NY) were used to better separate organic and aqueous phases after the addition of chloroform. DNA was digested with Ambion rDNAse I (Life Technologies, Carlsbad, CA) for 30 min at 37°C. Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 (Agilent Technologies, Santa Clara, CA). Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit (Life Technologies, Carlsbad, CA) and were used for library construction. PGCGROWTHCONDITIONS	SRR6449117	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Experiments were performed at <Temp> 37 °C </Temp> and followed three steps : seed culture , pre-culture and experimental culture . In the seed culture the cells were grown overnight in Luria Broth , then diluted 1:100 in either <Med> M9 minimal media </Med> with glycerol or glucose for the pre-cultures . Finally , the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm ( OD600 ) of 0.05 . Cultures were harvested at mid-exponential phase , cells were immediately spun down and cell pellets stored at -80 °C until processed . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914323	CF108.4B_u1	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS	SRR6449117	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		RNA was extracted using Trizol and chloroform in conjunction with Qiagen 's RNeasy Mini kit ( Qiagen , Valencia , CA ) following the A. Untergasser protocol ( http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm ) with one modification : <Gtype> Phase Lock Gel </Gtype> tubes ( Eppendorf , Westbury , NY ) were used to better separate organic and aqueous phases after the addition of chloroform . DNA was digested with Ambion rDNAse I ( Life Technologies , Carlsbad , CA ) for <Supp> 30 min </Supp> at <Temp> 37 °C </Temp> . Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 ( Agilent Technologies , Santa Clara , CA ) . Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit ( Life Technologies , Carlsbad , CA ) and were used for library construction . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914324	CF108.4B_u2	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	RNA was extracted using Trizol and chloroform in conjunction with Qiagen’s RNeasy Mini kit (Qiagen, Valencia, CA) following the A. Untergasser protocol (http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm) with one modification: Phase Lock Gel tubes (Eppendorf, Westbury, NY) were used to better separate organic and aqueous phases after the addition of chloroform. DNA was digested with Ambion rDNAse I (Life Technologies, Carlsbad, CA) for 30 min at 37°C. Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 (Agilent Technologies, Santa Clara, CA). Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit (Life Technologies, Carlsbad, CA) and were used for library construction. PGCGROWTHCONDITIONS	SRR6449118	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Experiments were performed at <Temp> 37 °C </Temp> and followed three steps : seed culture , pre-culture and experimental culture . In the seed culture the cells were grown overnight in Luria Broth , then diluted 1:100 in either <Med> M9 minimal media </Med> with glycerol or glucose for the pre-cultures . Finally , the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm ( OD600 ) of 0.05 . Cultures were harvested at mid-exponential phase , cells were immediately spun down and cell pellets stored at -80 °C until processed . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914324	CF108.4B_u2	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS	SRR6449118	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		RNA was extracted using Trizol and chloroform in conjunction with Qiagen 's RNeasy Mini kit ( Qiagen , Valencia , CA ) following the A. Untergasser protocol ( http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm ) with one modification : <Gtype> Phase Lock Gel </Gtype> tubes ( Eppendorf , Westbury , NY ) were used to better separate organic and aqueous phases after the addition of chloroform . DNA was digested with Ambion rDNAse I ( Life Technologies , Carlsbad , CA ) for <Supp> 30 min </Supp> at <Temp> 37 °C </Temp> . Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 ( Agilent Technologies , Santa Clara , CA ) . Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit ( Life Technologies , Carlsbad , CA ) and were used for library construction . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914325	CON206.3A_u1	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	RNA was extracted using Trizol and chloroform in conjunction with Qiagen’s RNeasy Mini kit (Qiagen, Valencia, CA) following the A. Untergasser protocol (http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm) with one modification: Phase Lock Gel tubes (Eppendorf, Westbury, NY) were used to better separate organic and aqueous phases after the addition of chloroform. DNA was digested with Ambion rDNAse I (Life Technologies, Carlsbad, CA) for 30 min at 37°C. Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 (Agilent Technologies, Santa Clara, CA). Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit (Life Technologies, Carlsbad, CA) and were used for library construction. PGCGROWTHCONDITIONS	SRR6449119	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Experiments were performed at <Temp> 37 °C </Temp> and followed three steps : seed culture , pre-culture and experimental culture . In the seed culture the cells were grown overnight in Luria Broth , then diluted 1:100 in either <Med> M9 minimal media </Med> with glycerol or glucose for the pre-cultures . Finally , the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm ( OD600 ) of 0.05 . Cultures were harvested at mid-exponential phase , cells were immediately spun down and cell pellets stored at -80 °C until processed . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914325	CON206.3A_u1	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS	SRR6449119	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		RNA was extracted using Trizol and chloroform in conjunction with Qiagen 's RNeasy Mini kit ( Qiagen , Valencia , CA ) following the A. Untergasser protocol ( http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm ) with one modification : <Gtype> Phase Lock Gel </Gtype> tubes ( Eppendorf , Westbury , NY ) were used to better separate organic and aqueous phases after the addition of chloroform . DNA was digested with Ambion rDNAse I ( Life Technologies , Carlsbad , CA ) for <Supp> 30 min </Supp> at <Temp> 37 °C </Temp> . Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 ( Agilent Technologies , Santa Clara , CA ) . Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit ( Life Technologies , Carlsbad , CA ) and were used for library construction . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914326	CON206.3A_u2	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	RNA was extracted using Trizol and chloroform in conjunction with Qiagen’s RNeasy Mini kit (Qiagen, Valencia, CA) following the A. Untergasser protocol (http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm) with one modification: Phase Lock Gel tubes (Eppendorf, Westbury, NY) were used to better separate organic and aqueous phases after the addition of chloroform. DNA was digested with Ambion rDNAse I (Life Technologies, Carlsbad, CA) for 30 min at 37°C. Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 (Agilent Technologies, Santa Clara, CA). Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit (Life Technologies, Carlsbad, CA) and were used for library construction. PGCGROWTHCONDITIONS	SRR6449120	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Experiments were performed at <Temp> 37 °C </Temp> and followed three steps : seed culture , pre-culture and experimental culture . In the seed culture the cells were grown overnight in Luria Broth , then diluted 1:100 in either <Med> M9 minimal media </Med> with glycerol or glucose for the pre-cultures . Finally , the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm ( OD600 ) of 0.05 . Cultures were harvested at mid-exponential phase , cells were immediately spun down and cell pellets stored at -80 °C until processed . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914326	CON206.3A_u2	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS	SRR6449120	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		RNA was extracted using Trizol and chloroform in conjunction with Qiagen 's RNeasy Mini kit ( Qiagen , Valencia , CA ) following the A. Untergasser protocol ( http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm ) with one modification : <Gtype> Phase Lock Gel </Gtype> tubes ( Eppendorf , Westbury , NY ) were used to better separate organic and aqueous phases after the addition of chloroform . DNA was digested with Ambion rDNAse I ( Life Technologies , Carlsbad , CA ) for <Supp> 30 min </Supp> at <Temp> 37 °C </Temp> . Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 ( Agilent Technologies , Santa Clara , CA ) . Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit ( Life Technologies , Carlsbad , CA ) and were used for library construction . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914327	CON208.3A_u1	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	RNA was extracted using Trizol and chloroform in conjunction with Qiagen’s RNeasy Mini kit (Qiagen, Valencia, CA) following the A. Untergasser protocol (http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm) with one modification: Phase Lock Gel tubes (Eppendorf, Westbury, NY) were used to better separate organic and aqueous phases after the addition of chloroform. DNA was digested with Ambion rDNAse I (Life Technologies, Carlsbad, CA) for 30 min at 37°C. Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 (Agilent Technologies, Santa Clara, CA). Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit (Life Technologies, Carlsbad, CA) and were used for library construction. PGCGROWTHCONDITIONS	SRR6449121	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Experiments were performed at <Temp> 37 °C </Temp> and followed three steps : seed culture , pre-culture and experimental culture . In the seed culture the cells were grown overnight in Luria Broth , then diluted 1:100 in either <Med> M9 minimal media </Med> with glycerol or glucose for the pre-cultures . Finally , the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm ( OD600 ) of 0.05 . Cultures were harvested at mid-exponential phase , cells were immediately spun down and cell pellets stored at -80 °C until processed . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914327	CON208.3A_u1	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS	SRR6449121	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		RNA was extracted using Trizol and chloroform in conjunction with Qiagen 's RNeasy Mini kit ( Qiagen , Valencia , CA ) following the A. Untergasser protocol ( http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm ) with one modification : <Gtype> Phase Lock Gel </Gtype> tubes ( Eppendorf , Westbury , NY ) were used to better separate organic and aqueous phases after the addition of chloroform . DNA was digested with Ambion rDNAse I ( Life Technologies , Carlsbad , CA ) for <Supp> 30 min </Supp> at <Temp> 37 °C </Temp> . Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 ( Agilent Technologies , Santa Clara , CA ) . Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit ( Life Technologies , Carlsbad , CA ) and were used for library construction . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914328	CON208.3A_u8	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	RNA was extracted using Trizol and chloroform in conjunction with Qiagen’s RNeasy Mini kit (Qiagen, Valencia, CA) following the A. Untergasser protocol (http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm) with one modification: Phase Lock Gel tubes (Eppendorf, Westbury, NY) were used to better separate organic and aqueous phases after the addition of chloroform. DNA was digested with Ambion rDNAse I (Life Technologies, Carlsbad, CA) for 30 min at 37°C. Total RNA was further cleaned using the RNeasy Mini kit and quality was assessed by the RNA ScreenTape Assay on the TapeStation 2200 (Agilent Technologies, Santa Clara, CA). Samples with RIN values greater than 8.0 were treated with the Ambion MICROBExpress Bacterial mRNA Enrichment Kit (Life Technologies, Carlsbad, CA) and were used for library construction. PGCGROWTHCONDITIONS	SRR6449122	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Experiments were performed at <Temp> 37 °C </Temp> and followed three steps : seed culture , pre-culture and experimental culture . In the seed culture the cells were grown overnight in Luria Broth , then diluted 1:100 in either <Med> M9 minimal media </Med> with glycerol or glucose for the pre-cultures . Finally , the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm ( OD600 ) of 0.05 . Cultures were harvested at mid-exponential phase , cells were immediately spun down and cell pellets stored at -80 °C until processed . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914328	CON208.3A_u8	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS	SRR6449122	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG 1655 was grown in LB-Miller broth at <Temp> 37 °C </Temp> ,160 rpm to an O.D. 600 nm of 0 . 7 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE114917	Genetic response of E.coli to mild elevated pressure	GSM3154484	HP1	30016375	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE114917/GSE114917.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG 1655 was grown  in LB-Miller broth at 37°C ,160rpm to  an O.D.600 nm of 0. 7 PGCGROWTHCONDITIONS	SRR7217923	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG 1655 was grown in LB-Miller broth at <Temp> 37 °C </Temp> ,160 rpm to an O.D. 600 nm of 0 . 7 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE114917	Genetic response of E.coli to mild elevated pressure	GSM3154485	HP2	30016375	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE114917/GSE114917.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG 1655 was grown  in LB-Miller broth at 37°C ,160rpm to  an O.D.600 nm of 0. 7 PGCGROWTHCONDITIONS	SRR7217924	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG 1655 was grown in LB-Miller broth at <Temp> 37 °C </Temp> ,160 rpm to an O.D. 600 nm of 0 . 7 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE114917	Genetic response of E.coli to mild elevated pressure	GSM3154486	HP3	30016375	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE114917/GSE114917.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG 1655 was grown  in LB-Miller broth at 37°C ,160rpm to  an O.D.600 nm of 0. 7 PGCGROWTHCONDITIONS	SRR7217925	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG 1655 was grown in LB-Miller broth at <Temp> 37 °C </Temp> ,160 rpm to an O.D. 600 nm of 0 . 7 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE114917	Genetic response of E.coli to mild elevated pressure	GSM3154487	HP4	30016375	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE114917/GSE114917.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG 1655 was grown  in LB-Miller broth at 37°C ,160rpm to  an O.D.600 nm of 0. 7 PGCGROWTHCONDITIONS	SRR7217926	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG 1655 was grown in LB-Miller broth at <Temp> 37 °C </Temp> ,160 rpm to an O.D. 600 nm of 0 . 7 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE114917	Genetic response of E.coli to mild elevated pressure	GSM3154488	LP1	30016375	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE114917/GSE114917.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG 1655 was grown  in LB-Miller broth at 37°C ,160rpm to  an O.D.600 nm of 0. 7 PGCGROWTHCONDITIONS	SRR7217927	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG 1655 was grown in LB-Miller broth at <Temp> 37 °C </Temp> ,160 rpm to an O.D. 600 nm of 0 . 7 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE114917	Genetic response of E.coli to mild elevated pressure	GSM3154489	LP2	30016375	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE114917/GSE114917.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG 1655 was grown  in LB-Miller broth at 37°C ,160rpm to  an O.D.600 nm of 0. 7 PGCGROWTHCONDITIONS	SRR7217928	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG 1655 was grown in LB-Miller broth at <Temp> 37 °C </Temp> ,160 rpm to an O.D. 600 nm of 0 . 7 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE114917	Genetic response of E.coli to mild elevated pressure	GSM3154490	LP3	30016375	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE114917/GSE114917.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG 1655 was grown  in LB-Miller broth at 37°C ,160rpm to  an O.D.600 nm of 0. 7 PGCGROWTHCONDITIONS	SRR7217929	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG 1655 was grown in LB-Miller broth at <Temp> 37 °C </Temp> ,160 rpm to an O.D. 600 nm of 0 . 7 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE114917	Genetic response of E.coli to mild elevated pressure	GSM3154491	LP4	30016375	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE114917/GSE114917.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG 1655 was grown  in LB-Miller broth at 37°C ,160rpm to  an O.D.600 nm of 0. 7 PGCGROWTHCONDITIONS	SRR7217930	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Plasmid pLCenvZ or pLCenvZM was co-transformed with pPCB into the competent cells of E. coli JW3367 and spread on LB agar plates containing Ampicillin ( 50 ng/μl ) and Chloramphenicol ( 170 ng/μl ) at <Temp> 37 °C </Temp> overnight . A single colony was diluted in 2.5 ml LB medium containing Ampicillin ( 50 ng/μl ) and Chloramphenicol ( 170 ng/μl ) and was shaken at 250 rpm and <Temp> 37 °C </Temp> overnight . 	GPL25346	GPL25346: HiSeq X Ten (Escherichia coli)	GSE117326	Gene expression profiles in E. coli under different frequency signals	GSM3291044	envz600		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117326/GSE117326.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Plasmid pLCenvZ or pLCenvZM was co-transformed with pPCB into the competent cells of E. coli JW3367 and spread on LB agar plates containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) at 37°C overnight. A single colony was diluted in 2.5ml LB medium containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) and was shaken at 250 rpm and 37°C overnight. PGCGROWTHCONDITIONS	SRR7537397	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Plasmid pLCenvZ or pLCenvZM was co-transformed with pPCB into the competent cells of E. coli JW3367 and spread on LB agar plates containing Ampicillin ( 50 ng/μl ) and Chloramphenicol ( 170 ng/μl ) at <Temp> 37 °C </Temp> overnight . A single colony was diluted in 2.5 ml LB medium containing Ampicillin ( 50 ng/μl ) and Chloramphenicol ( 170 ng/μl ) and was shaken at 250 rpm and <Temp> 37 °C </Temp> overnight . 	GPL25346	GPL25346: HiSeq X Ten (Escherichia coli)	GSE117326	Gene expression profiles in E. coli under different frequency signals	GSM3291045	envz900		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117326/GSE117326.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Plasmid pLCenvZ or pLCenvZM was co-transformed with pPCB into the competent cells of E. coli JW3367 and spread on LB agar plates containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) at 37°C overnight. A single colony was diluted in 2.5ml LB medium containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) and was shaken at 250 rpm and 37°C overnight. PGCGROWTHCONDITIONS	SRR7537398	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Plasmid pLCenvZ or pLCenvZM was co-transformed with pPCB into the competent cells of E. coli JW3367 and spread on LB agar plates containing Ampicillin ( 50 ng/μl ) and Chloramphenicol ( 170 ng/μl ) at <Temp> 37 °C </Temp> overnight . A single colony was diluted in 2.5 ml LB medium containing Ampicillin ( 50 ng/μl ) and Chloramphenicol ( 170 ng/μl ) and was shaken at 250 rpm and <Temp> 37 °C </Temp> overnight . 	GPL25346	GPL25346: HiSeq X Ten (Escherichia coli)	GSE117326	Gene expression profiles in E. coli under different frequency signals	GSM3291049	envz3600		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117326/GSE117326.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Plasmid pLCenvZ or pLCenvZM was co-transformed with pPCB into the competent cells of E. coli JW3367 and spread on LB agar plates containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) at 37°C overnight. A single colony was diluted in 2.5ml LB medium containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) and was shaken at 250 rpm and 37°C overnight. PGCGROWTHCONDITIONS	SRR7537402	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Plasmid pLCenvZ or pLCenvZM was co-transformed with pPCB into the competent cells of E. coli JW3367 and spread on LB agar plates containing Ampicillin ( 50 ng/μl ) and Chloramphenicol ( 170 ng/μl ) at <Temp> 37 °C </Temp> overnight . A single colony was diluted in 2.5 ml LB medium containing Ampicillin ( 50 ng/μl ) and Chloramphenicol ( 170 ng/μl ) and was shaken at 250 rpm and <Temp> 37 °C </Temp> overnight . 	GPL25346	GPL25346: HiSeq X Ten (Escherichia coli)	GSE117326	Gene expression profiles in E. coli under different frequency signals	GSM3291050	envzM600		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117326/GSE117326.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Plasmid pLCenvZ or pLCenvZM was co-transformed with pPCB into the competent cells of E. coli JW3367 and spread on LB agar plates containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) at 37°C overnight. A single colony was diluted in 2.5ml LB medium containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) and was shaken at 250 rpm and 37°C overnight. PGCGROWTHCONDITIONS	SRR7537403	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Plasmid pLCenvZ or pLCenvZM was co-transformed with pPCB into the competent cells of E. coli JW3367 and spread on LB agar plates containing Ampicillin ( 50 ng/μl ) and Chloramphenicol ( 170 ng/μl ) at <Temp> 37 °C </Temp> overnight . A single colony was diluted in 2.5 ml LB medium containing Ampicillin ( 50 ng/μl ) and Chloramphenicol ( 170 ng/μl ) and was shaken at 250 rpm and <Temp> 37 °C </Temp> overnight . 	GPL25346	GPL25346: HiSeq X Ten (Escherichia coli)	GSE117326	Gene expression profiles in E. coli under different frequency signals	GSM3291051	envzM900		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117326/GSE117326.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Plasmid pLCenvZ or pLCenvZM was co-transformed with pPCB into the competent cells of E. coli JW3367 and spread on LB agar plates containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) at 37°C overnight. A single colony was diluted in 2.5ml LB medium containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) and was shaken at 250 rpm and 37°C overnight. PGCGROWTHCONDITIONS	SRR7537404	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Plasmid pLCenvZ or pLCenvZM was co-transformed with pPCB into the competent cells of E. coli JW3367 and spread on LB agar plates containing Ampicillin ( 50 ng/μl ) and Chloramphenicol ( 170 ng/μl ) at <Temp> 37 °C </Temp> overnight . A single colony was diluted in 2.5 ml LB medium containing Ampicillin ( 50 ng/μl ) and Chloramphenicol ( 170 ng/μl ) and was shaken at 250 rpm and <Temp> 37 °C </Temp> overnight . 	GPL25346	GPL25346: HiSeq X Ten (Escherichia coli)	GSE117326	Gene expression profiles in E. coli under different frequency signals	GSM3291052	envzM1200		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117326/GSE117326.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Plasmid pLCenvZ or pLCenvZM was co-transformed with pPCB into the competent cells of E. coli JW3367 and spread on LB agar plates containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) at 37°C overnight. A single colony was diluted in 2.5ml LB medium containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) and was shaken at 250 rpm and 37°C overnight. PGCGROWTHCONDITIONS	SRR7537405	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Plasmid pLCenvZ or pLCenvZM was co-transformed with pPCB into the competent cells of E. coli JW3367 and spread on LB agar plates containing Ampicillin ( 50 ng/μl ) and Chloramphenicol ( 170 ng/μl ) at <Temp> 37 °C </Temp> overnight . A single colony was diluted in 2.5 ml LB medium containing Ampicillin ( 50 ng/μl ) and Chloramphenicol ( 170 ng/μl ) and was shaken at 250 rpm and <Temp> 37 °C </Temp> overnight . 	GPL25346	GPL25346: HiSeq X Ten (Escherichia coli)	GSE117326	Gene expression profiles in E. coli under different frequency signals	GSM3291054	envzM2400		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117326/GSE117326.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Plasmid pLCenvZ or pLCenvZM was co-transformed with pPCB into the competent cells of E. coli JW3367 and spread on LB agar plates containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) at 37°C overnight. A single colony was diluted in 2.5ml LB medium containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) and was shaken at 250 rpm and 37°C overnight. PGCGROWTHCONDITIONS	SRR7537407	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Plasmid pLCenvZ or pLCenvZM was co-transformed with pPCB into the competent cells of E. coli JW3367 and spread on LB agar plates containing Ampicillin ( 50 ng/μl ) and Chloramphenicol ( 170 ng/μl ) at <Temp> 37 °C </Temp> overnight . A single colony was diluted in 2.5 ml LB medium containing Ampicillin ( 50 ng/μl ) and Chloramphenicol ( 170 ng/μl ) and was shaken at 250 rpm and <Temp> 37 °C </Temp> overnight . 	GPL25346	GPL25346: HiSeq X Ten (Escherichia coli)	GSE117326	Gene expression profiles in E. coli under different frequency signals	GSM3291055	envzM3600		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117326/GSE117326.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Plasmid pLCenvZ or pLCenvZM was co-transformed with pPCB into the competent cells of E. coli JW3367 and spread on LB agar plates containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) at 37°C overnight. A single colony was diluted in 2.5ml LB medium containing Ampicillin (50 ng/μl) and Chloramphenicol (170 ng/μl) and was shaken at 250 rpm and 37°C overnight. PGCGROWTHCONDITIONS	SRR7537408	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		For the RNA-seq samples , the E. coli cells were quenched by adding 0.5 volume of cold Stop Buffer ( 5 % phenol in ethanol ) immediately to the culture medium before harvest and stay on the ice for 15 minutes . Cell pellets were collected by centrifugation ( 6,000 rpm , 5 minutes at 4 °C ) , thoroughly resuspended in 100 μl of lysozyme solution [ 2 mg/ml in TE buffer ( 10 mM Tris-HCl and 1 mM EDTA ) ] , and incubated for 2 minutes . The cells were immediately lysed by adding 1 ml of TRIzol Reagent ( Invitrogen , 15596 ) and the RNA was extracted following manufacture 's instruction . For the ChIP-seq samples , the E. coli cells were fixed with 1 % formaldehyde with continued shaking at <Temp> 37 °C </Temp> for 10 minutes before quenching with glycine ( 100 mM final concentration ) . Cells were then lysed and DNA was sheared by sonication followed by the treatment with micrococcal nuclease and RNase A. Antibody against RNAP β was used for target DNA enrichment . 	GPL16085-GPL21222	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE117737	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GSM3566393	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 4	31308523	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the RNA-seq samples, the E. coli cells were quenched by adding 0.5 volume of cold Stop Buffer (5% phenol in ethanol) immediately to the culture medium before harvest and stay on the ice for 15 minutes. Cell pellets were collected by centrifugation (6,000 rpm, 5 minutes at 4 °C), thoroughly resuspended in 100 μl of lysozyme solution [2 mg/ml in TE buffer (10 mM Tris-HCl and 1 mM EDTA)], and incubated for 2 minutes. The cells were immediately lysed by adding 1 ml of TRIzol Reagent (Invitrogen, 15596) and the RNA was extracted following manufacture’s instruction. For the ChIP-seq samples, the E. coli cells were fixed with 1% formaldehyde with continued shaking at 37 °C for 10 minutes before quenching with glycine (100 mM final concentration). Cells were then lysed and DNA was sheared by sonication followed by the treatment with micrococcal nuclease and RNase A. Antibody against RNAP β was used for target DNA enrichment. PGCGROWTHCONDITIONS	SRR8449235	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Escherichia coli K-12 MG1655 were cultured in <Med> LB media </Med> ( 10 g/L tryptone , 5 g/L yeast extract , 10 g/L NaCl , pH 7.4 ) under aerobic conditions at <Temp> 37 °C </Temp> . The temperature-sensitive RNase E mutant E.coli strain [ rne-3071 ( ts ) ] was cultured in <Med> LB media </Med> at 28 °C for normal culture and shift to 44 °C to deactive RNase E activity . 	GPL16085-GPL21222	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE117737	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GSM3566393	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 4	31308523	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Escherichia coli K-12 MG1655 were cultured in LB media (10 g/L tryptone, 5 g/L yeast extract, 10 g/L NaCl, pH 7.4) under aerobic conditions at 37 °C. The temperature-sensitive RNase E mutant E.coli strain [rne-3071(ts)] was cultured in LB media at 28 °C  for normal culture and shift to 44 °C to deactive RNase E activity. PGCGROWTHCONDITIONS	SRR8449235	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		<Gtype> Wild type </Gtype> E. coli , pnp knoctout , rnb knoctout and rnr knoct out strains were cultured in <Med> LB media </Med> at <Temp> 37 °C </Temp> , RNA samples and ChIP-seq samples were collected when the growth stage of indicated cells reached to log phase or stationary phase . rne-3071 ( ts ) mutation strain was cultured in <Med> LB media </Med> at 28 °C to retain the RNase E activity or shifted to 44 °C in water bath for 30 minutes to deactivate RNase E . In order to <Gtype> inactive the rho activity , the wild type ( WT ) Wild type </Gtype> E. coli was cultured in <Med> LB media </Med> with 50 μg/ml bicyclomycin at <Temp> 37 °C </Temp> for 15 min at indicated growth condition . 	GPL16085-GPL21222	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE117737	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GSM3566393	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 4	31308523	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Wild type E. coli, pnp knoctout, rnb knoctout and rnr knoct out strains were cultured in LB media at 37 °C, RNA samples and ChIP-seq samples were collected when the growth stage of indicated cells reached to log phase or stationary phase.  rne-3071(ts) mutation strain was cultured in LB media at 28 °C to retain the RNase E activity or shifted to 44 °C in water bath for 30 minutes to deactivate RNase E. In order to inactive the rho activity, the wild type (WT) Wild type E. coli was cultured in LB media with 50 μg/ml bicyclomycin at 37 °C for 15 min at indicated growth condition. PGCGROWTHCONDITIONS	SRR8449235	MCO000003199	37 °C	Temperature	True
characteristics	35.7 C		treatment : <Temp> 37 °C </Temp> culture 	GPL16085-GPL21222	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE117737	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GSM3566393	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 4	31308523	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 37°C culture PGCGROWTHCONDITIONS	SRR8449235	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		For the RNA-seq samples , the E. coli cells were quenched by adding 0.5 volume of cold Stop Buffer ( 5 % phenol in ethanol ) immediately to the culture medium before harvest and stay on the ice for 15 minutes . Cell pellets were collected by centrifugation ( 6,000 rpm , 5 minutes at 4 °C ) , thoroughly resuspended in 100 μl of lysozyme solution [ 2 mg/ml in TE buffer ( 10 mM Tris-HCl and 1 mM EDTA ) ] , and incubated for 2 minutes . The cells were immediately lysed by adding 1 ml of TRIzol Reagent ( Invitrogen , 15596 ) and the RNA was extracted following manufacture 's instruction . For the ChIP-seq samples , the E. coli cells were fixed with 1 % formaldehyde with continued shaking at <Temp> 37 °C </Temp> for 10 minutes before quenching with glycine ( 100 mM final concentration ) . Cells were then lysed and DNA was sheared by sonication followed by the treatment with micrococcal nuclease and RNase A. Antibody against RNAP β was used for target DNA enrichment . 	GPL16085-GPL21222	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE117737	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GSM3566394	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 5	31308523	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the RNA-seq samples, the E. coli cells were quenched by adding 0.5 volume of cold Stop Buffer (5% phenol in ethanol) immediately to the culture medium before harvest and stay on the ice for 15 minutes. Cell pellets were collected by centrifugation (6,000 rpm, 5 minutes at 4 °C), thoroughly resuspended in 100 μl of lysozyme solution [2 mg/ml in TE buffer (10 mM Tris-HCl and 1 mM EDTA)], and incubated for 2 minutes. The cells were immediately lysed by adding 1 ml of TRIzol Reagent (Invitrogen, 15596) and the RNA was extracted following manufacture’s instruction. For the ChIP-seq samples, the E. coli cells were fixed with 1% formaldehyde with continued shaking at 37 °C for 10 minutes before quenching with glycine (100 mM final concentration). Cells were then lysed and DNA was sheared by sonication followed by the treatment with micrococcal nuclease and RNase A. Antibody against RNAP β was used for target DNA enrichment. PGCGROWTHCONDITIONS	SRR8449236	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Escherichia coli K-12 MG1655 were cultured in <Med> LB media </Med> ( 10 g/L tryptone , 5 g/L yeast extract , 10 g/L NaCl , pH 7.4 ) under aerobic conditions at <Temp> 37 °C </Temp> . The temperature-sensitive RNase E mutant E.coli strain [ rne-3071 ( ts ) ] was cultured in <Med> LB media </Med> at 28 °C for normal culture and shift to 44 °C to deactive RNase E activity . 	GPL16085-GPL21222	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE117737	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GSM3566394	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 5	31308523	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Escherichia coli K-12 MG1655 were cultured in LB media (10 g/L tryptone, 5 g/L yeast extract, 10 g/L NaCl, pH 7.4) under aerobic conditions at 37 °C. The temperature-sensitive RNase E mutant E.coli strain [rne-3071(ts)] was cultured in LB media at 28 °C  for normal culture and shift to 44 °C to deactive RNase E activity. PGCGROWTHCONDITIONS	SRR8449236	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		<Gtype> Wild type </Gtype> E. coli , pnp knoctout , rnb knoctout and rnr knoct out strains were cultured in <Med> LB media </Med> at <Temp> 37 °C </Temp> , RNA samples and ChIP-seq samples were collected when the growth stage of indicated cells reached to log phase or stationary phase . rne-3071 ( ts ) mutation strain was cultured in <Med> LB media </Med> at 28 °C to retain the RNase E activity or shifted to 44 °C in water bath for 30 minutes to deactivate RNase E . In order to <Gtype> inactive the rho activity , the wild type ( WT ) Wild type </Gtype> E. coli was cultured in <Med> LB media </Med> with 50 μg/ml bicyclomycin at <Temp> 37 °C </Temp> for 15 min at indicated growth condition . 	GPL16085-GPL21222	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE117737	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GSM3566394	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 5	31308523	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Wild type E. coli, pnp knoctout, rnb knoctout and rnr knoct out strains were cultured in LB media at 37 °C, RNA samples and ChIP-seq samples were collected when the growth stage of indicated cells reached to log phase or stationary phase.  rne-3071(ts) mutation strain was cultured in LB media at 28 °C to retain the RNase E activity or shifted to 44 °C in water bath for 30 minutes to deactivate RNase E. In order to inactive the rho activity, the wild type (WT) Wild type E. coli was cultured in LB media with 50 μg/ml bicyclomycin at 37 °C for 15 min at indicated growth condition. PGCGROWTHCONDITIONS	SRR8449236	MCO000003199	37 °C	Temperature	True
characteristics	35.7 C		treatment : <Temp> 37 °C </Temp> culture 	GPL16085-GPL21222	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE117737	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GSM3566394	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 5	31308523	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 37°C culture PGCGROWTHCONDITIONS	SRR8449236	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		For the RNA-seq samples , the E. coli cells were quenched by adding 0.5 volume of cold Stop Buffer ( 5 % phenol in ethanol ) immediately to the culture medium before harvest and stay on the ice for 15 minutes . Cell pellets were collected by centrifugation ( 6,000 rpm , 5 minutes at 4 °C ) , thoroughly resuspended in 100 μl of lysozyme solution [ 2 mg/ml in TE buffer ( 10 mM Tris-HCl and 1 mM EDTA ) ] , and incubated for 2 minutes . The cells were immediately lysed by adding 1 ml of TRIzol Reagent ( Invitrogen , 15596 ) and the RNA was extracted following manufacture 's instruction . For the ChIP-seq samples , the E. coli cells were fixed with 1 % formaldehyde with continued shaking at <Temp> 37 °C </Temp> for 10 minutes before quenching with glycine ( 100 mM final concentration ) . Cells were then lysed and DNA was sheared by sonication followed by the treatment with micrococcal nuclease and RNase A. Antibody against RNAP β was used for target DNA enrichment . 	GPL16085-GPL21222	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE117737	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GSM3566395	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 6	31308523	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the RNA-seq samples, the E. coli cells were quenched by adding 0.5 volume of cold Stop Buffer (5% phenol in ethanol) immediately to the culture medium before harvest and stay on the ice for 15 minutes. Cell pellets were collected by centrifugation (6,000 rpm, 5 minutes at 4 °C), thoroughly resuspended in 100 μl of lysozyme solution [2 mg/ml in TE buffer (10 mM Tris-HCl and 1 mM EDTA)], and incubated for 2 minutes. The cells were immediately lysed by adding 1 ml of TRIzol Reagent (Invitrogen, 15596) and the RNA was extracted following manufacture’s instruction. For the ChIP-seq samples, the E. coli cells were fixed with 1% formaldehyde with continued shaking at 37 °C for 10 minutes before quenching with glycine (100 mM final concentration). Cells were then lysed and DNA was sheared by sonication followed by the treatment with micrococcal nuclease and RNase A. Antibody against RNAP β was used for target DNA enrichment. PGCGROWTHCONDITIONS	SRR8449237	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Escherichia coli K-12 MG1655 were cultured in <Med> LB media </Med> ( 10 g/L tryptone , 5 g/L yeast extract , 10 g/L NaCl , pH 7.4 ) under aerobic conditions at <Temp> 37 °C </Temp> . The temperature-sensitive RNase E mutant E.coli strain [ rne-3071 ( ts ) ] was cultured in <Med> LB media </Med> at 28 °C for normal culture and shift to 44 °C to deactive RNase E activity . 	GPL16085-GPL21222	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE117737	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GSM3566395	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 6	31308523	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Escherichia coli K-12 MG1655 were cultured in LB media (10 g/L tryptone, 5 g/L yeast extract, 10 g/L NaCl, pH 7.4) under aerobic conditions at 37 °C. The temperature-sensitive RNase E mutant E.coli strain [rne-3071(ts)] was cultured in LB media at 28 °C  for normal culture and shift to 44 °C to deactive RNase E activity. PGCGROWTHCONDITIONS	SRR8449237	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		<Gtype> Wild type </Gtype> E. coli , pnp knoctout , rnb knoctout and rnr knoct out strains were cultured in <Med> LB media </Med> at <Temp> 37 °C </Temp> , RNA samples and ChIP-seq samples were collected when the growth stage of indicated cells reached to log phase or stationary phase . rne-3071 ( ts ) mutation strain was cultured in <Med> LB media </Med> at 28 °C to retain the RNase E activity or shifted to 44 °C in water bath for 30 minutes to deactivate RNase E . In order to <Gtype> inactive the rho activity , the wild type ( WT ) Wild type </Gtype> E. coli was cultured in <Med> LB media </Med> with 50 μg/ml bicyclomycin at <Temp> 37 °C </Temp> for 15 min at indicated growth condition . 	GPL16085-GPL21222	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE117737	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GSM3566395	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 6	31308523	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Wild type E. coli, pnp knoctout, rnb knoctout and rnr knoct out strains were cultured in LB media at 37 °C, RNA samples and ChIP-seq samples were collected when the growth stage of indicated cells reached to log phase or stationary phase.  rne-3071(ts) mutation strain was cultured in LB media at 28 °C to retain the RNase E activity or shifted to 44 °C in water bath for 30 minutes to deactivate RNase E. In order to inactive the rho activity, the wild type (WT) Wild type E. coli was cultured in LB media with 50 μg/ml bicyclomycin at 37 °C for 15 min at indicated growth condition. PGCGROWTHCONDITIONS	SRR8449237	MCO000003199	37 °C	Temperature	True
characteristics	35.7 C		treatment : <Temp> 37 °C </Temp> culture 	GPL16085-GPL21222	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE117737	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GSM3566395	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 6	31308523	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 37°C culture PGCGROWTHCONDITIONS	SRR8449237	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		For the RNA-seq samples , the E. coli cells were quenched by adding 0.5 volume of cold Stop Buffer ( 5 % phenol in ethanol ) immediately to the culture medium before harvest and stay on the ice for 15 minutes . Cell pellets were collected by centrifugation ( 6,000 rpm , 5 minutes at 4 °C ) , thoroughly resuspended in 100 μl of lysozyme solution [ 2 mg/ml in TE buffer ( 10 mM Tris-HCl and 1 mM EDTA ) ] , and incubated for 2 minutes . The cells were immediately lysed by adding 1 ml of TRIzol Reagent ( Invitrogen , 15596 ) and the RNA was extracted following manufacture 's instruction . For the ChIP-seq samples , the E. coli cells were fixed with 1 % formaldehyde with continued shaking at <Temp> 37 °C </Temp> for 10 minutes before quenching with glycine ( 100 mM final concentration ) . Cells were then lysed and DNA was sheared by sonication followed by the treatment with micrococcal nuclease and RNase A. Antibody against RNAP β was used for target DNA enrichment . 	GPL16085-GPL21222	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE117737	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GSM3566396	RNA-seq WT log phase related to total SEnd-seq WT stationary phase rep4	31308523	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the RNA-seq samples, the E. coli cells were quenched by adding 0.5 volume of cold Stop Buffer (5% phenol in ethanol) immediately to the culture medium before harvest and stay on the ice for 15 minutes. Cell pellets were collected by centrifugation (6,000 rpm, 5 minutes at 4 °C), thoroughly resuspended in 100 μl of lysozyme solution [2 mg/ml in TE buffer (10 mM Tris-HCl and 1 mM EDTA)], and incubated for 2 minutes. The cells were immediately lysed by adding 1 ml of TRIzol Reagent (Invitrogen, 15596) and the RNA was extracted following manufacture’s instruction. For the ChIP-seq samples, the E. coli cells were fixed with 1% formaldehyde with continued shaking at 37 °C for 10 minutes before quenching with glycine (100 mM final concentration). Cells were then lysed and DNA was sheared by sonication followed by the treatment with micrococcal nuclease and RNase A. Antibody against RNAP β was used for target DNA enrichment. PGCGROWTHCONDITIONS	SRR8449238	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Escherichia coli K-12 MG1655 were cultured in <Med> LB media </Med> ( 10 g/L tryptone , 5 g/L yeast extract , 10 g/L NaCl , pH 7.4 ) under aerobic conditions at <Temp> 37 °C </Temp> . The temperature-sensitive RNase E mutant E.coli strain [ rne-3071 ( ts ) ] was cultured in <Med> LB media </Med> at 28 °C for normal culture and shift to 44 °C to deactive RNase E activity . 	GPL16085-GPL21222	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE117737	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GSM3566396	RNA-seq WT log phase related to total SEnd-seq WT stationary phase rep4	31308523	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Escherichia coli K-12 MG1655 were cultured in LB media (10 g/L tryptone, 5 g/L yeast extract, 10 g/L NaCl, pH 7.4) under aerobic conditions at 37 °C. The temperature-sensitive RNase E mutant E.coli strain [rne-3071(ts)] was cultured in LB media at 28 °C  for normal culture and shift to 44 °C to deactive RNase E activity. PGCGROWTHCONDITIONS	SRR8449238	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		<Gtype> Wild type </Gtype> E. coli , pnp knoctout , rnb knoctout and rnr knoct out strains were cultured in <Med> LB media </Med> at <Temp> 37 °C </Temp> , RNA samples and ChIP-seq samples were collected when the growth stage of indicated cells reached to log phase or stationary phase . rne-3071 ( ts ) mutation strain was cultured in <Med> LB media </Med> at 28 °C to retain the RNase E activity or shifted to 44 °C in water bath for 30 minutes to deactivate RNase E . In order to <Gtype> inactive the rho activity , the wild type ( WT ) Wild type </Gtype> E. coli was cultured in <Med> LB media </Med> with 50 μg/ml bicyclomycin at <Temp> 37 °C </Temp> for 15 min at indicated growth condition . 	GPL16085-GPL21222	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE117737	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GSM3566396	RNA-seq WT log phase related to total SEnd-seq WT stationary phase rep4	31308523	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Wild type E. coli, pnp knoctout, rnb knoctout and rnr knoct out strains were cultured in LB media at 37 °C, RNA samples and ChIP-seq samples were collected when the growth stage of indicated cells reached to log phase or stationary phase.  rne-3071(ts) mutation strain was cultured in LB media at 28 °C to retain the RNase E activity or shifted to 44 °C in water bath for 30 minutes to deactivate RNase E. In order to inactive the rho activity, the wild type (WT) Wild type E. coli was cultured in LB media with 50 μg/ml bicyclomycin at 37 °C for 15 min at indicated growth condition. PGCGROWTHCONDITIONS	SRR8449238	MCO000003199	37 °C	Temperature	True
characteristics	35.7 C		treatment : <Temp> 37 °C </Temp> culture 	GPL16085-GPL21222	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE117737	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GSM3566396	RNA-seq WT log phase related to total SEnd-seq WT stationary phase rep4	31308523	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 37°C culture PGCGROWTHCONDITIONS	SRR8449238	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		After inoculation and growth , 3 mL of cell broth ( OD600 ~ 0.5 ) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent ( 6 mL ) , vortexed for 5 seconds , incubated at room temperature for 5 min , and immediately centrifuged for 10 min at 17,500 RPMs . The supernatant was decanted , and the cell pellet was stored in the -80 °C . Cell pellets were thawed and incubated with Readylyse Lysozyme , SuperaseIn , Protease K , and 20 % SDS for 20 minutes at <Temp> 37 °C </Temp> . Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures . An on-column DNase-treatment was performed for 30 minutes at room temperature . RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer . The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria . A KAPA Stranded RNA-Seq Kit ( Kapa Biosystems KK8401 ) was used following the manufacturer 's protocol to create sequencing libraries with an average insert length of around ~ 300 bp . 	GPL17024-GPL17439-GPL18995-GPL25769	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	GSE122211	Expression profiling of E. coli K-12 MG1655	GSM3461156	MG_no_te_1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS	SRR8164476	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		After inoculation and growth , 3 mL of cell broth ( OD600 ~ 0.5 ) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent ( 6 mL ) , vortexed for 5 seconds , incubated at room temperature for 5 min , and immediately centrifuged for 10 min at 17,500 RPMs . The supernatant was decanted , and the cell pellet was stored in the -80 °C . Cell pellets were thawed and incubated with Readylyse Lysozyme , SuperaseIn , Protease K , and 20 % SDS for 20 minutes at <Temp> 37 °C </Temp> . Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures . An on-column DNase-treatment was performed for 30 minutes at room temperature . RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer . The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria . A KAPA Stranded RNA-Seq Kit ( Kapa Biosystems KK8401 ) was used following the manufacturer 's protocol to create sequencing libraries with an average insert length of around ~ 300 bp . 	GPL17024-GPL17439-GPL18995-GPL25769	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	GSE122211	Expression profiling of E. coli K-12 MG1655	GSM3461157	MG_no_te_2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS	SRR8164477	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		After inoculation and growth , 3 mL of cell broth ( OD600 ~ 0.5 ) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent ( 6 mL ) , vortexed for 5 seconds , incubated at room temperature for 5 min , and immediately centrifuged for 10 min at 17,500 RPMs . The supernatant was decanted , and the cell pellet was stored in the -80 °C . Cell pellets were thawed and incubated with Readylyse Lysozyme , SuperaseIn , Protease K , and 20 % SDS for 20 minutes at <Temp> 37 °C </Temp> . Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures . An on-column DNase-treatment was performed for 30 minutes at room temperature . RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer . The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria . A KAPA Stranded RNA-Seq Kit ( Kapa Biosystems KK8401 ) was used following the manufacturer 's protocol to create sequencing libraries with an average insert length of around ~ 300 bp . 	GPL17024-GPL17439-GPL18995-GPL25769	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	GSE122211	Expression profiling of E. coli K-12 MG1655	GSM3461164	MG_glu_1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS	SRR8164484	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		After inoculation and growth , 3 mL of cell broth ( OD600 ~ 0.5 ) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent ( 6 mL ) , vortexed for 5 seconds , incubated at room temperature for 5 min , and immediately centrifuged for 10 min at 17,500 RPMs . The supernatant was decanted , and the cell pellet was stored in the -80 °C . Cell pellets were thawed and incubated with Readylyse Lysozyme , SuperaseIn , Protease K , and 20 % SDS for 20 minutes at <Temp> 37 °C </Temp> . Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures . An on-column DNase-treatment was performed for 30 minutes at room temperature . RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer . The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria . A KAPA Stranded RNA-Seq Kit ( Kapa Biosystems KK8401 ) was used following the manufacturer 's protocol to create sequencing libraries with an average insert length of around ~ 300 bp . 	GPL17024-GPL17439-GPL18995-GPL25769	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	GSE122211	Expression profiling of E. coli K-12 MG1655	GSM3461165	MG_glu_2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS	SRR8164485	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		After inoculation and growth , 3 mL of cell broth ( OD600 ~ 0.5 ) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent ( 6 mL ) , vortexed for 5 seconds , incubated at room temperature for 5 min , and immediately centrifuged for 10 min at 17,500 RPMs . The supernatant was decanted , and the cell pellet was stored in the -80 °C . Cell pellets were thawed and incubated with Readylyse Lysozyme , SuperaseIn , Protease K , and 20 % SDS for 20 minutes at <Temp> 37 °C </Temp> . Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures . An on-column DNase-treatment was performed for 30 minutes at room temperature . RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer . The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria . A KAPA Stranded RNA-Seq Kit ( Kapa Biosystems KK8401 ) was used following the manufacturer 's protocol to create sequencing libraries with an average insert length of around ~ 300 bp . 	GPL17024-GPL17439-GPL18995-GPL25769	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	GSE122211	Expression profiling of E. coli K-12 MG1655	GSM3461166	MG_glc	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS	SRR8164486	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		After inoculation and growth , 3 mL of cell broth ( OD600 ~ 0.5 ) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent ( 6 mL ) , vortexed for 5 seconds , incubated at room temperature for 5 min , and immediately centrifuged for 10 min at 17,500 RPMs . The supernatant was decanted , and the cell pellet was stored in the -80 °C . Cell pellets were thawed and incubated with Readylyse Lysozyme , SuperaseIn , Protease K , and 20 % SDS for 20 minutes at <Temp> 37 °C </Temp> . Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures . An on-column DNase-treatment was performed for 30 minutes at room temperature . RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer . The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria . A KAPA Stranded RNA-Seq Kit ( Kapa Biosystems KK8401 ) was used following the manufacturer 's protocol to create sequencing libraries with an average insert length of around ~ 300 bp . 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463565	wt_glc__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS	SRR8173227	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		After inoculation and growth , 3 mL of cell broth ( OD600 ~ 0.5 ) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent ( 6 mL ) , vortexed for 5 seconds , incubated at room temperature for 5 min , and immediately centrifuged for 10 min at 17,500 RPMs . The supernatant was decanted , and the cell pellet was stored in the -80 °C . Cell pellets were thawed and incubated with Readylyse Lysozyme , SuperaseIn , Protease K , and 20 % SDS for 20 minutes at <Temp> 37 °C </Temp> . Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures . An on-column DNase-treatment was performed for 30 minutes at room temperature . RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer . The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria . A KAPA Stranded RNA-Seq Kit ( Kapa Biosystems KK8401 ) was used following the manufacturer 's protocol to create sequencing libraries with an average insert length of around ~ 300 bp . 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463566	wt_glc__2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS	SRR8173228	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		After inoculation and growth , 3 mL of cell broth ( OD600 ~ 0.5 ) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent ( 6 mL ) , vortexed for 5 seconds , incubated at room temperature for 5 min , and immediately centrifuged for 10 min at 17,500 RPMs . The supernatant was decanted , and the cell pellet was stored in the -80 °C . Cell pellets were thawed and incubated with Readylyse Lysozyme , SuperaseIn , Protease K , and 20 % SDS for 20 minutes at <Temp> 37 °C </Temp> . Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures . An on-column DNase-treatment was performed for 30 minutes at room temperature . RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer . The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria . A KAPA Stranded RNA-Seq Kit ( Kapa Biosystems KK8401 ) was used following the manufacturer 's protocol to create sequencing libraries with an average insert length of around ~ 300 bp . 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463567	wt_glc__3	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS	SRR8173229	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		After inoculation and growth , 3 mL of cell broth ( OD600 ~ 0.5 ) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent ( 6 mL ) , vortexed for 5 seconds , incubated at room temperature for 5 min , and immediately centrifuged for 10 min at 17,500 RPMs . The supernatant was decanted , and the cell pellet was stored in the -80 °C . Cell pellets were thawed and incubated with Readylyse Lysozyme , SuperaseIn , Protease K , and 20 % SDS for 20 minutes at <Temp> 37 °C </Temp> . Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures . An on-column DNase-treatment was performed for 30 minutes at room temperature . RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer . The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria . A KAPA Stranded RNA-Seq Kit ( Kapa Biosystems KK8401 ) was used following the manufacturer 's protocol to create sequencing libraries with an average insert length of around ~ 300 bp . 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463568	wt_glc__4	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS	SRR8173230	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		After inoculation and growth , 3 mL of cell broth ( OD600 ~ 0.5 ) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent ( 6 mL ) , vortexed for 5 seconds , incubated at room temperature for 5 min , and immediately centrifuged for 10 min at 17,500 RPMs . The supernatant was decanted , and the cell pellet was stored in the -80 °C . Cell pellets were thawed and incubated with Readylyse Lysozyme , SuperaseIn , Protease K , and 20 % SDS for 20 minutes at <Temp> 37 °C </Temp> . Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures . An on-column DNase-treatment was performed for 30 minutes at room temperature . RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer . The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria . A KAPA Stranded RNA-Seq Kit ( Kapa Biosystems KK8401 ) was used following the manufacturer 's protocol to create sequencing libraries with an average insert length of around ~ 300 bp . 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463569	arg_sbt__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS	SRR8173231	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		After inoculation and growth , 3 mL of cell broth ( OD600 ~ 0.5 ) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent ( 6 mL ) , vortexed for 5 seconds , incubated at room temperature for 5 min , and immediately centrifuged for 10 min at 17,500 RPMs . The supernatant was decanted , and the cell pellet was stored in the -80 °C . Cell pellets were thawed and incubated with Readylyse Lysozyme , SuperaseIn , Protease K , and 20 % SDS for 20 minutes at <Temp> 37 °C </Temp> . Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures . An on-column DNase-treatment was performed for 30 minutes at room temperature . RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer . The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria . A KAPA Stranded RNA-Seq Kit ( Kapa Biosystems KK8401 ) was used following the manufacturer 's protocol to create sequencing libraries with an average insert length of around ~ 300 bp . 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463570	arg_sbt__2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS	SRR8173232	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		After inoculation and growth , 3 mL of cell broth ( OD600 ~ 0.5 ) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent ( 6 mL ) , vortexed for 5 seconds , incubated at room temperature for 5 min , and immediately centrifuged for 10 min at 17,500 RPMs . The supernatant was decanted , and the cell pellet was stored in the -80 °C . Cell pellets were thawed and incubated with Readylyse Lysozyme , SuperaseIn , Protease K , and 20 % SDS for 20 minutes at <Temp> 37 °C </Temp> . Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures . An on-column DNase-treatment was performed for 30 minutes at room temperature . RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer . The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria . A KAPA Stranded RNA-Seq Kit ( Kapa Biosystems KK8401 ) was used following the manufacturer 's protocol to create sequencing libraries with an average insert length of around ~ 300 bp . 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463571	cytd_rib__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS	SRR8173233	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		After inoculation and growth , 3 mL of cell broth ( OD600 ~ 0.5 ) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent ( 6 mL ) , vortexed for 5 seconds , incubated at room temperature for 5 min , and immediately centrifuged for 10 min at 17,500 RPMs . The supernatant was decanted , and the cell pellet was stored in the -80 °C . Cell pellets were thawed and incubated with Readylyse Lysozyme , SuperaseIn , Protease K , and 20 % SDS for 20 minutes at <Temp> 37 °C </Temp> . Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures . An on-column DNase-treatment was performed for 30 minutes at room temperature . RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer . The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria . A KAPA Stranded RNA-Seq Kit ( Kapa Biosystems KK8401 ) was used following the manufacturer 's protocol to create sequencing libraries with an average insert length of around ~ 300 bp . 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463572	cytd_rib__2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS	SRR8173234	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		After inoculation and growth , 3 mL of cell broth ( OD600 ~ 0.5 ) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent ( 6 mL ) , vortexed for 5 seconds , incubated at room temperature for 5 min , and immediately centrifuged for 10 min at 17,500 RPMs . The supernatant was decanted , and the cell pellet was stored in the -80 °C . Cell pellets were thawed and incubated with Readylyse Lysozyme , SuperaseIn , Protease K , and 20 % SDS for 20 minutes at <Temp> 37 °C </Temp> . Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures . An on-column DNase-treatment was performed for 30 minutes at room temperature . RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer . The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria . A KAPA Stranded RNA-Seq Kit ( Kapa Biosystems KK8401 ) was used following the manufacturer 's protocol to create sequencing libraries with an average insert length of around ~ 300 bp . 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463573	gth__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS	SRR8173235	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		After inoculation and growth , 3 mL of cell broth ( OD600 ~ 0.5 ) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent ( 6 mL ) , vortexed for 5 seconds , incubated at room temperature for 5 min , and immediately centrifuged for 10 min at 17,500 RPMs . The supernatant was decanted , and the cell pellet was stored in the -80 °C . Cell pellets were thawed and incubated with Readylyse Lysozyme , SuperaseIn , Protease K , and 20 % SDS for 20 minutes at <Temp> 37 °C </Temp> . Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures . An on-column DNase-treatment was performed for 30 minutes at room temperature . RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer . The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria . A KAPA Stranded RNA-Seq Kit ( Kapa Biosystems KK8401 ) was used following the manufacturer 's protocol to create sequencing libraries with an average insert length of around ~ 300 bp . 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463574	gth__2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS	SRR8173236	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		After inoculation and growth , 3 mL of cell broth ( OD600 ~ 0.5 ) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent ( 6 mL ) , vortexed for 5 seconds , incubated at room temperature for 5 min , and immediately centrifuged for 10 min at 17,500 RPMs . The supernatant was decanted , and the cell pellet was stored in the -80 °C . Cell pellets were thawed and incubated with Readylyse Lysozyme , SuperaseIn , Protease K , and 20 % SDS for 20 minutes at <Temp> 37 °C </Temp> . Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures . An on-column DNase-treatment was performed for 30 minutes at room temperature . RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer . The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria . A KAPA Stranded RNA-Seq Kit ( Kapa Biosystems KK8401 ) was used following the manufacturer 's protocol to create sequencing libraries with an average insert length of around ~ 300 bp . 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463575	leu_glcr__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS	SRR8173237	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		After inoculation and growth , 3 mL of cell broth ( OD600 ~ 0.5 ) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent ( 6 mL ) , vortexed for 5 seconds , incubated at room temperature for 5 min , and immediately centrifuged for 10 min at 17,500 RPMs . The supernatant was decanted , and the cell pellet was stored in the -80 °C . Cell pellets were thawed and incubated with Readylyse Lysozyme , SuperaseIn , Protease K , and 20 % SDS for 20 minutes at <Temp> 37 °C </Temp> . Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures . An on-column DNase-treatment was performed for 30 minutes at room temperature . RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer . The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria . A KAPA Stranded RNA-Seq Kit ( Kapa Biosystems KK8401 ) was used following the manufacturer 's protocol to create sequencing libraries with an average insert length of around ~ 300 bp . 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463576	leu_glcr__2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS	SRR8173238	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		After inoculation and growth , 3 mL of cell broth ( OD600 ~ 0.5 ) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent ( 6 mL ) , vortexed for 5 seconds , incubated at room temperature for 5 min , and immediately centrifuged for 10 min at 17,500 RPMs . The supernatant was decanted , and the cell pellet was stored in the -80 °C . Cell pellets were thawed and incubated with Readylyse Lysozyme , SuperaseIn , Protease K , and 20 % SDS for 20 minutes at <Temp> 37 °C </Temp> . Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures . An on-column DNase-treatment was performed for 30 minutes at room temperature . RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer . The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria . A KAPA Stranded RNA-Seq Kit ( Kapa Biosystems KK8401 ) was used following the manufacturer 's protocol to create sequencing libraries with an average insert length of around ~ 300 bp . 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463577	met_glc__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS	SRR8173239	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		After inoculation and growth , 3 mL of cell broth ( OD600 ~ 0.5 ) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent ( 6 mL ) , vortexed for 5 seconds , incubated at room temperature for 5 min , and immediately centrifuged for 10 min at 17,500 RPMs . The supernatant was decanted , and the cell pellet was stored in the -80 °C . Cell pellets were thawed and incubated with Readylyse Lysozyme , SuperaseIn , Protease K , and 20 % SDS for 20 minutes at <Temp> 37 °C </Temp> . Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures . An on-column DNase-treatment was performed for 30 minutes at room temperature . RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer . The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria . A KAPA Stranded RNA-Seq Kit ( Kapa Biosystems KK8401 ) was used following the manufacturer 's protocol to create sequencing libraries with an average insert length of around ~ 300 bp . 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463578	met_glc__2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS	SRR8173240	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		After inoculation and growth , 3 mL of cell broth ( OD600 ~ 0.5 ) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent ( 6 mL ) , vortexed for 5 seconds , incubated at room temperature for 5 min , and immediately centrifuged for 10 min at 17,500 RPMs . The supernatant was decanted , and the cell pellet was stored in the -80 °C . Cell pellets were thawed and incubated with Readylyse Lysozyme , SuperaseIn , Protease K , and 20 % SDS for 20 minutes at <Temp> 37 °C </Temp> . Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures . An on-column DNase-treatment was performed for 30 minutes at room temperature . RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer . The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria . A KAPA Stranded RNA-Seq Kit ( Kapa Biosystems KK8401 ) was used following the manufacturer 's protocol to create sequencing libraries with an average insert length of around ~ 300 bp . 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463579	no3_anaero__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS	SRR8173241	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		After inoculation and growth , 3 mL of cell broth ( OD600 ~ 0.5 ) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent ( 6 mL ) , vortexed for 5 seconds , incubated at room temperature for 5 min , and immediately centrifuged for 10 min at 17,500 RPMs . The supernatant was decanted , and the cell pellet was stored in the -80 °C . Cell pellets were thawed and incubated with Readylyse Lysozyme , SuperaseIn , Protease K , and 20 % SDS for 20 minutes at <Temp> 37 °C </Temp> . Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures . An on-column DNase-treatment was performed for 30 minutes at room temperature . RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer . The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria . A KAPA Stranded RNA-Seq Kit ( Kapa Biosystems KK8401 ) was used following the manufacturer 's protocol to create sequencing libraries with an average insert length of around ~ 300 bp . 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463580	no3_anaero__2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS	SRR8173242	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		After inoculation and growth , 3 mL of cell broth ( OD600 ~ 0.5 ) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent ( 6 mL ) , vortexed for 5 seconds , incubated at room temperature for 5 min , and immediately centrifuged for 10 min at 17,500 RPMs . The supernatant was decanted , and the cell pellet was stored in the -80 °C . Cell pellets were thawed and incubated with Readylyse Lysozyme , SuperaseIn , Protease K , and 20 % SDS for 20 minutes at <Temp> 37 °C </Temp> . Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures . An on-column DNase-treatment was performed for 30 minutes at room temperature . RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer . The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria . A KAPA Stranded RNA-Seq Kit ( Kapa Biosystems KK8401 ) was used following the manufacturer 's protocol to create sequencing libraries with an average insert length of around ~ 300 bp . 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463581	phe_acgam__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS	SRR8173243	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		After inoculation and growth , 3 mL of cell broth ( OD600 ~ 0.5 ) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent ( 6 mL ) , vortexed for 5 seconds , incubated at room temperature for 5 min , and immediately centrifuged for 10 min at 17,500 RPMs . The supernatant was decanted , and the cell pellet was stored in the -80 °C . Cell pellets were thawed and incubated with Readylyse Lysozyme , SuperaseIn , Protease K , and 20 % SDS for 20 minutes at <Temp> 37 °C </Temp> . Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures . An on-column DNase-treatment was performed for 30 minutes at room temperature . RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer . The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria . A KAPA Stranded RNA-Seq Kit ( Kapa Biosystems KK8401 ) was used following the manufacturer 's protocol to create sequencing libraries with an average insert length of around ~ 300 bp . 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463582	phe_acgam__2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS	SRR8173244	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		After inoculation and growth , 3 mL of cell broth ( OD600 ~ 0.5 ) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent ( 6 mL ) , vortexed for 5 seconds , incubated at room temperature for 5 min , and immediately centrifuged for 10 min at 17,500 RPMs . The supernatant was decanted , and the cell pellet was stored in the -80 °C . Cell pellets were thawed and incubated with Readylyse Lysozyme , SuperaseIn , Protease K , and 20 % SDS for 20 minutes at <Temp> 37 °C </Temp> . Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures . An on-column DNase-treatment was performed for 30 minutes at room temperature . RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer . The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria . A KAPA Stranded RNA-Seq Kit ( Kapa Biosystems KK8401 ) was used following the manufacturer 's protocol to create sequencing libraries with an average insert length of around ~ 300 bp . 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463583	thm_gal__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS	SRR8173245	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		After inoculation and growth , 3 mL of cell broth ( OD600 ~ 0.5 ) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent ( 6 mL ) , vortexed for 5 seconds , incubated at room temperature for 5 min , and immediately centrifuged for 10 min at 17,500 RPMs . The supernatant was decanted , and the cell pellet was stored in the -80 °C . Cell pellets were thawed and incubated with Readylyse Lysozyme , SuperaseIn , Protease K , and 20 % SDS for 20 minutes at <Temp> 37 °C </Temp> . Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures . An on-column DNase-treatment was performed for 30 minutes at room temperature . RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer . The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria . A KAPA Stranded RNA-Seq Kit ( Kapa Biosystems KK8401 ) was used following the manufacturer 's protocol to create sequencing libraries with an average insert length of around ~ 300 bp . 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463584	thm_gal__2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS	SRR8173246	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		After inoculation and growth , 3 mL of cell broth ( OD600 ~ 0.5 ) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent ( 6 mL ) , vortexed for 5 seconds , incubated at room temperature for 5 min , and immediately centrifuged for 10 min at 17,500 RPMs . The supernatant was decanted , and the cell pellet was stored in the -80 °C . Cell pellets were thawed and incubated with Readylyse Lysozyme , SuperaseIn , Protease K , and 20 % SDS for 20 minutes at <Temp> 37 °C </Temp> . Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures . An on-column DNase-treatment was performed for 30 minutes at room temperature . RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer . The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria . A KAPA Stranded RNA-Seq Kit ( Kapa Biosystems KK8401 ) was used following the manufacturer 's protocol to create sequencing libraries with an average insert length of around ~ 300 bp . 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463585	tyr_glcn__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS	SRR8173247	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		After inoculation and growth , 3 mL of cell broth ( OD600 ~ 0.5 ) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent ( 6 mL ) , vortexed for 5 seconds , incubated at room temperature for 5 min , and immediately centrifuged for 10 min at 17,500 RPMs . The supernatant was decanted , and the cell pellet was stored in the -80 °C . Cell pellets were thawed and incubated with Readylyse Lysozyme , SuperaseIn , Protease K , and 20 % SDS for 20 minutes at <Temp> 37 °C </Temp> . Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures . An on-column DNase-treatment was performed for 30 minutes at room temperature . RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer . The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria . A KAPA Stranded RNA-Seq Kit ( Kapa Biosystems KK8401 ) was used following the manufacturer 's protocol to create sequencing libraries with an average insert length of around ~ 300 bp . 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463586	tyr_glcn__2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS	SRR8173248	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		After inoculation and growth , 3 mL of cell broth ( OD600 ~ 0.5 ) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent ( 6 mL ) , vortexed for 5 seconds , incubated at room temperature for 5 min , and immediately centrifuged for 10 min at 17,500 RPMs . The supernatant was decanted , and the cell pellet was stored in the -80 °C . Cell pellets were thawed and incubated with Readylyse Lysozyme , SuperaseIn , Protease K , and 20 % SDS for 20 minutes at <Temp> 37 °C </Temp> . Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures . An on-column DNase-treatment was performed for 30 minutes at room temperature . RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer . The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria . A KAPA Stranded RNA-Seq Kit ( Kapa Biosystems KK8401 ) was used following the manufacturer 's protocol to create sequencing libraries with an average insert length of around ~ 300 bp . 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463587	ura_pyr__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS	SRR8173249	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		After inoculation and growth , 3 mL of cell broth ( OD600 ~ 0.5 ) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent ( 6 mL ) , vortexed for 5 seconds , incubated at room temperature for 5 min , and immediately centrifuged for 10 min at 17,500 RPMs . The supernatant was decanted , and the cell pellet was stored in the -80 °C . Cell pellets were thawed and incubated with Readylyse Lysozyme , SuperaseIn , Protease K , and 20 % SDS for 20 minutes at <Temp> 37 °C </Temp> . Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures . An on-column DNase-treatment was performed for 30 minutes at room temperature . RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer . The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria . A KAPA Stranded RNA-Seq Kit ( Kapa Biosystems KK8401 ) was used following the manufacturer 's protocol to create sequencing libraries with an average insert length of around ~ 300 bp . 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463588	ura_pyr__2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS	SRR8173250	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		After inoculation and growth , 3 mL of cell broth ( OD600 ~ 0.5 ) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent ( 6 mL ) , vortexed for 5 seconds , incubated at room temperature for 5 min , and immediately centrifuged for 10 min at 17,500 RPMs . The supernatant was decanted , and the cell pellet was stored in the -80 °C . Cell pellets were thawed and incubated with Readylyse Lysozyme , SuperaseIn , Protease K , and 20 % SDS for 20 minutes at <Temp> 37 °C </Temp> . Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures . An on-column DNase-treatment was performed for 30 minutes at room temperature . RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer . The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria . A KAPA Stranded RNA-Seq Kit ( Kapa Biosystems KK8401 ) was used following the manufacturer 's protocol to create sequencing libraries with an average insert length of around ~ 300 bp . 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3854833	wt_glc_5__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS	SRR9204648	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		After inoculation and growth , 3 mL of cell broth ( OD600 ~ 0.5 ) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent ( 6 mL ) , vortexed for 5 seconds , incubated at room temperature for 5 min , and immediately centrifuged for 10 min at 17,500 RPMs . The supernatant was decanted , and the cell pellet was stored in the -80 °C . Cell pellets were thawed and incubated with Readylyse Lysozyme , SuperaseIn , Protease K , and 20 % SDS for 20 minutes at <Temp> 37 °C </Temp> . Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures . An on-column DNase-treatment was performed for 30 minutes at room temperature . RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer . The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria . A KAPA Stranded RNA-Seq Kit ( Kapa Biosystems KK8401 ) was used following the manufacturer 's protocol to create sequencing libraries with an average insert length of around ~ 300 bp . 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3854834	wt_glc_6__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS	SRR9204649	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		After inoculation and growth , 3 mL of cell broth ( OD600 ~ 0.5 ) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent ( 6 mL ) , vortexed for 5 seconds , incubated at room temperature for 5 min , and immediately centrifuged for 10 min at 17,500 RPMs . The supernatant was decanted , and the cell pellet was stored in the -80 °C . Cell pellets were thawed and incubated with Readylyse Lysozyme , SuperaseIn , Protease K , and 20 % SDS for 20 minutes at <Temp> 37 °C </Temp> . Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures . An on-column DNase-treatment was performed for 30 minutes at room temperature . RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer . The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria . A KAPA Stranded RNA-Seq Kit ( Kapa Biosystems KK8401 ) was used following the manufacturer 's protocol to create sequencing libraries with an average insert length of around ~ 300 bp . 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3854835	bw_delpurR_cytd__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS	SRR9204650	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		After inoculation and growth , 3 mL of cell broth ( OD600 ~ 0.5 ) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent ( 6 mL ) , vortexed for 5 seconds , incubated at room temperature for 5 min , and immediately centrifuged for 10 min at 17,500 RPMs . The supernatant was decanted , and the cell pellet was stored in the -80 °C . Cell pellets were thawed and incubated with Readylyse Lysozyme , SuperaseIn , Protease K , and 20 % SDS for 20 minutes at <Temp> 37 °C </Temp> . Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures . An on-column DNase-treatment was performed for 30 minutes at room temperature . RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer . The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria . A KAPA Stranded RNA-Seq Kit ( Kapa Biosystems KK8401 ) was used following the manufacturer 's protocol to create sequencing libraries with an average insert length of around ~ 300 bp . 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3854836	bw_delpurR_cytd__2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS	SRR9204651	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		After inoculation and growth , 3 mL of cell broth ( OD600 ~ 0.5 ) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent ( 6 mL ) , vortexed for 5 seconds , incubated at room temperature for 5 min , and immediately centrifuged for 10 min at 17,500 RPMs . The supernatant was decanted , and the cell pellet was stored in the -80 °C . Cell pellets were thawed and incubated with Readylyse Lysozyme , SuperaseIn , Protease K , and 20 % SDS for 20 minutes at <Temp> 37 °C </Temp> . Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures . An on-column DNase-treatment was performed for 30 minutes at room temperature . RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer . The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria . A KAPA Stranded RNA-Seq Kit ( Kapa Biosystems KK8401 ) was used following the manufacturer 's protocol to create sequencing libraries with an average insert length of around ~ 300 bp . 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3854837	ade_glc__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS	SRR9204652	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		After inoculation and growth , 3 mL of cell broth ( OD600 ~ 0.5 ) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent ( 6 mL ) , vortexed for 5 seconds , incubated at room temperature for 5 min , and immediately centrifuged for 10 min at 17,500 RPMs . The supernatant was decanted , and the cell pellet was stored in the -80 °C . Cell pellets were thawed and incubated with Readylyse Lysozyme , SuperaseIn , Protease K , and 20 % SDS for 20 minutes at <Temp> 37 °C </Temp> . Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures . An on-column DNase-treatment was performed for 30 minutes at room temperature . RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer . The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria . A KAPA Stranded RNA-Seq Kit ( Kapa Biosystems KK8401 ) was used following the manufacturer 's protocol to create sequencing libraries with an average insert length of around ~ 300 bp . 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3854838	ade_glc__2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS	SRR9204653	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		After inoculation and growth , 3 mL of cell broth ( OD600 ~ 0.5 ) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent ( 6 mL ) , vortexed for 5 seconds , incubated at room temperature for 5 min , and immediately centrifuged for 10 min at 17,500 RPMs . The supernatant was decanted , and the cell pellet was stored in the -80 °C . Cell pellets were thawed and incubated with Readylyse Lysozyme , SuperaseIn , Protease K , and 20 % SDS for 20 minutes at <Temp> 37 °C </Temp> . Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures . An on-column DNase-treatment was performed for 30 minutes at room temperature . RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer . The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria . A KAPA Stranded RNA-Seq Kit ( Kapa Biosystems KK8401 ) was used following the manufacturer 's protocol to create sequencing libraries with an average insert length of around ~ 300 bp . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE122296	Expression profiling of multiple Escherichia coli strains on glucose minimal media	GSM3463601	MG1655_1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122296/GSE122296.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS	SRR8173221	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		After inoculation and growth , 3 mL of cell broth ( OD600 ~ 0.5 ) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent ( 6 mL ) , vortexed for 5 seconds , incubated at room temperature for 5 min , and immediately centrifuged for 10 min at 17,500 RPMs . The supernatant was decanted , and the cell pellet was stored in the -80 °C . Cell pellets were thawed and incubated with Readylyse Lysozyme , SuperaseIn , Protease K , and 20 % SDS for 20 minutes at <Temp> 37 °C </Temp> . Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures . An on-column DNase-treatment was performed for 30 minutes at room temperature . RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer . The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria . A KAPA Stranded RNA-Seq Kit ( Kapa Biosystems KK8401 ) was used following the manufacturer 's protocol to create sequencing libraries with an average insert length of around ~ 300 bp . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE122296	Expression profiling of multiple Escherichia coli strains on glucose minimal media	GSM3463602	MG1655_2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122296/GSE122296.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	After inoculation and growth, 3 mL of cell broth (OD600 ~ 0.5) was immediately added to 2 volumes Qiagen RNA-protect Bacteria Reagent (6 mL), vortexed for 5 seconds, incubated at room temperature for 5 min, and immediately centrifuged for 10 min at 17,500 RPMs.  The supernatant was decanted, and the cell pellet was stored in the -80°C. Cell pellets were thawed and incubated with Readylyse Lysozyme, SuperaseIn, Protease K, and 20% SDS for 20 minutes at 37°C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase-treatment was performed for 30 minutes at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA-nano chip on a bioanalyzer. The rRNA was removed using Illumina Ribo-Zero rRNA removal kit for Gram Negative Bacteria. A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around ~300 bp. PGCGROWTHCONDITIONS	SRR8173222	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT , Δfis and Δhns were grown in Luria-Bertani ( LB ) broth and agar ( 15g/l ) . Where needed , kanamycin was used at final concentration of 50µg/ml . For RNA extraction , E. coli cultures were grown to mid-exponential growth phase <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with 40 % ( w/v ) glucose . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE123554	Reconstruction of transcriptional regulatory networks of Fis and H-NS in Escherichia coli from genome wide data analysis	GSM3507068	delta-fis rep1		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE123554/GSE123554.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, Δfis and Δhns were grown in Luria-Bertani (LB) broth and agar (15g/l). Where needed, kanamycin was used at final concentration of 50µg/ml. For RNA extraction, E. coli cultures were grown to mid-exponential growth phase aerobically at 37°C in M9 minimal media supplemented with 40% (w/v) glucose. PGCGROWTHCONDITIONS	SRR8309841	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT , Δfis and Δhns were grown in Luria-Bertani ( LB ) broth and agar ( 15g/l ) . Where needed , kanamycin was used at final concentration of 50µg/ml . For RNA extraction , E. coli cultures were grown to mid-exponential growth phase <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with 40 % ( w/v ) glucose . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE123554	Reconstruction of transcriptional regulatory networks of Fis and H-NS in Escherichia coli from genome wide data analysis	GSM3507069	delta-fis rep2		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE123554/GSE123554.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, Δfis and Δhns were grown in Luria-Bertani (LB) broth and agar (15g/l). Where needed, kanamycin was used at final concentration of 50µg/ml. For RNA extraction, E. coli cultures were grown to mid-exponential growth phase aerobically at 37°C in M9 minimal media supplemented with 40% (w/v) glucose. PGCGROWTHCONDITIONS	SRR8309842	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT , Δfis and Δhns were grown in Luria-Bertani ( LB ) broth and agar ( 15g/l ) . Where needed , kanamycin was used at final concentration of 50µg/ml . For RNA extraction , E. coli cultures were grown to mid-exponential growth phase <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with 40 % ( w/v ) glucose . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE123554	Reconstruction of transcriptional regulatory networks of Fis and H-NS in Escherichia coli from genome wide data analysis	GSM3507070	delta-hns rep1		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE123554/GSE123554.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, Δfis and Δhns were grown in Luria-Bertani (LB) broth and agar (15g/l). Where needed, kanamycin was used at final concentration of 50µg/ml. For RNA extraction, E. coli cultures were grown to mid-exponential growth phase aerobically at 37°C in M9 minimal media supplemented with 40% (w/v) glucose. PGCGROWTHCONDITIONS	SRR8309843	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT , Δfis and Δhns were grown in Luria-Bertani ( LB ) broth and agar ( 15g/l ) . Where needed , kanamycin was used at final concentration of 50µg/ml . For RNA extraction , E. coli cultures were grown to mid-exponential growth phase <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with 40 % ( w/v ) glucose . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE123554	Reconstruction of transcriptional regulatory networks of Fis and H-NS in Escherichia coli from genome wide data analysis	GSM3507071	delta-hns rep2		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE123554/GSE123554.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, Δfis and Δhns were grown in Luria-Bertani (LB) broth and agar (15g/l). Where needed, kanamycin was used at final concentration of 50µg/ml. For RNA extraction, E. coli cultures were grown to mid-exponential growth phase aerobically at 37°C in M9 minimal media supplemented with 40% (w/v) glucose. PGCGROWTHCONDITIONS	SRR8309844	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		Total RNA was extracted using the Trizol reagent ( Thermo Fisher Scientific ) and the concentration and purity of the samples were determined using Nano Drop . RNA integrity was monitored using the R6K ScreenTape system on the Agilent 2200 TapeStation . gDNA was removed by Turbo DNase ( Thermo Fisher Scientific ) in the presence of RiboLock RNase Inhibitor ( Thermo Fisher Scientific ) for 60 min at <Temp> 37 °C </Temp> . Following organic extraction ( 1x 25:24:1 v/v phenol/chloroform / isoamyalcohol , 1x chloroform ) , RNA was recovered by overnight precipitation with 3 volumes of 30:1 100 % ethanol/3 M sodium acetate ( pH 5.2 ) . The RNA preparations were further treated with RiboZero ( Illumina ) and the concentration of the samples was determined with Qubit . 	GPL26204	GPL26204: NextSeq 550 (Escherichia coli K-12)	GSE126710	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GSM3611666	E. coli K-12 MG1655_R1 [MG_1]	31208335	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE126710/GSE126710.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Total RNA was extracted using the Trizol reagent (Thermo Fisher Scientific) and the concentration and purity of the samples were determined using Nano Drop. RNA integrity was monitored using the R6K ScreenTape system on the Agilent 2200 TapeStation. gDNA was removed by Turbo DNase (Thermo Fisher Scientific) in the presence of RiboLock RNase Inhibitor (Thermo Fisher Scientific) for 60 min at 37°C. Following organic extraction (1x 25:24:1 v/v phenol/chloroform/ isoamyalcohol, 1x chloroform), RNA was recovered by overnight precipitation with 3 volumes of 30:1 100 % ethanol/3 M sodium acetate (pH 5.2). The RNA preparations were further treated with RiboZero (Illumina) and the concentration of the samples was determined with Qubit. PGCGROWTHCONDITIONS	SRR8587784	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		Total RNA was extracted using the Trizol reagent ( Thermo Fisher Scientific ) and the concentration and purity of the samples were determined using Nano Drop . RNA integrity was monitored using the R6K ScreenTape system on the Agilent 2200 TapeStation . gDNA was removed by Turbo DNase ( Thermo Fisher Scientific ) in the presence of RiboLock RNase Inhibitor ( Thermo Fisher Scientific ) for 60 min at <Temp> 37 °C </Temp> . Following organic extraction ( 1x 25:24:1 v/v phenol/chloroform / isoamyalcohol , 1x chloroform ) , RNA was recovered by overnight precipitation with 3 volumes of 30:1 100 % ethanol/3 M sodium acetate ( pH 5.2 ) . The RNA preparations were further treated with RiboZero ( Illumina ) and the concentration of the samples was determined with Qubit . 	GPL26204	GPL26204: NextSeq 550 (Escherichia coli K-12)	GSE126710	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GSM3611667	E. coli K-12 MG1655_R2 [MG_2]	31208335	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE126710/GSE126710.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Total RNA was extracted using the Trizol reagent (Thermo Fisher Scientific) and the concentration and purity of the samples were determined using Nano Drop. RNA integrity was monitored using the R6K ScreenTape system on the Agilent 2200 TapeStation. gDNA was removed by Turbo DNase (Thermo Fisher Scientific) in the presence of RiboLock RNase Inhibitor (Thermo Fisher Scientific) for 60 min at 37°C. Following organic extraction (1x 25:24:1 v/v phenol/chloroform/ isoamyalcohol, 1x chloroform), RNA was recovered by overnight precipitation with 3 volumes of 30:1 100 % ethanol/3 M sodium acetate (pH 5.2). The RNA preparations were further treated with RiboZero (Illumina) and the concentration of the samples was determined with Qubit. PGCGROWTHCONDITIONS	SRR8587785	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		Total RNA was extracted using the Trizol reagent ( Thermo Fisher Scientific ) and the concentration and purity of the samples were determined using Nano Drop . RNA integrity was monitored using the R6K ScreenTape system on the Agilent 2200 TapeStation . gDNA was removed by Turbo DNase ( Thermo Fisher Scientific ) in the presence of RiboLock RNase Inhibitor ( Thermo Fisher Scientific ) for 60 min at <Temp> 37 °C </Temp> . Following organic extraction ( 1x 25:24:1 v/v phenol/chloroform / isoamyalcohol , 1x chloroform ) , RNA was recovered by overnight precipitation with 3 volumes of 30:1 100 % ethanol/3 M sodium acetate ( pH 5.2 ) . The RNA preparations were further treated with RiboZero ( Illumina ) and the concentration of the samples was determined with Qubit . 	GPL26204	GPL26204: NextSeq 550 (Escherichia coli K-12)	GSE126710	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GSM3611668	E. coli K-12 MG1655_R3 [MG_3]	31208335	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE126710/GSE126710.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Total RNA was extracted using the Trizol reagent (Thermo Fisher Scientific) and the concentration and purity of the samples were determined using Nano Drop. RNA integrity was monitored using the R6K ScreenTape system on the Agilent 2200 TapeStation. gDNA was removed by Turbo DNase (Thermo Fisher Scientific) in the presence of RiboLock RNase Inhibitor (Thermo Fisher Scientific) for 60 min at 37°C. Following organic extraction (1x 25:24:1 v/v phenol/chloroform/ isoamyalcohol, 1x chloroform), RNA was recovered by overnight precipitation with 3 volumes of 30:1 100 % ethanol/3 M sodium acetate (pH 5.2). The RNA preparations were further treated with RiboZero (Illumina) and the concentration of the samples was determined with Qubit. PGCGROWTHCONDITIONS	SRR8587786	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		Total RNA was extracted using the Trizol reagent ( Thermo Fisher Scientific ) and the concentration and purity of the samples were determined using Nano Drop . RNA integrity was monitored using the R6K ScreenTape system on the Agilent 2200 TapeStation . gDNA was removed by Turbo DNase ( Thermo Fisher Scientific ) in the presence of RiboLock RNase Inhibitor ( Thermo Fisher Scientific ) for 60 min at <Temp> 37 °C </Temp> . Following organic extraction ( 1x 25:24:1 v/v phenol/chloroform / isoamyalcohol , 1x chloroform ) , RNA was recovered by overnight precipitation with 3 volumes of 30:1 100 % ethanol/3 M sodium acetate ( pH 5.2 ) . The RNA preparations were further treated with RiboZero ( Illumina ) and the concentration of the samples was determined with Qubit . 	GPL26204	GPL26204: NextSeq 550 (Escherichia coli K-12)	GSE126710	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GSM3611669	E. coli K-12 MG1655::φO104_R1 [O104_1]	31208335	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE126710/GSE126710.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Total RNA was extracted using the Trizol reagent (Thermo Fisher Scientific) and the concentration and purity of the samples were determined using Nano Drop. RNA integrity was monitored using the R6K ScreenTape system on the Agilent 2200 TapeStation. gDNA was removed by Turbo DNase (Thermo Fisher Scientific) in the presence of RiboLock RNase Inhibitor (Thermo Fisher Scientific) for 60 min at 37°C. Following organic extraction (1x 25:24:1 v/v phenol/chloroform/ isoamyalcohol, 1x chloroform), RNA was recovered by overnight precipitation with 3 volumes of 30:1 100 % ethanol/3 M sodium acetate (pH 5.2). The RNA preparations were further treated with RiboZero (Illumina) and the concentration of the samples was determined with Qubit. PGCGROWTHCONDITIONS	SRR8587787	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		Total RNA was extracted using the Trizol reagent ( Thermo Fisher Scientific ) and the concentration and purity of the samples were determined using Nano Drop . RNA integrity was monitored using the R6K ScreenTape system on the Agilent 2200 TapeStation . gDNA was removed by Turbo DNase ( Thermo Fisher Scientific ) in the presence of RiboLock RNase Inhibitor ( Thermo Fisher Scientific ) for 60 min at <Temp> 37 °C </Temp> . Following organic extraction ( 1x 25:24:1 v/v phenol/chloroform / isoamyalcohol , 1x chloroform ) , RNA was recovered by overnight precipitation with 3 volumes of 30:1 100 % ethanol/3 M sodium acetate ( pH 5.2 ) . The RNA preparations were further treated with RiboZero ( Illumina ) and the concentration of the samples was determined with Qubit . 	GPL26204	GPL26204: NextSeq 550 (Escherichia coli K-12)	GSE126710	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GSM3611670	E. coli K-12 MG1655::φO104_R2 [O104_2]	31208335	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE126710/GSE126710.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Total RNA was extracted using the Trizol reagent (Thermo Fisher Scientific) and the concentration and purity of the samples were determined using Nano Drop. RNA integrity was monitored using the R6K ScreenTape system on the Agilent 2200 TapeStation. gDNA was removed by Turbo DNase (Thermo Fisher Scientific) in the presence of RiboLock RNase Inhibitor (Thermo Fisher Scientific) for 60 min at 37°C. Following organic extraction (1x 25:24:1 v/v phenol/chloroform/ isoamyalcohol, 1x chloroform), RNA was recovered by overnight precipitation with 3 volumes of 30:1 100 % ethanol/3 M sodium acetate (pH 5.2). The RNA preparations were further treated with RiboZero (Illumina) and the concentration of the samples was determined with Qubit. PGCGROWTHCONDITIONS	SRR8587788	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		Total RNA was extracted using the Trizol reagent ( Thermo Fisher Scientific ) and the concentration and purity of the samples were determined using Nano Drop . RNA integrity was monitored using the R6K ScreenTape system on the Agilent 2200 TapeStation . gDNA was removed by Turbo DNase ( Thermo Fisher Scientific ) in the presence of RiboLock RNase Inhibitor ( Thermo Fisher Scientific ) for 60 min at <Temp> 37 °C </Temp> . Following organic extraction ( 1x 25:24:1 v/v phenol/chloroform / isoamyalcohol , 1x chloroform ) , RNA was recovered by overnight precipitation with 3 volumes of 30:1 100 % ethanol/3 M sodium acetate ( pH 5.2 ) . The RNA preparations were further treated with RiboZero ( Illumina ) and the concentration of the samples was determined with Qubit . 	GPL26204	GPL26204: NextSeq 550 (Escherichia coli K-12)	GSE126710	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GSM3611671	E. coli K-12 MG1655::φO104_R3 [O104_3]	31208335	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE126710/GSE126710.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Total RNA was extracted using the Trizol reagent (Thermo Fisher Scientific) and the concentration and purity of the samples were determined using Nano Drop. RNA integrity was monitored using the R6K ScreenTape system on the Agilent 2200 TapeStation. gDNA was removed by Turbo DNase (Thermo Fisher Scientific) in the presence of RiboLock RNase Inhibitor (Thermo Fisher Scientific) for 60 min at 37°C. Following organic extraction (1x 25:24:1 v/v phenol/chloroform/ isoamyalcohol, 1x chloroform), RNA was recovered by overnight precipitation with 3 volumes of 30:1 100 % ethanol/3 M sodium acetate (pH 5.2). The RNA preparations were further treated with RiboZero (Illumina) and the concentration of the samples was determined with Qubit. PGCGROWTHCONDITIONS	SRR8587789	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		Total RNA was extracted using the Trizol reagent ( Thermo Fisher Scientific ) and the concentration and purity of the samples were determined using Nano Drop . RNA integrity was monitored using the R6K ScreenTape system on the Agilent 2200 TapeStation . gDNA was removed by Turbo DNase ( Thermo Fisher Scientific ) in the presence of RiboLock RNase Inhibitor ( Thermo Fisher Scientific ) for 60 min at <Temp> 37 °C </Temp> . Following organic extraction ( 1x 25:24:1 v/v phenol/chloroform / isoamyalcohol , 1x chloroform ) , RNA was recovered by overnight precipitation with 3 volumes of 30:1 100 % ethanol/3 M sodium acetate ( pH 5.2 ) . The RNA preparations were further treated with RiboZero ( Illumina ) and the concentration of the samples was determined with Qubit . 	GPL26204	GPL26204: NextSeq 550 (Escherichia coli K-12)	GSE126710	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GSM3611672	E. coli K-12 MG1655_φPA8_R1 [PA8_1]	31208335	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE126710/GSE126710.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Total RNA was extracted using the Trizol reagent (Thermo Fisher Scientific) and the concentration and purity of the samples were determined using Nano Drop. RNA integrity was monitored using the R6K ScreenTape system on the Agilent 2200 TapeStation. gDNA was removed by Turbo DNase (Thermo Fisher Scientific) in the presence of RiboLock RNase Inhibitor (Thermo Fisher Scientific) for 60 min at 37°C. Following organic extraction (1x 25:24:1 v/v phenol/chloroform/ isoamyalcohol, 1x chloroform), RNA was recovered by overnight precipitation with 3 volumes of 30:1 100 % ethanol/3 M sodium acetate (pH 5.2). The RNA preparations were further treated with RiboZero (Illumina) and the concentration of the samples was determined with Qubit. PGCGROWTHCONDITIONS	SRR8587790	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		Total RNA was extracted using the Trizol reagent ( Thermo Fisher Scientific ) and the concentration and purity of the samples were determined using Nano Drop . RNA integrity was monitored using the R6K ScreenTape system on the Agilent 2200 TapeStation . gDNA was removed by Turbo DNase ( Thermo Fisher Scientific ) in the presence of RiboLock RNase Inhibitor ( Thermo Fisher Scientific ) for 60 min at <Temp> 37 °C </Temp> . Following organic extraction ( 1x 25:24:1 v/v phenol/chloroform / isoamyalcohol , 1x chloroform ) , RNA was recovered by overnight precipitation with 3 volumes of 30:1 100 % ethanol/3 M sodium acetate ( pH 5.2 ) . The RNA preparations were further treated with RiboZero ( Illumina ) and the concentration of the samples was determined with Qubit . 	GPL26204	GPL26204: NextSeq 550 (Escherichia coli K-12)	GSE126710	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GSM3611673	E. coli K-12 MG1655_φPA8_R2 [PA8_2]	31208335	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE126710/GSE126710.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Total RNA was extracted using the Trizol reagent (Thermo Fisher Scientific) and the concentration and purity of the samples were determined using Nano Drop. RNA integrity was monitored using the R6K ScreenTape system on the Agilent 2200 TapeStation. gDNA was removed by Turbo DNase (Thermo Fisher Scientific) in the presence of RiboLock RNase Inhibitor (Thermo Fisher Scientific) for 60 min at 37°C. Following organic extraction (1x 25:24:1 v/v phenol/chloroform/ isoamyalcohol, 1x chloroform), RNA was recovered by overnight precipitation with 3 volumes of 30:1 100 % ethanol/3 M sodium acetate (pH 5.2). The RNA preparations were further treated with RiboZero (Illumina) and the concentration of the samples was determined with Qubit. PGCGROWTHCONDITIONS	SRR8587791	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		Total RNA was extracted using the Trizol reagent ( Thermo Fisher Scientific ) and the concentration and purity of the samples were determined using Nano Drop . RNA integrity was monitored using the R6K ScreenTape system on the Agilent 2200 TapeStation . gDNA was removed by Turbo DNase ( Thermo Fisher Scientific ) in the presence of RiboLock RNase Inhibitor ( Thermo Fisher Scientific ) for 60 min at <Temp> 37 °C </Temp> . Following organic extraction ( 1x 25:24:1 v/v phenol/chloroform / isoamyalcohol , 1x chloroform ) , RNA was recovered by overnight precipitation with 3 volumes of 30:1 100 % ethanol/3 M sodium acetate ( pH 5.2 ) . The RNA preparations were further treated with RiboZero ( Illumina ) and the concentration of the samples was determined with Qubit . 	GPL26204	GPL26204: NextSeq 550 (Escherichia coli K-12)	GSE126710	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GSM3611674	E. coli K-12 MG1655_fastφPA8_R3 [PA8_3]	31208335	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE126710/GSE126710.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Total RNA was extracted using the Trizol reagent (Thermo Fisher Scientific) and the concentration and purity of the samples were determined using Nano Drop. RNA integrity was monitored using the R6K ScreenTape system on the Agilent 2200 TapeStation. gDNA was removed by Turbo DNase (Thermo Fisher Scientific) in the presence of RiboLock RNase Inhibitor (Thermo Fisher Scientific) for 60 min at 37°C. Following organic extraction (1x 25:24:1 v/v phenol/chloroform/ isoamyalcohol, 1x chloroform), RNA was recovered by overnight precipitation with 3 volumes of 30:1 100 % ethanol/3 M sodium acetate (pH 5.2). The RNA preparations were further treated with RiboZero (Illumina) and the concentration of the samples was determined with Qubit. PGCGROWTHCONDITIONS	SRR8587792	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275442	WT_LB_R1	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907640	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275443	WT_LB_R2	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907641	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275444	WT_EtOH_R1	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907642	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275446	BaeR_KO_LB_R1	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907644	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275447	BaeR_KO_ LB_R2	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907645	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275448	BaeR_KO_EtOH_R1	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907646	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275450	CpxR_KO_LB_R1	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907648	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275451	CpxR_KO_LB_R2	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907649	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275454	KdpE_KO_01-KCl_R1	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907652	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275455	KdpE_KO_01-KCl_R2	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907653	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275456	KdpE_KO_115-KCl_R1	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907654	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275457	KdpE_KO_115-KCl_R2	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907655	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275458	WT_01-KCl_R1	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907656	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275459	WT_01-KCl_R2	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907657	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275460	WT_115-KCl_R1	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907658	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275461	WT_115-KCl_R2	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907659	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275462	PhoB_KO_M9_R1	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907660	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275463	PhoB_KO_M9_R2	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907661	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275464	PhoB_KO_M9-P_R1	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907662	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275465	PhoB_KO_M9-P_R2	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907663	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275466	WT_M9-P_R1	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907664	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275467	WT_M9-P_R2	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907665	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275469	ZraR_KO_LB_R2	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907667	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275470	ZraR_KO_ZnCl2_R1	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907668	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275471	ZraR_KO_ZnCl2_R2	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907669	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275472	WT_ZnCl2_R1	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907670	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275473	WT_ZnCl2_R2	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907671	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		An overnight culture was diluted to an <OD> OD600 of 0.02 </OD> in <Med> LB media </Med> supplemented with 100 µg/ml of carbenicillin , 40 µg/ml biotin , and <Supp> 70 µM IPTG </Supp> . The back diluted culture was grown at <Temp> 37 °C </Temp> until reaching an OD600 of 0.45 . 	GPL10328	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	GSE33671	Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo	GSM832606	DSP1_AP	22153074	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE33671/GSE33671.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	An overnight culture was diluted to an OD600 of 0.02 in LB media supplemented with 100 µg/ml of carbenicillin, 40 µg/ml biotin, and 70 µM IPTG. The back diluted culture was grown at 37°C until reaching an OD600 of 0.45. PGCGROWTHCONDITIONS	SRR364363	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		An overnight culture was diluted to an <OD> OD600 of 0.02 </OD> in <Med> LB media </Med> supplemented with 100 µg/ml of carbenicillin , 40 µg/ml biotin , and <Supp> 70 µM IPTG </Supp> . The back diluted culture was grown at <Temp> 37 °C </Temp> until reaching an OD600 of 0.45 . 	GPL10328	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	GSE33671	Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo	GSM832607	DSP1_Total	22153074	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE33671/GSE33671.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	An overnight culture was diluted to an OD600 of 0.02 in LB media supplemented with 100 µg/ml of carbenicillin, 40 µg/ml biotin, and 70 µM IPTG. The back diluted culture was grown at 37°C until reaching an OD600 of 0.45. PGCGROWTHCONDITIONS	SRR364364	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		An overnight culture was diluted to an <OD> OD600 of 0.02 </OD> in <Med> LB media </Med> supplemented with 100 µg/ml of carbenicillin , 40 µg/ml biotin , and <Supp> 70 µM IPTG </Supp> . The back diluted culture was grown at <Temp> 37 °C </Temp> until reaching an OD600 of 0.45 . 	GPL10328	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	GSE33671	Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo	GSM832608	DSP2_AP	22153074	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE33671/GSE33671.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	An overnight culture was diluted to an OD600 of 0.02 in LB media supplemented with 100 µg/ml of carbenicillin, 40 µg/ml biotin, and 70 µM IPTG. The back diluted culture was grown at 37°C until reaching an OD600 of 0.45. PGCGROWTHCONDITIONS	SRR364365	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		An overnight culture was diluted to an <OD> OD600 of 0.02 </OD> in <Med> LB media </Med> supplemented with 100 µg/ml of carbenicillin , 40 µg/ml biotin , and <Supp> 70 µM IPTG </Supp> . The back diluted culture was grown at <Temp> 37 °C </Temp> until reaching an OD600 of 0.45 . 	GPL10328	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	GSE33671	Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo	GSM832609	DSP2_Total	22153074	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE33671/GSE33671.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	An overnight culture was diluted to an OD600 of 0.02 in LB media supplemented with 100 µg/ml of carbenicillin, 40 µg/ml biotin, and 70 µM IPTG. The back diluted culture was grown at 37°C until reaching an OD600 of 0.45. PGCGROWTHCONDITIONS	SRR364366	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		An overnight culture was diluted to an <OD> OD600 of 0.02 </OD> in <Med> LB media </Med> supplemented with 100 µg/ml of carbenicillin , 40 µg/ml biotin , and <Supp> 70 µM IPTG </Supp> . The back diluted culture was grown at <Temp> 37 °C </Temp> until reaching an OD600 of 0.45 . 	GPL10328	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	GSE33671	Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo	GSM832610	DSP3_AP	22153074	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE33671/GSE33671.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	An overnight culture was diluted to an OD600 of 0.02 in LB media supplemented with 100 µg/ml of carbenicillin, 40 µg/ml biotin, and 70 µM IPTG. The back diluted culture was grown at 37°C until reaching an OD600 of 0.45. PGCGROWTHCONDITIONS	SRR364367	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		An overnight culture was diluted to an <OD> OD600 of 0.02 </OD> in <Med> LB media </Med> supplemented with 100 µg/ml of carbenicillin , 40 µg/ml biotin , and <Supp> 70 µM IPTG </Supp> . The back diluted culture was grown at <Temp> 37 °C </Temp> until reaching an OD600 of 0.45 . 	GPL10328	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	GSE33671	Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo	GSM832611	DSP3_Total	22153074	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE33671/GSE33671.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	An overnight culture was diluted to an OD600 of 0.02 in LB media supplemented with 100 µg/ml of carbenicillin, 40 µg/ml biotin, and 70 µM IPTG. The back diluted culture was grown at 37°C until reaching an OD600 of 0.45. PGCGROWTHCONDITIONS	SRR364368	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		An overnight culture was diluted to an <OD> OD600 of 0.02 </OD> in <Med> LB media </Med> supplemented with 100 µg/ml of carbenicillin , 40 µg/ml biotin , and <Supp> 70 µM IPTG </Supp> . The back diluted culture was grown at <Temp> 37 °C </Temp> until reaching an OD600 of 0.45 . 	GPL10328	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	GSE33671	Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo	GSM832612	EDC1_AP	22153074	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE33671/GSE33671.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	An overnight culture was diluted to an OD600 of 0.02 in LB media supplemented with 100 µg/ml of carbenicillin, 40 µg/ml biotin, and 70 µM IPTG. The back diluted culture was grown at 37°C until reaching an OD600 of 0.45. PGCGROWTHCONDITIONS	SRR364369	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		An overnight culture was diluted to an <OD> OD600 of 0.02 </OD> in <Med> LB media </Med> supplemented with 100 µg/ml of carbenicillin , 40 µg/ml biotin , and <Supp> 70 µM IPTG </Supp> . The back diluted culture was grown at <Temp> 37 °C </Temp> until reaching an OD600 of 0.45 . 	GPL10328	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	GSE33671	Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo	GSM832613	EDC1_Total	22153074	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE33671/GSE33671.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	An overnight culture was diluted to an OD600 of 0.02 in LB media supplemented with 100 µg/ml of carbenicillin, 40 µg/ml biotin, and 70 µM IPTG. The back diluted culture was grown at 37°C until reaching an OD600 of 0.45. PGCGROWTHCONDITIONS	SRR364370	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		Total RNA was isolated with TRIzol ( invitrogen , Carlsbad , CA ) according to the manufacture [ linebreak ] s instruction . DNA was removed from RNA extracts with RNase-free DNase I ( New England Biolabs , Beverly , MA , USA ) by incubation at <Temp> 37 °C </Temp> for <Supp> 30 min </Supp> . The quality of total RNA was assessed by using 2100 Bioanalyzer ( Agilent , Santa Clara , USA ) and also checked by agarose gel electrophoresis . rRNAs was subsquently removed from the total mRNA following the instruction of the Ribo-Zero rRNATM Removal kit ( Epicentre , Madison , WI , USA ) . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE43408	Quantitative Different Analysis of antimicrobial peptide LL37 expressed in E.coli Top 10 under aerobic and anaerobic condition.	GSM1217967	pHerd30T CK+aerobic	23856776	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE43408/GSE43408.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Total RNA was isolated with TRIzol (invitrogen, Carlsbad, CA) according to the manufacture[linebreak]s instruction. DNA was removed from RNA extracts with RNase-free DNase I (New England Biolabs, Beverly, MA, USA) by incubation at 37°C for 30 min. The quality of total RNA was assessed by using 2100 Bioanalyzer (Agilent, Santa Clara, USA) and also checked by agarose gel electrophoresis. rRNAs was subsquently removed from the total mRNA following the instruction of the Ribo-Zero rRNATM Removal kit (Epicentre, Madison, WI, USA). PGCGROWTHCONDITIONS	SRR958658	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		Total RNA was isolated with TRIzol ( invitrogen , Carlsbad , CA ) according to the manufacture [ linebreak ] s instruction . DNA was removed from RNA extracts with RNase-free DNase I ( New England Biolabs , Beverly , MA , USA ) by incubation at <Temp> 37 °C </Temp> for <Supp> 30 min </Supp> . The quality of total RNA was assessed by using 2100 Bioanalyzer ( Agilent , Santa Clara , USA ) and also checked by agarose gel electrophoresis . rRNAs was subsquently removed from the total mRNA following the instruction of the Ribo-Zero rRNATM Removal kit ( Epicentre , Madison , WI , USA ) . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE43408	Quantitative Different Analysis of antimicrobial peptide LL37 expressed in E.coli Top 10 under aerobic and anaerobic condition.	GSM1217968	pHerd30T-LL37 induced+aerobic	23856776	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE43408/GSE43408.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Total RNA was isolated with TRIzol (invitrogen, Carlsbad, CA) according to the manufacture[linebreak]s instruction. DNA was removed from RNA extracts with RNase-free DNase I (New England Biolabs, Beverly, MA, USA) by incubation at 37°C for 30 min. The quality of total RNA was assessed by using 2100 Bioanalyzer (Agilent, Santa Clara, USA) and also checked by agarose gel electrophoresis. rRNAs was subsquently removed from the total mRNA following the instruction of the Ribo-Zero rRNATM Removal kit (Epicentre, Madison, WI, USA). PGCGROWTHCONDITIONS	SRR958659	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		Total RNA was isolated with TRIzol ( invitrogen , Carlsbad , CA ) according to the manufacture [ linebreak ] s instruction . DNA was removed from RNA extracts with RNase-free DNase I ( New England Biolabs , Beverly , MA , USA ) by incubation at <Temp> 37 °C </Temp> for <Supp> 30 min </Supp> . The quality of total RNA was assessed by using 2100 Bioanalyzer ( Agilent , Santa Clara , USA ) and also checked by agarose gel electrophoresis . rRNAs was subsquently removed from the total mRNA following the instruction of the Ribo-Zero rRNATM Removal kit ( Epicentre , Madison , WI , USA ) . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE43408	Quantitative Different Analysis of antimicrobial peptide LL37 expressed in E.coli Top 10 under aerobic and anaerobic condition.	GSM1217969	pHerd30T-LL37 CK+ anaerobic	23856776	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE43408/GSE43408.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Total RNA was isolated with TRIzol (invitrogen, Carlsbad, CA) according to the manufacture[linebreak]s instruction. DNA was removed from RNA extracts with RNase-free DNase I (New England Biolabs, Beverly, MA, USA) by incubation at 37°C for 30 min. The quality of total RNA was assessed by using 2100 Bioanalyzer (Agilent, Santa Clara, USA) and also checked by agarose gel electrophoresis. rRNAs was subsquently removed from the total mRNA following the instruction of the Ribo-Zero rRNATM Removal kit (Epicentre, Madison, WI, USA). PGCGROWTHCONDITIONS	SRR958660	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		Total RNA was isolated with TRIzol ( invitrogen , Carlsbad , CA ) according to the manufacture [ linebreak ] s instruction . DNA was removed from RNA extracts with RNase-free DNase I ( New England Biolabs , Beverly , MA , USA ) by incubation at <Temp> 37 °C </Temp> for <Supp> 30 min </Supp> . The quality of total RNA was assessed by using 2100 Bioanalyzer ( Agilent , Santa Clara , USA ) and also checked by agarose gel electrophoresis . rRNAs was subsquently removed from the total mRNA following the instruction of the Ribo-Zero rRNATM Removal kit ( Epicentre , Madison , WI , USA ) . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE43408	Quantitative Different Analysis of antimicrobial peptide LL37 expressed in E.coli Top 10 under aerobic and anaerobic condition.	GSM1217970	pHerd30T-LL37 induced +anaerobic	23856776	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE43408/GSE43408.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Total RNA was isolated with TRIzol (invitrogen, Carlsbad, CA) according to the manufacture[linebreak]s instruction. DNA was removed from RNA extracts with RNase-free DNase I (New England Biolabs, Beverly, MA, USA) by incubation at 37°C for 30 min. The quality of total RNA was assessed by using 2100 Bioanalyzer (Agilent, Santa Clara, USA) and also checked by agarose gel electrophoresis. rRNAs was subsquently removed from the total mRNA following the instruction of the Ribo-Zero rRNATM Removal kit (Epicentre, Madison, WI, USA). PGCGROWTHCONDITIONS	SRR958661	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104381	pHDB3_1	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794827	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104386	pLCV1_3	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794832	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104387	MG1655-aMG_1	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794833	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104388	MG1655-aMG_2	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794834	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104389	MG1655-aMG_3	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794835	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104390	MG1655+aMG_1	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794836	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104391	MG1655+aMG_2	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794837	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104392	MG1655+aMG_3	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794838	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104393	SgrR_1	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794839	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104394	SgrR_2	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794840	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104395	SgrR_3	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794841	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104396	sgrS_T_1	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794842	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104397	sgrS_T_2	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794843	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104398	sgrS_T_3	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794844	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104399	sgrS_un_1	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794845	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104400	sgrS_un_2	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794846	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104401	sgrS_un_3	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794847	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104402	WT_1	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794848	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104403	WT_2	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794849	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104404	WT_3	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794850	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104405	wt_T_1	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794851	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104406	wt_T_2	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794852	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104407	wt_T_3	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794853	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104408	wt_un_1	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794854	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104410	wt_un_3	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794856	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104411	CV108_minus_aMG_1	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794857	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104412	CV108_minus_aMG_2	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794858	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104413	CV108_minus_aMG_3	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794859	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104414	CV108_plus_aMG_1	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794860	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104415	CV108_plus_aMG_2	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794861	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104416	CV108_plus_aMG_3	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794862	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104417	MG1655_minus_aMG_1	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794863	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104418	MG1655_minus_aMG_2	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794864	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104419	MG1655_minus_aMG_3	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794865	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104420	MG1655_plus_aMG_1	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794866	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104421	MG1655_plus_aMG_2	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794867	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104422	MG1655_plus_aMG_3	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794868	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104423	WT_minus_2DG_1	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794869	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104424	WT_minus_2DG_2	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794870	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104425	WT_minus_2DG_3	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794871	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104426	WT_plus_2DG_1	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794872	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104427	WT_plus_2DG_2	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794873	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104428	WT_plus_2DG_3	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794874	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174823	Mid log_wildtype_glc minimal media_aerobic rep1	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922260	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174824	Mid log_wildtype_glc minimal media_aerobic rep2	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922261	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174825	Mid log_wildtype_glc minimal media_aerobic rep3	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922262	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174826	Mid log_wildtype_glc minimal media + adenine_aerobic	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922263	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174827	Mid log_wildtype_glc minimal media + L-tryptophan_aerobic	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922264	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174828	Mid log_wildtype_glc minimal media_anaerobic rep1	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922265	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174829	Mid log_wildtype_glc minimal media_anaerobic rep2	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922266	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174830	Mid log_wildtype_glc minimal media_anaerobic rep3	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922267	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174831	Mid log_nac KO_glc minimal media_aerobic	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922268	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174832	Mid log_nac KO_glc minimal media + adenine_aerobic	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922269	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174833	Mid log_cra KO_glc minimal media_aerobic	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922270	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174834	Mid log_cra KO_glc minimal media + L-tryptophan_aerobic	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922271	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174835	Mid log_mntR KO_glc minimal media_aerobic	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922272	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174836	Mid log_mntR KO_glc minimal media_anaerobic	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922273	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT and Δfur were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . For iron treated cells , 0.1 mM of FeCl2 were treated from the beginning of culture , and for DPD treated cells , <Supp> 0.2 mM of DPD </Supp> were added at early-log phase and continued to culture for additional <Supp> 2h </Supp> . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE54900	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GSM1326347	WT with Fe 1 (RNA-seq)	25222563	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT and Δfur were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. PGCGROWTHCONDITIONS	SRR1168133	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT and Δfur were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . For iron treated cells , 0.1 mM of FeCl2 were treated from the beginning of culture , and for DPD treated cells , <Supp> 0.2 mM of DPD </Supp> were added at early-log phase and continued to culture for additional <Supp> 2h </Supp> . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE54900	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GSM1326348	WT with Fe 2 (RNA-seq)	25222563	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT and Δfur were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. PGCGROWTHCONDITIONS	SRR1168134	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT and Δfur were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . For iron treated cells , 0.1 mM of FeCl2 were treated from the beginning of culture , and for DPD treated cells , <Supp> 0.2 mM of DPD </Supp> were added at early-log phase and continued to culture for additional <Supp> 2h </Supp> . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE54900	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GSM1326349	WT with DPD 1 (RNA-seq)	25222563	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT and Δfur were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. PGCGROWTHCONDITIONS	SRR1168135	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT and Δfur were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . For iron treated cells , 0.1 mM of FeCl2 were treated from the beginning of culture , and for DPD treated cells , <Supp> 0.2 mM of DPD </Supp> were added at early-log phase and continued to culture for additional <Supp> 2h </Supp> . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE54900	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GSM1326350	WT with DPD 2 (RNA-seq)	25222563	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT and Δfur were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. PGCGROWTHCONDITIONS	SRR1168136	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT and Δfur were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . For iron treated cells , 0.1 mM of FeCl2 were treated from the beginning of culture , and for DPD treated cells , <Supp> 0.2 mM of DPD </Supp> were added at early-log phase and continued to culture for additional <Supp> 2h </Supp> . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE54900	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GSM1326351	Δfur with Fe 1 (RNA-seq)	25222563	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT and Δfur were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. PGCGROWTHCONDITIONS	SRR1168137	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT and Δfur were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . For iron treated cells , 0.1 mM of FeCl2 were treated from the beginning of culture , and for DPD treated cells , <Supp> 0.2 mM of DPD </Supp> were added at early-log phase and continued to culture for additional <Supp> 2h </Supp> . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE54900	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GSM1326352	Δfur with Fe 2 (RNA-seq)	25222563	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT and Δfur were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. PGCGROWTHCONDITIONS	SRR1168138	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT and Δfur were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . For iron treated cells , 0.1 mM of FeCl2 were treated from the beginning of culture , and for DPD treated cells , <Supp> 0.2 mM of DPD </Supp> were added at early-log phase and continued to culture for additional <Supp> 2h </Supp> . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE54900	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GSM1326353	Δfur with DPD 1 (RNA-seq)	25222563	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT and Δfur were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. PGCGROWTHCONDITIONS	SRR1168139	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT and Δfur were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . For iron treated cells , 0.1 mM of FeCl2 were treated from the beginning of culture , and for DPD treated cells , <Supp> 0.2 mM of DPD </Supp> were added at early-log phase and continued to culture for additional <Supp> 2h </Supp> . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE54900	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GSM1326354	Δfur with DPD 2 (RNA-seq)	25222563	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT and Δfur were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. PGCGROWTHCONDITIONS	SRR1168140	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Cultures were grown aerobically at <Temp> 37 °C </Temp> in 1 L volumes of M9 minimal medium , supplemented with MgSO4 ( 1 mM ) , CaCl2 ( 0.1 mM ) , and glucose ( 10 g/L ) in vigorously shaken ( 225 rpm ) Fernbach flasks . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360031	Wild-type (MG1655) T0 RNA rep 2	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS	SRR1211036	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Cultures were grown aerobically at <Temp> 37 °C </Temp> in 1 L volumes of M9 minimal medium , supplemented with MgSO4 ( 1 mM ) , CaCl2 ( 0.1 mM ) , and glucose ( 10 g/L ) in vigorously shaken ( 225 rpm ) Fernbach flasks . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360032	Wild-type (MG1655) T1 RNA rep 1	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS	SRR1211037	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Cultures were grown aerobically at <Temp> 37 °C </Temp> in 1 L volumes of M9 minimal medium , supplemented with MgSO4 ( 1 mM ) , CaCl2 ( 0.1 mM ) , and glucose ( 10 g/L ) in vigorously shaken ( 225 rpm ) Fernbach flasks . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360033	Wild-type (MG1655) T1 RNA rep 2	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS	SRR1211038	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Cultures were grown aerobically at <Temp> 37 °C </Temp> in 1 L volumes of M9 minimal medium , supplemented with MgSO4 ( 1 mM ) , CaCl2 ( 0.1 mM ) , and glucose ( 10 g/L ) in vigorously shaken ( 225 rpm ) Fernbach flasks . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360034	Wild-type (MG1655) T2 RNA rep 1	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS	SRR1211039	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Cultures were grown aerobically at <Temp> 37 °C </Temp> in 1 L volumes of M9 minimal medium , supplemented with MgSO4 ( 1 mM ) , CaCl2 ( 0.1 mM ) , and glucose ( 10 g/L ) in vigorously shaken ( 225 rpm ) Fernbach flasks . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360035	Wild-type (MG1655) T2 RNA rep 2	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS	SRR1211040	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Cultures were grown aerobically at <Temp> 37 °C </Temp> in 1 L volumes of M9 minimal medium , supplemented with MgSO4 ( 1 mM ) , CaCl2 ( 0.1 mM ) , and glucose ( 10 g/L ) in vigorously shaken ( 225 rpm ) Fernbach flasks . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360036	Mutant (EP61) T0 RNA rep 1	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS	SRR1211041	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Cultures were grown aerobically at <Temp> 37 °C </Temp> in 1 L volumes of M9 minimal medium , supplemented with MgSO4 ( 1 mM ) , CaCl2 ( 0.1 mM ) , and glucose ( 10 g/L ) in vigorously shaken ( 225 rpm ) Fernbach flasks . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360037	Mutant (EP61) T0 RNA rep 2	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS	SRR1211042	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Cultures were grown aerobically at <Temp> 37 °C </Temp> in 1 L volumes of M9 minimal medium , supplemented with MgSO4 ( 1 mM ) , CaCl2 ( 0.1 mM ) , and glucose ( 10 g/L ) in vigorously shaken ( 225 rpm ) Fernbach flasks . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360038	Mutant (EP61) T1 RNA rep 1	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS	SRR1211043	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Cultures were grown aerobically at <Temp> 37 °C </Temp> in 1 L volumes of M9 minimal medium , supplemented with MgSO4 ( 1 mM ) , CaCl2 ( 0.1 mM ) , and glucose ( 10 g/L ) in vigorously shaken ( 225 rpm ) Fernbach flasks . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360039	Mutant (EP61) T1 RNA rep 2	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS	SRR1211044	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Cultures were grown aerobically at <Temp> 37 °C </Temp> in 1 L volumes of M9 minimal medium , supplemented with MgSO4 ( 1 mM ) , CaCl2 ( 0.1 mM ) , and glucose ( 10 g/L ) in vigorously shaken ( 225 rpm ) Fernbach flasks . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360040	Mutant (EP61) T2 RNA rep 1	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS	SRR1211045	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Cultures were grown aerobically at <Temp> 37 °C </Temp> in 1 L volumes of M9 minimal medium , supplemented with MgSO4 ( 1 mM ) , CaCl2 ( 0.1 mM ) , and glucose ( 10 g/L ) in vigorously shaken ( 225 rpm ) Fernbach flasks . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360041	Mutant (EP61) T2 RNA rep 2	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS	SRR1211046	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Cultures were grown aerobically at <Temp> 37 °C </Temp> in 1 L volumes of M9 minimal medium , supplemented with MgSO4 ( 1 mM ) , CaCl2 ( 0.1 mM ) , and glucose ( 10 g/L ) in vigorously shaken ( 225 rpm ) Fernbach flasks . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360042	Wild-type (MG1655) T0 RP rep 1	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS	SRR1211047	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Cultures were grown aerobically at <Temp> 37 °C </Temp> in 1 L volumes of M9 minimal medium , supplemented with MgSO4 ( 1 mM ) , CaCl2 ( 0.1 mM ) , and glucose ( 10 g/L ) in vigorously shaken ( 225 rpm ) Fernbach flasks . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360043	Wild-type (MG1655) T0 RP rep 2	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS	SRR1211048	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Cultures were grown aerobically at <Temp> 37 °C </Temp> in 1 L volumes of M9 minimal medium , supplemented with MgSO4 ( 1 mM ) , CaCl2 ( 0.1 mM ) , and glucose ( 10 g/L ) in vigorously shaken ( 225 rpm ) Fernbach flasks . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360044	Wild-type (MG1655) T1 RP rep 1	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS	SRR1211049	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Cultures were grown aerobically at <Temp> 37 °C </Temp> in 1 L volumes of M9 minimal medium , supplemented with MgSO4 ( 1 mM ) , CaCl2 ( 0.1 mM ) , and glucose ( 10 g/L ) in vigorously shaken ( 225 rpm ) Fernbach flasks . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360045	Wild-type (MG1655) T1 RP rep 2	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS	SRR1211050	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Cultures were grown aerobically at <Temp> 37 °C </Temp> in 1 L volumes of M9 minimal medium , supplemented with MgSO4 ( 1 mM ) , CaCl2 ( 0.1 mM ) , and glucose ( 10 g/L ) in vigorously shaken ( 225 rpm ) Fernbach flasks . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360046	Wild-type (MG1655) T2 RP rep 1	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS	SRR1211051	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Cultures were grown aerobically at <Temp> 37 °C </Temp> in 1 L volumes of M9 minimal medium , supplemented with MgSO4 ( 1 mM ) , CaCl2 ( 0.1 mM ) , and glucose ( 10 g/L ) in vigorously shaken ( 225 rpm ) Fernbach flasks . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360047	Wild-type (MG1655) T2 RP rep 2	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS	SRR1211052	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Cultures were grown aerobically at <Temp> 37 °C </Temp> in 1 L volumes of M9 minimal medium , supplemented with MgSO4 ( 1 mM ) , CaCl2 ( 0.1 mM ) , and glucose ( 10 g/L ) in vigorously shaken ( 225 rpm ) Fernbach flasks . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360048	Mutant (EP61) T0 RP rep 1	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS	SRR1211053	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Cultures were grown aerobically at <Temp> 37 °C </Temp> in 1 L volumes of M9 minimal medium , supplemented with MgSO4 ( 1 mM ) , CaCl2 ( 0.1 mM ) , and glucose ( 10 g/L ) in vigorously shaken ( 225 rpm ) Fernbach flasks . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360049	Mutant (EP61) T0 RP rep 2	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS	SRR1211054	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Cultures were grown aerobically at <Temp> 37 °C </Temp> in 1 L volumes of M9 minimal medium , supplemented with MgSO4 ( 1 mM ) , CaCl2 ( 0.1 mM ) , and glucose ( 10 g/L ) in vigorously shaken ( 225 rpm ) Fernbach flasks . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360050	Mutant (EP61) T1 RP rep 1	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS	SRR1211055	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Cultures were grown aerobically at <Temp> 37 °C </Temp> in 1 L volumes of M9 minimal medium , supplemented with MgSO4 ( 1 mM ) , CaCl2 ( 0.1 mM ) , and glucose ( 10 g/L ) in vigorously shaken ( 225 rpm ) Fernbach flasks . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360051	Mutant (EP61) T1 RP rep 2	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS	SRR1211056	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Cultures were grown aerobically at <Temp> 37 °C </Temp> in 1 L volumes of M9 minimal medium , supplemented with MgSO4 ( 1 mM ) , CaCl2 ( 0.1 mM ) , and glucose ( 10 g/L ) in vigorously shaken ( 225 rpm ) Fernbach flasks . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360052	Mutant (EP61) T2 RP rep 1	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS	SRR1211057	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Cultures were grown aerobically at <Temp> 37 °C </Temp> in 1 L volumes of M9 minimal medium , supplemented with MgSO4 ( 1 mM ) , CaCl2 ( 0.1 mM ) , and glucose ( 10 g/L ) in vigorously shaken ( 225 rpm ) Fernbach flasks . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360053	Mutant (EP61) T2 RP rep 2	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cultures were grown aerobically at 37 °C in 1 L volumes of M9 minimal medium, supplemented with MgSO4 (1 mM), CaCl2 (0.1 mM), and glucose (10 g/L) in vigorously shaken (225 rpm) Fernbach flasks. PGCGROWTHCONDITIONS	SRR1211058	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All cultures grown up to 0.6 OD600 with shaking at 200 rpm . Samples 1,2,5 and 6 were grown at 30 °C whereas samples 3 and 4 were grown at <Temp> 37 °C </Temp> . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE58285	Direct entry by RNase E is a major pathway for the degradation and processing of RNA in Escherichia coli	GSM1405877	rne wild-type	25237058	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE58285/GSE58285.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All cultures grown up to 0.6 OD600 with shaking at 200 rpm. Samples 1,2,5 and 6 were grown at 30°C whereas samples 3 and 4 were grown at 37°C. PGCGROWTHCONDITIONS	SRR1363864	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All cultures grown up to 0.6 OD600 with shaking at 200 rpm . Samples 1,2,5 and 6 were grown at 30 °C whereas samples 3 and 4 were grown at <Temp> 37 °C </Temp> . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE58285	Direct entry by RNase E is a major pathway for the degradation and processing of RNA in Escherichia coli	GSM1405878	rne-3071 ts	25237058	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE58285/GSE58285.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All cultures grown up to 0.6 OD600 with shaking at 200 rpm. Samples 1,2,5 and 6 were grown at 30°C whereas samples 3 and 4 were grown at 37°C. PGCGROWTHCONDITIONS	SRR1363865	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All cultures grown up to 0.6 OD600 with shaking at 200 rpm . Samples 1,2,5 and 6 were grown at 30 °C whereas samples 3 and 4 were grown at <Temp> 37 °C </Temp> . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE58285	Direct entry by RNase E is a major pathway for the degradation and processing of RNA in Escherichia coli	GSM1405879	T170V 0 min	25237058	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE58285/GSE58285.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All cultures grown up to 0.6 OD600 with shaking at 200 rpm. Samples 1,2,5 and 6 were grown at 30°C whereas samples 3 and 4 were grown at 37°C. PGCGROWTHCONDITIONS	SRR1363866	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All cultures grown up to 0.6 OD600 with shaking at 200 rpm . Samples 1,2,5 and 6 were grown at 30 °C whereas samples 3 and 4 were grown at <Temp> 37 °C </Temp> . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE58285	Direct entry by RNase E is a major pathway for the degradation and processing of RNA in Escherichia coli	GSM1405880	T170V 10 min	25237058	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE58285/GSE58285.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All cultures grown up to 0.6 OD600 with shaking at 200 rpm. Samples 1,2,5 and 6 were grown at 30°C whereas samples 3 and 4 were grown at 37°C. PGCGROWTHCONDITIONS	SRR1363867	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All cultures grown up to 0.6 OD600 with shaking at 200 rpm . Samples 1,2,5 and 6 were grown at 30 °C whereas samples 3 and 4 were grown at <Temp> 37 °C </Temp> . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE58285	Direct entry by RNase E is a major pathway for the degradation and processing of RNA in Escherichia coli	GSM1405882	rng mutant	25237058	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE58285/GSE58285.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All cultures grown up to 0.6 OD600 with shaking at 200 rpm. Samples 1,2,5 and 6 were grown at 30°C whereas samples 3 and 4 were grown at 37°C. PGCGROWTHCONDITIONS	SRR1363869	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Gtype> Wild type </Gtype> E. coli K-12 ( strain BW38038 ) and BW39452 ( ΔrpoS ) cultures were grown on <Med> MOPS glucose minimal medium </Med> with <Supp> 0.2 % glucose </Supp> as sole carbon source at <Temp> 37 °C </Temp> , pH was initially 7.4 , and the agitation speed was 500 rpm . Culture samples were harvested during logarithmic growth and following entry into stationary phase for the WT and rpoS mutant . OD600 measurements were made on a Beckman Coulter DU 800 spectrophotometer . Samples were harvested directly into ice-cold RNAlater at a 1:1 dilution to protect RNA from degradation and cells then were pelleted by centrifugation at 8000rpm for 10 minutes . Cell pellets were stored at -80 °C in an equal volume of RNAlater prior to RNA extraction . 	GPL18814	GPL18814: Illumina HiSeq 2000 (Escherichia coli BW38028)	GSE58556	RNA sequencing based analysis of the bacterial transcriptome	GSM1413874	WT_glucose_log	25483350	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE58556/GSE58556.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Wild type E. coli K-12 (strain BW38038) and BW39452(ΔrpoS) cultures were grown on MOPS glucose minimal medium with 0.2% glucose as sole carbon source at 37°C, pH was initially 7.4,  and the agitation speed was 500 rpm. Culture samples were harvested during logarithmic growth and  following entry into stationary phase for the WT and rpoS mutant. OD600 measurements were made on a Beckman Coulter DU 800 spectrophotometer. Samples were harvested directly into ice-cold RNAlater at a 1:1 dilution to protect RNA from degradation and cells then were pelleted by centrifugation at 8000rpm for 10 minutes. Cell pellets were stored at -80°C in an equal volume of RNAlater prior to RNA extraction. PGCGROWTHCONDITIONS	SRR1411272	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		Total RNA was extracted using TRIzol reagent ( Invitrogen ) and the sample was enriched in mRNA , depleting small RNAs with GeneJET ™ RNA Purification Kit ( Fermentas ) and ribosomal RNA with two cycle of MICROBExpress ™ Bacterial mRNA Enrichment Kit ( Ambion ) . To probe the RNA structure two µg of enriched mRNA were resuspended in 45 µl of DEPC water and denatured for 3 min at 95 °C , refolded at <Temp> 37 °C </Temp> , after addition of 10x RNA-structure buffer with pH 7.0 ( 100 mM Tris , 1 M KCl , 100 mM MgCl2 ) and digested for 1 min at <Temp> 37 °C </Temp> with either 0.05 U RNase V1 ( Life Technologies ) or a combination of 2 µg RNase A and 5 U RNase T1 ( Thermo Scientific ) . The reaction was stopped by extracting the RNA with phenol-chlorophorm . The RNase A/T1-digested sample was phosphorylated with T4 PNK ( NEB ) and purified with RNA Clean & Concentrator ™ kit ( Zymo Research ) . Both the V1 and A/T1 digested samples were randomly fragmented in buffer with pH 9.2 ( 100 mM Na2CO3 , 2 mM EDTA ) for 12 min at 95 °C . 	GPL14548-GPL18945	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	GSE63817	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GSM1558078	LB mRNA	26495981	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE63817/GSE63817.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Total RNA was extracted using TRIzol reagent (Invitrogen) and the sample was enriched in mRNA, depleting small RNAs with GeneJET™ RNA Purification Kit (Fermentas) and ribosomal RNA with two cycle of MICROBExpress™Bacterial mRNA Enrichment Kit (Ambion). To probe the RNA structure two µg of enriched mRNA were resuspended in 45 µl of DEPC water and denatured for 3 min at 95°C,refolded at 37 °C, after addition of 10x RNA-structure buffer with pH 7.0 (100 mM Tris, 1 M KCl, 100 mM MgCl2) and digested for 1 min at 37 °C with either 0.05 U RNase V1 (Life Technologies) or a combination of 2 µg RNase A and 5 U RNase T1 (Thermo Scientific). The reaction was stopped by extracting the RNA with phenol-chlorophorm. The RNase A/T1-digested sample was phosphorylated with T4 PNK (NEB) and purified with RNA Clean & Concentrator™ kit (Zymo Research). Both the V1 and A/T1 digested samples were randomly fragmented in buffer with pH 9.2 (100 mM Na2CO3, 2 mM EDTA) for 12 min at 95°C. PGCGROWTHCONDITIONS	SRR1692165	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli MC4100 strain was cultured at <Temp> 37 °C </Temp> to <Phase> mid-log phase </Phase> ( OD600 ~ 0.4 ) in <Med> LB media </Med> 	GPL14548-GPL18945	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	GSE63817	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GSM1558078	LB mRNA	26495981	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE63817/GSE63817.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media PGCGROWTHCONDITIONS	SRR1692165	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		Total RNA was extracted using TRIzol reagent ( Invitrogen ) and the sample was enriched in mRNA , depleting small RNAs with GeneJET ™ RNA Purification Kit ( Fermentas ) and ribosomal RNA with two cycle of MICROBExpress ™ Bacterial mRNA Enrichment Kit ( Ambion ) . To probe the RNA structure two µg of enriched mRNA were resuspended in 45 µl of DEPC water and denatured for 3 min at 95 °C , refolded at <Temp> 37 °C </Temp> , after addition of 10x RNA-structure buffer with pH 7.0 ( 100 mM Tris , 1 M KCl , 100 mM MgCl2 ) and digested for 1 min at <Temp> 37 °C </Temp> with either 0.05 U RNase V1 ( Life Technologies ) or a combination of 2 µg RNase A and 5 U RNase T1 ( Thermo Scientific ) . The reaction was stopped by extracting the RNA with phenol-chlorophorm . The RNase A/T1-digested sample was phosphorylated with T4 PNK ( NEB ) and purified with RNA Clean & Concentrator ™ kit ( Zymo Research ) . Both the V1 and A/T1 digested samples were randomly fragmented in buffer with pH 9.2 ( 100 mM Na2CO3 , 2 mM EDTA ) for 12 min at 95 °C . 	GPL14548-GPL18945	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	GSE63817	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GSM1558079	LB RPF	26495981	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE63817/GSE63817.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Total RNA was extracted using TRIzol reagent (Invitrogen) and the sample was enriched in mRNA, depleting small RNAs with GeneJET™ RNA Purification Kit (Fermentas) and ribosomal RNA with two cycle of MICROBExpress™Bacterial mRNA Enrichment Kit (Ambion). To probe the RNA structure two µg of enriched mRNA were resuspended in 45 µl of DEPC water and denatured for 3 min at 95°C,refolded at 37 °C, after addition of 10x RNA-structure buffer with pH 7.0 (100 mM Tris, 1 M KCl, 100 mM MgCl2) and digested for 1 min at 37 °C with either 0.05 U RNase V1 (Life Technologies) or a combination of 2 µg RNase A and 5 U RNase T1 (Thermo Scientific). The reaction was stopped by extracting the RNA with phenol-chlorophorm. The RNase A/T1-digested sample was phosphorylated with T4 PNK (NEB) and purified with RNA Clean & Concentrator™ kit (Zymo Research). Both the V1 and A/T1 digested samples were randomly fragmented in buffer with pH 9.2 (100 mM Na2CO3, 2 mM EDTA) for 12 min at 95°C. PGCGROWTHCONDITIONS	SRR1692166	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli MC4100 strain was cultured at <Temp> 37 °C </Temp> to <Phase> mid-log phase </Phase> ( OD600 ~ 0.4 ) in <Med> LB media </Med> 	GPL14548-GPL18945	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	GSE63817	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GSM1558079	LB RPF	26495981	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE63817/GSE63817.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media PGCGROWTHCONDITIONS	SRR1692166	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		Total RNA was extracted using TRIzol reagent ( Invitrogen ) and the sample was enriched in mRNA , depleting small RNAs with GeneJET ™ RNA Purification Kit ( Fermentas ) and ribosomal RNA with two cycle of MICROBExpress ™ Bacterial mRNA Enrichment Kit ( Ambion ) . To probe the RNA structure two µg of enriched mRNA were resuspended in 45 µl of DEPC water and denatured for 3 min at 95 °C , refolded at <Temp> 37 °C </Temp> , after addition of 10x RNA-structure buffer with pH 7.0 ( 100 mM Tris , 1 M KCl , 100 mM MgCl2 ) and digested for 1 min at <Temp> 37 °C </Temp> with either 0.05 U RNase V1 ( Life Technologies ) or a combination of 2 µg RNase A and 5 U RNase T1 ( Thermo Scientific ) . The reaction was stopped by extracting the RNA with phenol-chlorophorm . The RNase A/T1-digested sample was phosphorylated with T4 PNK ( NEB ) and purified with RNA Clean & Concentrator ™ kit ( Zymo Research ) . Both the V1 and A/T1 digested samples were randomly fragmented in buffer with pH 9.2 ( 100 mM Na2CO3 , 2 mM EDTA ) for 12 min at 95 °C . 	GPL14548-GPL18945	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	GSE63817	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GSM1558080	LB mRNA technical replicate	26495981	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE63817/GSE63817.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Total RNA was extracted using TRIzol reagent (Invitrogen) and the sample was enriched in mRNA, depleting small RNAs with GeneJET™ RNA Purification Kit (Fermentas) and ribosomal RNA with two cycle of MICROBExpress™Bacterial mRNA Enrichment Kit (Ambion). To probe the RNA structure two µg of enriched mRNA were resuspended in 45 µl of DEPC water and denatured for 3 min at 95°C,refolded at 37 °C, after addition of 10x RNA-structure buffer with pH 7.0 (100 mM Tris, 1 M KCl, 100 mM MgCl2) and digested for 1 min at 37 °C with either 0.05 U RNase V1 (Life Technologies) or a combination of 2 µg RNase A and 5 U RNase T1 (Thermo Scientific). The reaction was stopped by extracting the RNA with phenol-chlorophorm. The RNase A/T1-digested sample was phosphorylated with T4 PNK (NEB) and purified with RNA Clean & Concentrator™ kit (Zymo Research). Both the V1 and A/T1 digested samples were randomly fragmented in buffer with pH 9.2 (100 mM Na2CO3, 2 mM EDTA) for 12 min at 95°C. PGCGROWTHCONDITIONS	SRR1692167	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli MC4100 strain was cultured at <Temp> 37 °C </Temp> to <Phase> mid-log phase </Phase> ( OD600 ~ 0.4 ) in <Med> LB media </Med> 	GPL14548-GPL18945	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	GSE63817	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GSM1558080	LB mRNA technical replicate	26495981	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE63817/GSE63817.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media PGCGROWTHCONDITIONS	SRR1692167	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		Total RNA was extracted using TRIzol reagent ( Invitrogen ) and the sample was enriched in mRNA , depleting small RNAs with GeneJET ™ RNA Purification Kit ( Fermentas ) and ribosomal RNA with two cycle of MICROBExpress ™ Bacterial mRNA Enrichment Kit ( Ambion ) . To probe the RNA structure two µg of enriched mRNA were resuspended in 45 µl of DEPC water and denatured for 3 min at 95 °C , refolded at <Temp> 37 °C </Temp> , after addition of 10x RNA-structure buffer with pH 7.0 ( 100 mM Tris , 1 M KCl , 100 mM MgCl2 ) and digested for 1 min at <Temp> 37 °C </Temp> with either 0.05 U RNase V1 ( Life Technologies ) or a combination of 2 µg RNase A and 5 U RNase T1 ( Thermo Scientific ) . The reaction was stopped by extracting the RNA with phenol-chlorophorm . The RNase A/T1-digested sample was phosphorylated with T4 PNK ( NEB ) and purified with RNA Clean & Concentrator ™ kit ( Zymo Research ) . Both the V1 and A/T1 digested samples were randomly fragmented in buffer with pH 9.2 ( 100 mM Na2CO3 , 2 mM EDTA ) for 12 min at 95 °C . 	GPL14548-GPL18945	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	GSE63817	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GSM1558081	LB RPF biological replicate	26495981	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE63817/GSE63817.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Total RNA was extracted using TRIzol reagent (Invitrogen) and the sample was enriched in mRNA, depleting small RNAs with GeneJET™ RNA Purification Kit (Fermentas) and ribosomal RNA with two cycle of MICROBExpress™Bacterial mRNA Enrichment Kit (Ambion). To probe the RNA structure two µg of enriched mRNA were resuspended in 45 µl of DEPC water and denatured for 3 min at 95°C,refolded at 37 °C, after addition of 10x RNA-structure buffer with pH 7.0 (100 mM Tris, 1 M KCl, 100 mM MgCl2) and digested for 1 min at 37 °C with either 0.05 U RNase V1 (Life Technologies) or a combination of 2 µg RNase A and 5 U RNase T1 (Thermo Scientific). The reaction was stopped by extracting the RNA with phenol-chlorophorm. The RNase A/T1-digested sample was phosphorylated with T4 PNK (NEB) and purified with RNA Clean & Concentrator™ kit (Zymo Research). Both the V1 and A/T1 digested samples were randomly fragmented in buffer with pH 9.2 (100 mM Na2CO3, 2 mM EDTA) for 12 min at 95°C. PGCGROWTHCONDITIONS	SRR1692168	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli MC4100 strain was cultured at <Temp> 37 °C </Temp> to <Phase> mid-log phase </Phase> ( OD600 ~ 0.4 ) in <Med> LB media </Med> 	GPL14548-GPL18945	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	GSE63817	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GSM1558081	LB RPF biological replicate	26495981	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE63817/GSE63817.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media PGCGROWTHCONDITIONS	SRR1692168	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		Total RNA was extracted using TRIzol reagent ( Invitrogen ) and the sample was enriched in mRNA , depleting small RNAs with GeneJET ™ RNA Purification Kit ( Fermentas ) and ribosomal RNA with two cycle of MICROBExpress ™ Bacterial mRNA Enrichment Kit ( Ambion ) . To probe the RNA structure two µg of enriched mRNA were resuspended in 45 µl of DEPC water and denatured for 3 min at 95 °C , refolded at <Temp> 37 °C </Temp> , after addition of 10x RNA-structure buffer with pH 7.0 ( 100 mM Tris , 1 M KCl , 100 mM MgCl2 ) and digested for 1 min at <Temp> 37 °C </Temp> with either 0.05 U RNase V1 ( Life Technologies ) or a combination of 2 µg RNase A and 5 U RNase T1 ( Thermo Scientific ) . The reaction was stopped by extracting the RNA with phenol-chlorophorm . The RNase A/T1-digested sample was phosphorylated with T4 PNK ( NEB ) and purified with RNA Clean & Concentrator ™ kit ( Zymo Research ) . Both the V1 and A/T1 digested samples were randomly fragmented in buffer with pH 9.2 ( 100 mM Na2CO3 , 2 mM EDTA ) for 12 min at 95 °C . 	GPL14548-GPL18945	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	GSE63817	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GSM1558082	LB mRNA biological replicate	26495981	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE63817/GSE63817.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Total RNA was extracted using TRIzol reagent (Invitrogen) and the sample was enriched in mRNA, depleting small RNAs with GeneJET™ RNA Purification Kit (Fermentas) and ribosomal RNA with two cycle of MICROBExpress™Bacterial mRNA Enrichment Kit (Ambion). To probe the RNA structure two µg of enriched mRNA were resuspended in 45 µl of DEPC water and denatured for 3 min at 95°C,refolded at 37 °C, after addition of 10x RNA-structure buffer with pH 7.0 (100 mM Tris, 1 M KCl, 100 mM MgCl2) and digested for 1 min at 37 °C with either 0.05 U RNase V1 (Life Technologies) or a combination of 2 µg RNase A and 5 U RNase T1 (Thermo Scientific). The reaction was stopped by extracting the RNA with phenol-chlorophorm. The RNase A/T1-digested sample was phosphorylated with T4 PNK (NEB) and purified with RNA Clean & Concentrator™ kit (Zymo Research). Both the V1 and A/T1 digested samples were randomly fragmented in buffer with pH 9.2 (100 mM Na2CO3, 2 mM EDTA) for 12 min at 95°C. PGCGROWTHCONDITIONS	SRR1692169	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli MC4100 strain was cultured at <Temp> 37 °C </Temp> to <Phase> mid-log phase </Phase> ( OD600 ~ 0.4 ) in <Med> LB media </Med> 	GPL14548-GPL18945	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	GSE63817	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GSM1558082	LB mRNA biological replicate	26495981	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE63817/GSE63817.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media PGCGROWTHCONDITIONS	SRR1692169	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		Total RNA was extracted using TRIzol reagent ( Invitrogen ) and the sample was enriched in mRNA , depleting small RNAs with GeneJET ™ RNA Purification Kit ( Fermentas ) and ribosomal RNA with two cycle of MICROBExpress ™ Bacterial mRNA Enrichment Kit ( Ambion ) . To probe the RNA structure two µg of enriched mRNA were resuspended in 45 µl of DEPC water and denatured for 3 min at 95 °C , refolded at <Temp> 37 °C </Temp> , after addition of 10x RNA-structure buffer with pH 7.0 ( 100 mM Tris , 1 M KCl , 100 mM MgCl2 ) and digested for 1 min at <Temp> 37 °C </Temp> with either 0.05 U RNase V1 ( Life Technologies ) or a combination of 2 µg RNase A and 5 U RNase T1 ( Thermo Scientific ) . The reaction was stopped by extracting the RNA with phenol-chlorophorm . The RNase A/T1-digested sample was phosphorylated with T4 PNK ( NEB ) and purified with RNA Clean & Concentrator ™ kit ( Zymo Research ) . Both the V1 and A/T1 digested samples were randomly fragmented in buffer with pH 9.2 ( 100 mM Na2CO3 , 2 mM EDTA ) for 12 min at 95 °C . 	GPL14548-GPL18945	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	GSE63817	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GSM1558086	AT1 biological replicate	26495981	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE63817/GSE63817.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Total RNA was extracted using TRIzol reagent (Invitrogen) and the sample was enriched in mRNA, depleting small RNAs with GeneJET™ RNA Purification Kit (Fermentas) and ribosomal RNA with two cycle of MICROBExpress™Bacterial mRNA Enrichment Kit (Ambion). To probe the RNA structure two µg of enriched mRNA were resuspended in 45 µl of DEPC water and denatured for 3 min at 95°C,refolded at 37 °C, after addition of 10x RNA-structure buffer with pH 7.0 (100 mM Tris, 1 M KCl, 100 mM MgCl2) and digested for 1 min at 37 °C with either 0.05 U RNase V1 (Life Technologies) or a combination of 2 µg RNase A and 5 U RNase T1 (Thermo Scientific). The reaction was stopped by extracting the RNA with phenol-chlorophorm. The RNase A/T1-digested sample was phosphorylated with T4 PNK (NEB) and purified with RNA Clean & Concentrator™ kit (Zymo Research). Both the V1 and A/T1 digested samples were randomly fragmented in buffer with pH 9.2 (100 mM Na2CO3, 2 mM EDTA) for 12 min at 95°C. PGCGROWTHCONDITIONS	SRR1692173	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli MC4100 strain was cultured at <Temp> 37 °C </Temp> to <Phase> mid-log phase </Phase> ( OD600 ~ 0.4 ) in <Med> LB media </Med> 	GPL14548-GPL18945	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	GSE63817	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GSM1558086	AT1 biological replicate	26495981	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE63817/GSE63817.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media PGCGROWTHCONDITIONS	SRR1692173	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Med> LB medium , </Med> <Temp> 37 °C </Temp> , airated , constant pH 7.5 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE65244	Temporal gene expression in Escherichia coli	GSM1590712	Wt – 60 min		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65244/GSE65244.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS	SRR1771414	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Med> LB medium , </Med> <Temp> 37 °C </Temp> , airated , constant pH 7.5 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE65244	Temporal gene expression in Escherichia coli	GSM1590717	Fis – 60 min		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65244/GSE65244.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS	SRR1771419	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Med> LB medium , </Med> <Temp> 37 °C </Temp> , airated , constant pH 7.5 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE65244	Temporal gene expression in Escherichia coli	GSM1590718	Fis – 120 min		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65244/GSE65244.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS	SRR1771420	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Med> LB medium , </Med> <Temp> 37 °C </Temp> , airated , constant pH 7.5 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE65244	Temporal gene expression in Escherichia coli	GSM1590719	Fis – 180 min		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65244/GSE65244.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS	SRR1771421	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Med> LB medium , </Med> <Temp> 37 °C </Temp> , airated , constant pH 7.5 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE65244	Temporal gene expression in Escherichia coli	GSM1590720	Fis – 420 min		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65244/GSE65244.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS	SRR1771422	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Med> LB medium , </Med> <Temp> 37 °C </Temp> , airated , constant pH 7.5 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE65244	Temporal gene expression in Escherichia coli	GSM1590721	Hns – 60 min		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65244/GSE65244.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS	SRR1771423	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Med> LB medium , </Med> <Temp> 37 °C </Temp> , airated , constant pH 7.5 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE65244	Temporal gene expression in Escherichia coli	GSM1590722	Hns – 120 min		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65244/GSE65244.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS	SRR1771424	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT , and Δcra were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> , fructose and acetate . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602347	WT glucose 1	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, and Δcra were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS	SRR1787590	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT , and Δcra were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> , fructose and acetate . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602348	WT glucose 2	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, and Δcra were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS	SRR1787591	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT , and Δcra were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> , fructose and acetate . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602349	WT fructose 1	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, and Δcra were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS	SRR1787592	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT , and Δcra were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> , fructose and acetate . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602350	WT fructose 2	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, and Δcra were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS	SRR1787593	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT , and Δcra were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> , fructose and acetate . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602351	WT acetate 1	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, and Δcra were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS	SRR1787594	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT , and Δcra were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> , fructose and acetate . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602352	WT acetate 2	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, and Δcra were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS	SRR1787595	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT , and Δcra were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> , fructose and acetate . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602353	Δcra glucose 1	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, and Δcra were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS	SRR1787596	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT , and Δcra were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> , fructose and acetate . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602354	Δcra glucose 2	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, and Δcra were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS	SRR1787597	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT , and Δcra were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> , fructose and acetate . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602355	Δcra fructose 1	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, and Δcra were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS	SRR1787598	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT , and Δcra were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> , fructose and acetate . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602356	Δcra fructose 2	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, and Δcra were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS	SRR1787599	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT , and Δcra were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> , fructose and acetate . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602357	Δcra acetate 1	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, and Δcra were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS	SRR1787600	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT , and Δcra were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> , fructose and acetate . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602358	Δcra acetate 2	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, and Δcra were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS	SRR1787601	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT , ΔoxyR , ΔsoxR , and ΔsoxS were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65711	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GSM1603386	WT PQ 1	26279566	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, ΔoxyR, ΔsoxR, and ΔsoxS were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation. PGCGROWTHCONDITIONS	SRR1796598	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT , ΔoxyR , ΔsoxR , and ΔsoxS were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65711	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GSM1603387	WT PQ 2	26279566	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, ΔoxyR, ΔsoxR, and ΔsoxS were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation. PGCGROWTHCONDITIONS	SRR1796599	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT , ΔoxyR , ΔsoxR , and ΔsoxS were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65711	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GSM1603388	ΔoxyR PQ 1	26279566	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, ΔoxyR, ΔsoxR, and ΔsoxS were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation. PGCGROWTHCONDITIONS	SRR1796600	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT , ΔoxyR , ΔsoxR , and ΔsoxS were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65711	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GSM1603389	ΔoxyR PQ 2	26279566	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, ΔoxyR, ΔsoxR, and ΔsoxS were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation. PGCGROWTHCONDITIONS	SRR1796601	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT , ΔoxyR , ΔsoxR , and ΔsoxS were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65711	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GSM1603391	ΔsoxR PQ 2	26279566	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, ΔoxyR, ΔsoxR, and ΔsoxS were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation. PGCGROWTHCONDITIONS	SRR1796603	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT , ΔoxyR , ΔsoxR , and ΔsoxS were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65711	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GSM1603392	ΔsoxS PQ 1	26279566	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, ΔoxyR, ΔsoxR, and ΔsoxS were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation. PGCGROWTHCONDITIONS	SRR1796604	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT , ΔoxyR , ΔsoxR , and ΔsoxS were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65711	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GSM1603393	ΔsoxS PQ 2	26279566	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, ΔoxyR, ΔsoxR, and ΔsoxS were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation. PGCGROWTHCONDITIONS	SRR1796605	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT , gadE , gadW and gadX mutant cells were grown to <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) <Air> aerobically </Air> ( <Agit> 250 rpm </Agit> ) at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> at <pH> pH 5.5 </pH> . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623160	WT pH5.5 1	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5. PGCGROWTHCONDITIONS	SRR1824557	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT , gadE , gadW and gadX mutant cells were grown to <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) <Air> aerobically </Air> ( <Agit> 250 rpm </Agit> ) at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> at <pH> pH 5.5 </pH> . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623161	WT pH5.5 2	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5. PGCGROWTHCONDITIONS	SRR1824558	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT , gadE , gadW and gadX mutant cells were grown to <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) <Air> aerobically </Air> ( <Agit> 250 rpm </Agit> ) at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> at <pH> pH 5.5 </pH> . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623162	ΔgadE pH5.5 1	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5. PGCGROWTHCONDITIONS	SRR1824559	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT , gadE , gadW and gadX mutant cells were grown to <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) <Air> aerobically </Air> ( <Agit> 250 rpm </Agit> ) at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> at <pH> pH 5.5 </pH> . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623163	ΔgadE pH5.5 2	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5. PGCGROWTHCONDITIONS	SRR1824560	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT , gadE , gadW and gadX mutant cells were grown to <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) <Air> aerobically </Air> ( <Agit> 250 rpm </Agit> ) at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> at <pH> pH 5.5 </pH> . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623164	ΔgadW pH5.5 1	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5. PGCGROWTHCONDITIONS	SRR1824561	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT , gadE , gadW and gadX mutant cells were grown to <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) <Air> aerobically </Air> ( <Agit> 250 rpm </Agit> ) at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> at <pH> pH 5.5 </pH> . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623165	ΔgadW pH5.5 2	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5. PGCGROWTHCONDITIONS	SRR1824562	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT , gadE , gadW and gadX mutant cells were grown to <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) <Air> aerobically </Air> ( <Agit> 250 rpm </Agit> ) at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> at <pH> pH 5.5 </pH> . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623166	ΔgadX pH5.5 1	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5. PGCGROWTHCONDITIONS	SRR1824563	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT , gadE , gadW and gadX mutant cells were grown to <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) <Air> aerobically </Air> ( <Agit> 250 rpm </Agit> ) at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> at <pH> pH 5.5 </pH> . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623167	ΔgadX pH5.5 2	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5. PGCGROWTHCONDITIONS	SRR1824564	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900470	Parent LB rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547467	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900472	cysG KO LB rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547469	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900474	cysH KO LB rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547471	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900475	cysH KO LB rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547472	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900476	dcd KO LB rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547473	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900477	dcd KO LB rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547474	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900478	fadr KO LB rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547475	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900479	fadr KO LB rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547476	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900480	ppk KO LB rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547477	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900482	wzc KO LB rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547479	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900483	wzc KO LB rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547480	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900485	yghD KO LB rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547482	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900486	fepA KO LB rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547483	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900488	lacA KO LB rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547485	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900490	Parent M9 rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547487	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900491	Parent M9 rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547488	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900492	dcd KO M9 rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547489	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900493	dcd KO M9 rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547490	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900494	fadr KO M9 rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547491	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900495	fadr KO M9 rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547492	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900496	ppk KO M9 rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547493	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900497	ppk KO M9 rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547494	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900498	wzc KO M9 rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547495	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900499	wzc KO M9 rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547496	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900500	yghD KO M9 rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547497	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900501	yghD KO M9 rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547498	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900502	fepA KO M9 rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547499	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900507	WT rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547504	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900509	mgtA KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547506	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900510	mgtA KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547507	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900513	gabT KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547510	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900514	gabT KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547511	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900515	sdhC KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547512	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900516	sdhC KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547513	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900518	putP KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547515	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900520	putP KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547517	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900521	rfbA KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547518	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900522	rfbA KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547519	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900524	entF KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547521	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900525	entF KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547522	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900526	entF KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547523	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900527	kefB KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547524	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900529	kefB KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547526	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900530	cysA KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547527	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900531	cysA KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547528	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900532	cysA KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547529	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900534	galE KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547531	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900536	mhpD KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547533	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900537	mhpD KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547534	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900538	mhpD KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547535	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900539	fliY KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547536	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900540	fliY KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547537	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900541	fliY KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547538	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900542	lplA KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547539	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900543	lplA KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547540	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900544	lplA KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547541	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900545	khc KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547542	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900546	khc KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547543	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900547	khc KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547544	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900548	ugpC KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547545	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900549	ugpC KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547546	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900550	ugpC KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547547	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900551	trpD KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547548	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900552	trpD KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547549	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900553	trpD KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547550	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900554	aspC KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547551	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900555	aspC KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547552	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900556	aspC KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547553	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All cultures were based on MOPS media with <Supp> 0.2 % glucose </Supp> ( Teknova ) , with full supplement ( Neidhardt et al. , 1974 ) minus methionine . An overnight liquid culture was diluted 400-fold into 200 ml <Med> fresh media </Med> . The culture was kept in a 1 liter flask at <Temp> 37 °C </Temp> with aeration until OD420 reached 0.4 . 	GPL14548-GPL21433	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE77617	Operon mRNAs are organized into ORF-centric structures that predict translation efficiency	GSM2462936	mRNA-seq 37°C in WT with control plasmid	28139975	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE77617/GSE77617.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All cultures were based on MOPS media with 0.2% glucose (Teknova), with full supplement (Neidhardt et al., 1974) minus methionine. An overnight liquid culture was diluted 400-fold into 200 ml fresh media. The culture was kept in a 1 liter flask at 37°C with aeration until OD420 reached 0.4. PGCGROWTHCONDITIONS	SRR5186139	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		For in vivo DMS modification , 15 mL of exponentially growing E. coli were incubated with 750 µL DMS for 2 min at <Temp> 37 °C </Temp> . For kasugamycin ( ksg ) experiments , ksg was added to a final concentration of 10 mg/mL to ΔgcvB cells for 2 min at <Temp> 37 °C </Temp> prior to DMS modification . DMS was quenched by adding 30 mL 0 °C stop solution ( 30 % β-mercaptoethanol , 25 % isoamyl alcohol ) . For in vitro DMS modifications , mRNA was denatured at 95 °C for 2 min , cooled on ice and refolded in 90 µL RNA folding buffer ( 10 mM Tris pH 8.0 , 100 mM NaCl , 6 mM MgCl2 ) at <Temp> 37 °C </Temp> for 30 min then incubated in either .2 % DMS for 1 min ( 95 °C ) or 4 % DMS for 5 min ( <Temp> 37 °C </Temp> ) . 	GPL14548-GPL21433	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE77617	Operon mRNAs are organized into ORF-centric structures that predict translation efficiency	GSM2462936	mRNA-seq 37°C in WT with control plasmid	28139975	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE77617/GSE77617.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For in vivo DMS modification, 15 mL of exponentially growing E. coli were incubated with 750 µL DMS for 2 min at 37°C. For kasugamycin (ksg) experiments, ksg was added to a final concentration of 10 mg/mL to ΔgcvB cells for 2 min at 37°C prior to DMS modification. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol). For in vitro DMS modifications, mRNA was denatured at 95 °C for 2 min, cooled on ice and refolded in 90 µL RNA folding buffer (10 mM Tris pH 8.0, 100 mM NaCl, 6 mM MgCl2) at 37°C for 30 min then incubated in either .2% DMS for 1 min (95°C) or 4% DMS for 5 min (37°C). PGCGROWTHCONDITIONS	SRR5186139	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All cultures were based on MOPS media with <Supp> 0.2 % glucose </Supp> ( Teknova ) , with full supplement ( Neidhardt et al. , 1974 ) minus methionine . An overnight liquid culture was diluted 400-fold into 200 ml <Med> fresh media </Med> . The culture was kept in a 1 liter flask at <Temp> 37 °C </Temp> with aeration until OD420 reached 0.4 . 	GPL14548-GPL21433	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE77617	Operon mRNAs are organized into ORF-centric structures that predict translation efficiency	GSM2462937	mRNA-seq 37°C in WT with plasmid expressing mini-ORF CUA	28139975	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE77617/GSE77617.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All cultures were based on MOPS media with 0.2% glucose (Teknova), with full supplement (Neidhardt et al., 1974) minus methionine. An overnight liquid culture was diluted 400-fold into 200 ml fresh media. The culture was kept in a 1 liter flask at 37°C with aeration until OD420 reached 0.4. PGCGROWTHCONDITIONS	SRR5186140	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		For in vivo DMS modification , 15 mL of exponentially growing E. coli were incubated with 750 µL DMS for 2 min at <Temp> 37 °C </Temp> . For kasugamycin ( ksg ) experiments , ksg was added to a final concentration of 10 mg/mL to ΔgcvB cells for 2 min at <Temp> 37 °C </Temp> prior to DMS modification . DMS was quenched by adding 30 mL 0 °C stop solution ( 30 % β-mercaptoethanol , 25 % isoamyl alcohol ) . For in vitro DMS modifications , mRNA was denatured at 95 °C for 2 min , cooled on ice and refolded in 90 µL RNA folding buffer ( 10 mM Tris pH 8.0 , 100 mM NaCl , 6 mM MgCl2 ) at <Temp> 37 °C </Temp> for 30 min then incubated in either .2 % DMS for 1 min ( 95 °C ) or 4 % DMS for 5 min ( <Temp> 37 °C </Temp> ) . 	GPL14548-GPL21433	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE77617	Operon mRNAs are organized into ORF-centric structures that predict translation efficiency	GSM2462937	mRNA-seq 37°C in WT with plasmid expressing mini-ORF CUA	28139975	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE77617/GSE77617.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For in vivo DMS modification, 15 mL of exponentially growing E. coli were incubated with 750 µL DMS for 2 min at 37°C. For kasugamycin (ksg) experiments, ksg was added to a final concentration of 10 mg/mL to ΔgcvB cells for 2 min at 37°C prior to DMS modification. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol). For in vitro DMS modifications, mRNA was denatured at 95 °C for 2 min, cooled on ice and refolded in 90 µL RNA folding buffer (10 mM Tris pH 8.0, 100 mM NaCl, 6 mM MgCl2) at 37°C for 30 min then incubated in either .2% DMS for 1 min (95°C) or 4% DMS for 5 min (37°C). PGCGROWTHCONDITIONS	SRR5186140	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All cultures were based on MOPS media with <Supp> 0.2 % glucose </Supp> ( Teknova ) , with full supplement ( Neidhardt et al. , 1974 ) minus methionine . An overnight liquid culture was diluted 400-fold into 200 ml <Med> fresh media </Med> . The culture was kept in a 1 liter flask at <Temp> 37 °C </Temp> with aeration until OD420 reached 0.4 . 	GPL14548-GPL21433	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE77617	Operon mRNAs are organized into ORF-centric structures that predict translation efficiency	GSM2462938	mRNA-seq 37°C in WT with plasmid expressing mini-ORF CUG	28139975	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE77617/GSE77617.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All cultures were based on MOPS media with 0.2% glucose (Teknova), with full supplement (Neidhardt et al., 1974) minus methionine. An overnight liquid culture was diluted 400-fold into 200 ml fresh media. The culture was kept in a 1 liter flask at 37°C with aeration until OD420 reached 0.4. PGCGROWTHCONDITIONS	SRR5186141	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		For in vivo DMS modification , 15 mL of exponentially growing E. coli were incubated with 750 µL DMS for 2 min at <Temp> 37 °C </Temp> . For kasugamycin ( ksg ) experiments , ksg was added to a final concentration of 10 mg/mL to ΔgcvB cells for 2 min at <Temp> 37 °C </Temp> prior to DMS modification . DMS was quenched by adding 30 mL 0 °C stop solution ( 30 % β-mercaptoethanol , 25 % isoamyl alcohol ) . For in vitro DMS modifications , mRNA was denatured at 95 °C for 2 min , cooled on ice and refolded in 90 µL RNA folding buffer ( 10 mM Tris pH 8.0 , 100 mM NaCl , 6 mM MgCl2 ) at <Temp> 37 °C </Temp> for 30 min then incubated in either .2 % DMS for 1 min ( 95 °C ) or 4 % DMS for 5 min ( <Temp> 37 °C </Temp> ) . 	GPL14548-GPL21433	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE77617	Operon mRNAs are organized into ORF-centric structures that predict translation efficiency	GSM2462938	mRNA-seq 37°C in WT with plasmid expressing mini-ORF CUG	28139975	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE77617/GSE77617.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For in vivo DMS modification, 15 mL of exponentially growing E. coli were incubated with 750 µL DMS for 2 min at 37°C. For kasugamycin (ksg) experiments, ksg was added to a final concentration of 10 mg/mL to ΔgcvB cells for 2 min at 37°C prior to DMS modification. DMS was quenched by adding 30 mL 0°C stop solution (30% β-mercaptoethanol, 25% isoamyl alcohol). For in vitro DMS modifications, mRNA was denatured at 95 °C for 2 min, cooled on ice and refolded in 90 µL RNA folding buffer (10 mM Tris pH 8.0, 100 mM NaCl, 6 mM MgCl2) at 37°C for 30 min then incubated in either .2% DMS for 1 min (95°C) or 4% DMS for 5 min (37°C). PGCGROWTHCONDITIONS	SRR5186141	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		Total RNA was extracted using the Trizol reagent ( Thermo Fisher Scientific ) and the concentration and purity of the samples were determined using Nano Drop . RNA integrity was monitored using the R6K ScreenTape system on the Agilent 2200 TapeStation . gDNA was removed by Turbo DNase ( Thermo Fisher Scientific ) in the presence of 1U / L RiboLock RNase Inhibitor ( Thermo Fisher Scientific ) for 60 min at <Temp> 37 °C </Temp> . Following organic extraction ( 1x 25:24:1 v/v phenol/chloroform / isoamyalcohol , 1x chloroform ) , RNA was recovered by overnight precipitation with 3 volumes of 30:1 100 % ethanol/3 M sodium acetate ( pH 5.2 ) . Next , the sample ( TEX + ) was depleted of processed RNAs using 1U per 1μg of RNA Terminator 5 ' - Phosphate-Dependent Exonuclease ( TEX , Epicentre ) in the presence of 1U/μL RNase Inhibitor for 60 min at 30 ° C . A control reaction without TEX ( TEX - ) was run in parallel . Following organic extraction , RNA was recovered by overnight precipitation and resuspended in RNase-free water . 	GPL21475	GPL21475: Illumina HiSeq 2500 (Escherichia coli O104:H4)	GSE78041	Differential RNA-Seq (dRNA-seq)  of Escherichia coli O104:H4	GSM2065371	TEX-_E. coli O104:H4	27748404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE78041/GSE78041.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Total RNA was extracted using the Trizol reagent (Thermo Fisher Scientific) and the concentration and purity of the samples were determined using Nano Drop. RNA integrity was monitored using the R6K ScreenTape system on the Agilent 2200 TapeStation. gDNA was removed by Turbo DNase (Thermo Fisher Scientific) in the presence of 1U/L RiboLock RNase Inhibitor (Thermo Fisher Scientific) for 60 min at 37°C. Following organic extraction (1x 25:24:1 v/v phenol/chloroform/ isoamyalcohol, 1x chloroform), RNA was recovered by overnight precipitation with 3 volumes of 30:1 100 % ethanol/3 M sodium acetate (pH 5.2). Next, the sample (TEX+) was depleted of processed RNAs using 1U per 1μg of RNA Terminator 5´-Phosphate-Dependent Exonuclease (TEX, Epicentre) in the presence of 1U/μL RNase Inhibitor for 60 min at 30° C. A control reaction without TEX (TEX-) was run in parallel. Following organic extraction, RNA was recovered by overnight precipitation and resuspended in RNase-free water. PGCGROWTHCONDITIONS	SRR3176282	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		Total RNA was extracted using the Trizol reagent ( Thermo Fisher Scientific ) and the concentration and purity of the samples were determined using Nano Drop . RNA integrity was monitored using the R6K ScreenTape system on the Agilent 2200 TapeStation . gDNA was removed by Turbo DNase ( Thermo Fisher Scientific ) in the presence of 1U / L RiboLock RNase Inhibitor ( Thermo Fisher Scientific ) for 60 min at <Temp> 37 °C </Temp> . Following organic extraction ( 1x 25:24:1 v/v phenol/chloroform / isoamyalcohol , 1x chloroform ) , RNA was recovered by overnight precipitation with 3 volumes of 30:1 100 % ethanol/3 M sodium acetate ( pH 5.2 ) . Next , the sample ( TEX + ) was depleted of processed RNAs using 1U per 1μg of RNA Terminator 5 ' - Phosphate-Dependent Exonuclease ( TEX , Epicentre ) in the presence of 1U/μL RNase Inhibitor for 60 min at 30 ° C . A control reaction without TEX ( TEX - ) was run in parallel . Following organic extraction , RNA was recovered by overnight precipitation and resuspended in RNase-free water . 	GPL21475	GPL21475: Illumina HiSeq 2500 (Escherichia coli O104:H4)	GSE78041	Differential RNA-Seq (dRNA-seq)  of Escherichia coli O104:H4	GSM2065372	TEX+_E. coli O104:H4	27748404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE78041/GSE78041.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Total RNA was extracted using the Trizol reagent (Thermo Fisher Scientific) and the concentration and purity of the samples were determined using Nano Drop. RNA integrity was monitored using the R6K ScreenTape system on the Agilent 2200 TapeStation. gDNA was removed by Turbo DNase (Thermo Fisher Scientific) in the presence of 1U/L RiboLock RNase Inhibitor (Thermo Fisher Scientific) for 60 min at 37°C. Following organic extraction (1x 25:24:1 v/v phenol/chloroform/ isoamyalcohol, 1x chloroform), RNA was recovered by overnight precipitation with 3 volumes of 30:1 100 % ethanol/3 M sodium acetate (pH 5.2). Next, the sample (TEX+) was depleted of processed RNAs using 1U per 1μg of RNA Terminator 5´-Phosphate-Dependent Exonuclease (TEX, Epicentre) in the presence of 1U/μL RNase Inhibitor for 60 min at 30° C. A control reaction without TEX (TEX-) was run in parallel. Following organic extraction, RNA was recovered by overnight precipitation and resuspended in RNase-free water. PGCGROWTHCONDITIONS	SRR3176283	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Escherichia coli strains E.coli C ( DSMZ 4860 ) , E. coli Crooks ( DSMZ 1576 ) , E. coli DH5α ( DSMZ 6897 ) E. coli W ( DSMZ 1116 ) , E. coli W3110 ( DSMZ 5911 ) were obtained from DSMZ-German Collection of Microorganism and Cell Cultures ; E. coli BL21 ( DE3 ) was purchased as competent cells from Agilent ( Agilent Technologies Inc. , USA ) , E. coli K-12 MG1655 ( ATCC 700926 ) . All strains were cultured in <Med> M9 minimal medium </Med> ( 1 ) containing Na2HPO4 x 7H2O ( 6.8 g ) , KH2PO4 ( 3 g ) , NaCl ( 0.5 g ) , NH4Cl ( 1 g ) , MgSO4 ( 2 mmol ) , CaCl2 ( 0.1 mmol ) , trace elements , Wolf 's vitamin solution ( 2 ) and glucose ( 2 g L-1 ) . Anoxic <Med> M9 minimal media </Med> with <Supp> glucose </Supp> was obtained by flushing solution with oxygen free nitrogen ( 95 % ) . Overnight cultures from single colonies of each of seven E. coli strains were diluted to a starting optical density ( OD600 ) of 0.01 . Cultures were grown in 250 ml flasks or 300 ml oxygen-free sealed bottles containing 50 ml <Med> glucose-M9 minimal media </Med> in a shaking incubator at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> . 	GPL14548-GPL15010-GPL21530-GPL21531-GPL21532-GPL21533-GPL21534	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21530: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. W3110). GPL21531: Illumina HiSeq 2000 (Escherichia coli W). GPL21532: Illumina HiSeq 2000 (Escherichia coli C). GPL21533: Illumina HiSeq 2000 (Escherichia coli BL21). GPL21534: Illumina HiSeq 2000 (Escherichia coli DH5[alpha])	GSE78756	Quantifying variation within the bacterial species E. coli	GSM2075722	Crooks_aero	27667363	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE78756/GSE78756.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Escherichia coli strains E.coli C (DSMZ 4860), E. coli Crooks (DSMZ 1576), E. coli DH5α (DSMZ 6897) E. coli W (DSMZ 1116), E. coli W3110 (DSMZ 5911) were obtained from DSMZ-German Collection of Microorganism and Cell Cultures; E. coli BL21 (DE3) was purchased as competent cells from Agilent (Agilent Technologies Inc., USA), E. coli K-12 MG1655 (ATCC 700926). All strains were cultured in M9 minimal medium (1) containing Na2HPO4 x 7H2O (6.8 g), KH2PO4 (3 g), NaCl (0.5 g), NH4Cl (1 g), MgSO4 (2 mmol), CaCl2 (0.1 mmol), trace elements, Wolf’s vitamin solution (2) and glucose (2 g L-1). Anoxic M9 minimal media with glucose was obtained by flushing solution with oxygen free nitrogen (95%). Overnight cultures from single colonies of each of seven E. coli strains were diluted to a starting optical density (OD600) of 0.01. Cultures were grown in 250 ml flasks or 300 ml oxygen-free sealed bottles containing 50 ml glucose-M9 minimal media in a shaking incubator at 37°C and 250 rpm. PGCGROWTHCONDITIONS	SRR3194453	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Escherichia coli strains E.coli C ( DSMZ 4860 ) , E. coli Crooks ( DSMZ 1576 ) , E. coli DH5α ( DSMZ 6897 ) E. coli W ( DSMZ 1116 ) , E. coli W3110 ( DSMZ 5911 ) were obtained from DSMZ-German Collection of Microorganism and Cell Cultures ; E. coli BL21 ( DE3 ) was purchased as competent cells from Agilent ( Agilent Technologies Inc. , USA ) , E. coli K-12 MG1655 ( ATCC 700926 ) . All strains were cultured in <Med> M9 minimal medium </Med> ( 1 ) containing Na2HPO4 x 7H2O ( 6.8 g ) , KH2PO4 ( 3 g ) , NaCl ( 0.5 g ) , NH4Cl ( 1 g ) , MgSO4 ( 2 mmol ) , CaCl2 ( 0.1 mmol ) , trace elements , Wolf 's vitamin solution ( 2 ) and glucose ( 2 g L-1 ) . Anoxic <Med> M9 minimal media </Med> with <Supp> glucose </Supp> was obtained by flushing solution with oxygen free nitrogen ( 95 % ) . Overnight cultures from single colonies of each of seven E. coli strains were diluted to a starting optical density ( OD600 ) of 0.01 . Cultures were grown in 250 ml flasks or 300 ml oxygen-free sealed bottles containing 50 ml <Med> glucose-M9 minimal media </Med> in a shaking incubator at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> . 	GPL14548-GPL15010-GPL21530-GPL21531-GPL21532-GPL21533-GPL21534	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21530: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. W3110). GPL21531: Illumina HiSeq 2000 (Escherichia coli W). GPL21532: Illumina HiSeq 2000 (Escherichia coli C). GPL21533: Illumina HiSeq 2000 (Escherichia coli BL21). GPL21534: Illumina HiSeq 2000 (Escherichia coli DH5[alpha])	GSE78756	Quantifying variation within the bacterial species E. coli	GSM2075723	Crooks_anaero	27667363	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE78756/GSE78756.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Escherichia coli strains E.coli C (DSMZ 4860), E. coli Crooks (DSMZ 1576), E. coli DH5α (DSMZ 6897) E. coli W (DSMZ 1116), E. coli W3110 (DSMZ 5911) were obtained from DSMZ-German Collection of Microorganism and Cell Cultures; E. coli BL21 (DE3) was purchased as competent cells from Agilent (Agilent Technologies Inc., USA), E. coli K-12 MG1655 (ATCC 700926). All strains were cultured in M9 minimal medium (1) containing Na2HPO4 x 7H2O (6.8 g), KH2PO4 (3 g), NaCl (0.5 g), NH4Cl (1 g), MgSO4 (2 mmol), CaCl2 (0.1 mmol), trace elements, Wolf’s vitamin solution (2) and glucose (2 g L-1). Anoxic M9 minimal media with glucose was obtained by flushing solution with oxygen free nitrogen (95%). Overnight cultures from single colonies of each of seven E. coli strains were diluted to a starting optical density (OD600) of 0.01. Cultures were grown in 250 ml flasks or 300 ml oxygen-free sealed bottles containing 50 ml glucose-M9 minimal media in a shaking incubator at 37°C and 250 rpm. PGCGROWTHCONDITIONS	SRR3194455SRR3194456	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		The cells were untreated , or treated with ( 100µg/mL Erythromycin or 50 µg/mL Clindamycin in 70 % Ethanol ) . After 10 minutes at <Temp> 37 °C </Temp> , 1 mL samples were subjected to hot phenol-chloroform extraction . Ref : <Gtype> Chuang </Gtype> SE , Daniels DL , and Blattner FR ( 1993 ) Global regulation of gene expression in Escherichia coli . J. Bacteriol . 175:2026-2036 . 	GPL21726	GPL21726: Ion Torrent Proton (Escherichia coli)	GSE80251	Genome-wide transcriptome analyses of E. coli treated with ribosome-targeting antibiotics	GSM2122743	Untreated_replicate_1	27645242	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80251/GSE80251.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	The cells were untreated, or treated with  (100µg/mL Erythromycin or 50 µg/mL Clindamycin in 70% Ethanol). After 10 minutes at 37°C, 1 mL samples were subjected to hot phenol-chloroform extraction. Ref: Chuang SE, Daniels DL, and Blattner FR (1993) Global regulation of gene expression in Escherichia coli. J. Bacteriol. 175:2026-2036. PGCGROWTHCONDITIONS	SRR3379590	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		The cells were untreated , or treated with ( 100µg/mL Erythromycin or 50 µg/mL Clindamycin in 70 % Ethanol ) . After 10 minutes at <Temp> 37 °C </Temp> , 1 mL samples were subjected to hot phenol-chloroform extraction . Ref : <Gtype> Chuang </Gtype> SE , Daniels DL , and Blattner FR ( 1993 ) Global regulation of gene expression in Escherichia coli . J. Bacteriol . 175:2026-2036 . 	GPL21726	GPL21726: Ion Torrent Proton (Escherichia coli)	GSE80251	Genome-wide transcriptome analyses of E. coli treated with ribosome-targeting antibiotics	GSM2122744	Untreated_replicate_2	27645242	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80251/GSE80251.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	The cells were untreated, or treated with  (100µg/mL Erythromycin or 50 µg/mL Clindamycin in 70% Ethanol). After 10 minutes at 37°C, 1 mL samples were subjected to hot phenol-chloroform extraction. Ref: Chuang SE, Daniels DL, and Blattner FR (1993) Global regulation of gene expression in Escherichia coli. J. Bacteriol. 175:2026-2036. PGCGROWTHCONDITIONS	SRR3379591	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		The cells were untreated , or treated with ( 100µg/mL Erythromycin or 50 µg/mL Clindamycin in 70 % Ethanol ) . After 10 minutes at <Temp> 37 °C </Temp> , 1 mL samples were subjected to hot phenol-chloroform extraction . Ref : <Gtype> Chuang </Gtype> SE , Daniels DL , and Blattner FR ( 1993 ) Global regulation of gene expression in Escherichia coli . J. Bacteriol . 175:2026-2036 . 	GPL21726	GPL21726: Ion Torrent Proton (Escherichia coli)	GSE80251	Genome-wide transcriptome analyses of E. coli treated with ribosome-targeting antibiotics	GSM2122745	Untreated_replicate_3	27645242	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80251/GSE80251.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	The cells were untreated, or treated with  (100µg/mL Erythromycin or 50 µg/mL Clindamycin in 70% Ethanol). After 10 minutes at 37°C, 1 mL samples were subjected to hot phenol-chloroform extraction. Ref: Chuang SE, Daniels DL, and Blattner FR (1993) Global regulation of gene expression in Escherichia coli. J. Bacteriol. 175:2026-2036. PGCGROWTHCONDITIONS	SRR3379592	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		The cells were untreated , or treated with ( 100µg/mL Erythromycin or 50 µg/mL Clindamycin in 70 % Ethanol ) . After 10 minutes at <Temp> 37 °C </Temp> , 1 mL samples were subjected to hot phenol-chloroform extraction . Ref : <Gtype> Chuang </Gtype> SE , Daniels DL , and Blattner FR ( 1993 ) Global regulation of gene expression in Escherichia coli . J. Bacteriol . 175:2026-2036 . 	GPL21726	GPL21726: Ion Torrent Proton (Escherichia coli)	GSE80251	Genome-wide transcriptome analyses of E. coli treated with ribosome-targeting antibiotics	GSM2122746	Erythromycin_replicate_1	27645242	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80251/GSE80251.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	The cells were untreated, or treated with  (100µg/mL Erythromycin or 50 µg/mL Clindamycin in 70% Ethanol). After 10 minutes at 37°C, 1 mL samples were subjected to hot phenol-chloroform extraction. Ref: Chuang SE, Daniels DL, and Blattner FR (1993) Global regulation of gene expression in Escherichia coli. J. Bacteriol. 175:2026-2036. PGCGROWTHCONDITIONS	SRR3379593	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		The cells were untreated , or treated with ( 100µg/mL Erythromycin or 50 µg/mL Clindamycin in 70 % Ethanol ) . After 10 minutes at <Temp> 37 °C </Temp> , 1 mL samples were subjected to hot phenol-chloroform extraction . Ref : <Gtype> Chuang </Gtype> SE , Daniels DL , and Blattner FR ( 1993 ) Global regulation of gene expression in Escherichia coli . J. Bacteriol . 175:2026-2036 . 	GPL21726	GPL21726: Ion Torrent Proton (Escherichia coli)	GSE80251	Genome-wide transcriptome analyses of E. coli treated with ribosome-targeting antibiotics	GSM2122747	Erythromycin_replicate_2	27645242	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80251/GSE80251.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	The cells were untreated, or treated with  (100µg/mL Erythromycin or 50 µg/mL Clindamycin in 70% Ethanol). After 10 minutes at 37°C, 1 mL samples were subjected to hot phenol-chloroform extraction. Ref: Chuang SE, Daniels DL, and Blattner FR (1993) Global regulation of gene expression in Escherichia coli. J. Bacteriol. 175:2026-2036. PGCGROWTHCONDITIONS	SRR3379594	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		The cells were untreated , or treated with ( 100µg/mL Erythromycin or 50 µg/mL Clindamycin in 70 % Ethanol ) . After 10 minutes at <Temp> 37 °C </Temp> , 1 mL samples were subjected to hot phenol-chloroform extraction . Ref : <Gtype> Chuang </Gtype> SE , Daniels DL , and Blattner FR ( 1993 ) Global regulation of gene expression in Escherichia coli . J. Bacteriol . 175:2026-2036 . 	GPL21726	GPL21726: Ion Torrent Proton (Escherichia coli)	GSE80251	Genome-wide transcriptome analyses of E. coli treated with ribosome-targeting antibiotics	GSM2122748	Erythromycin_replicate_3	27645242	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80251/GSE80251.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	The cells were untreated, or treated with  (100µg/mL Erythromycin or 50 µg/mL Clindamycin in 70% Ethanol). After 10 minutes at 37°C, 1 mL samples were subjected to hot phenol-chloroform extraction. Ref: Chuang SE, Daniels DL, and Blattner FR (1993) Global regulation of gene expression in Escherichia coli. J. Bacteriol. 175:2026-2036. PGCGROWTHCONDITIONS	SRR3379595	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		The cells were untreated , or treated with ( 100µg/mL Erythromycin or 50 µg/mL Clindamycin in 70 % Ethanol ) . After 10 minutes at <Temp> 37 °C </Temp> , 1 mL samples were subjected to hot phenol-chloroform extraction . Ref : <Gtype> Chuang </Gtype> SE , Daniels DL , and Blattner FR ( 1993 ) Global regulation of gene expression in Escherichia coli . J. Bacteriol . 175:2026-2036 . 	GPL21726	GPL21726: Ion Torrent Proton (Escherichia coli)	GSE80251	Genome-wide transcriptome analyses of E. coli treated with ribosome-targeting antibiotics	GSM2122749	Clindamycin_replicate_1	27645242	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80251/GSE80251.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	The cells were untreated, or treated with  (100µg/mL Erythromycin or 50 µg/mL Clindamycin in 70% Ethanol). After 10 minutes at 37°C, 1 mL samples were subjected to hot phenol-chloroform extraction. Ref: Chuang SE, Daniels DL, and Blattner FR (1993) Global regulation of gene expression in Escherichia coli. J. Bacteriol. 175:2026-2036. PGCGROWTHCONDITIONS	SRR3379596	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		The cells were untreated , or treated with ( 100µg/mL Erythromycin or 50 µg/mL Clindamycin in 70 % Ethanol ) . After 10 minutes at <Temp> 37 °C </Temp> , 1 mL samples were subjected to hot phenol-chloroform extraction . Ref : <Gtype> Chuang </Gtype> SE , Daniels DL , and Blattner FR ( 1993 ) Global regulation of gene expression in Escherichia coli . J. Bacteriol . 175:2026-2036 . 	GPL21726	GPL21726: Ion Torrent Proton (Escherichia coli)	GSE80251	Genome-wide transcriptome analyses of E. coli treated with ribosome-targeting antibiotics	GSM2122750	Clindamycin_replicate_2	27645242	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80251/GSE80251.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	The cells were untreated, or treated with  (100µg/mL Erythromycin or 50 µg/mL Clindamycin in 70% Ethanol). After 10 minutes at 37°C, 1 mL samples were subjected to hot phenol-chloroform extraction. Ref: Chuang SE, Daniels DL, and Blattner FR (1993) Global regulation of gene expression in Escherichia coli. J. Bacteriol. 175:2026-2036. PGCGROWTHCONDITIONS	SRR3379597	MCO000003199	37 °C	Temperature	True
treatment_protocol	35.7 C		The cells were untreated , or treated with ( 100µg/mL Erythromycin or 50 µg/mL Clindamycin in 70 % Ethanol ) . After 10 minutes at <Temp> 37 °C </Temp> , 1 mL samples were subjected to hot phenol-chloroform extraction . Ref : <Gtype> Chuang </Gtype> SE , Daniels DL , and Blattner FR ( 1993 ) Global regulation of gene expression in Escherichia coli . J. Bacteriol . 175:2026-2036 . 	GPL21726	GPL21726: Ion Torrent Proton (Escherichia coli)	GSE80251	Genome-wide transcriptome analyses of E. coli treated with ribosome-targeting antibiotics	GSM2122751	Clindamycin_replicate_3	27645242	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80251/GSE80251.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	The cells were untreated, or treated with  (100µg/mL Erythromycin or 50 µg/mL Clindamycin in 70% Ethanol). After 10 minutes at 37°C, 1 mL samples were subjected to hot phenol-chloroform extraction. Ref: Chuang SE, Daniels DL, and Blattner FR (1993) Global regulation of gene expression in Escherichia coli. J. Bacteriol. 175:2026-2036. PGCGROWTHCONDITIONS	SRR3379598	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic and anaerobic </Air> cultures were grown in 600 mL aliquots of DM25 and incubated at <Temp> 37 °C </Temp> with an orbital shaking of 150 RPM and inoculated with 1/100th volume of overnight culture . Aerobic cultures were grown for 9 h while anaerobic cultures were grown for 16 h. 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE80451	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GSM2127617	Aerobic 1	28103245	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80451/GSE80451.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic and anaerobic cultures were grown in 600 mL aliquots of DM25 and incubated at 37°C with an orbital shaking of 150 RPM and inoculated with 1/100th volume of overnight culture. Aerobic cultures were grown for 9 h while anaerobic cultures were grown for 16 h. PGCGROWTHCONDITIONS	SRR3403686	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic and anaerobic </Air> cultures were grown in 600 mL aliquots of DM25 and incubated at <Temp> 37 °C </Temp> with an orbital shaking of 150 RPM and inoculated with 1/100th volume of overnight culture . Aerobic cultures were grown for 9 h while anaerobic cultures were grown for 16 h. 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE80451	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GSM2127618	Aerobic 2	28103245	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80451/GSE80451.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic and anaerobic cultures were grown in 600 mL aliquots of DM25 and incubated at 37°C with an orbital shaking of 150 RPM and inoculated with 1/100th volume of overnight culture. Aerobic cultures were grown for 9 h while anaerobic cultures were grown for 16 h. PGCGROWTHCONDITIONS	SRR3403687	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		<Air> Aerobic and anaerobic </Air> cultures were grown in 600 mL aliquots of DM25 and incubated at <Temp> 37 °C </Temp> with an orbital shaking of 150 RPM and inoculated with 1/100th volume of overnight culture . Aerobic cultures were grown for 9 h while anaerobic cultures were grown for 16 h. 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE80451	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GSM2127619	Aerobic 3	28103245	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80451/GSE80451.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic and anaerobic cultures were grown in 600 mL aliquots of DM25 and incubated at 37°C with an orbital shaking of 150 RPM and inoculated with 1/100th volume of overnight culture. Aerobic cultures were grown for 9 h while anaerobic cultures were grown for 16 h. PGCGROWTHCONDITIONS	SRR3403688	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		Cell pellets were lysed and RNA collected using Qiagen 's RNeasy Plus Mini Kit with Qiagen Bacteria Protect RNA kit . RNA samples were then treated with DNase ( New England Biolabs ) for <Supp> 30 min </Supp> at <Temp> 37 °C </Temp> . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE81584	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GSM2157648	MG1655_1		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE81584/GSE81584.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cell pellets were lysed and RNA collected using Qiagen’s RNeasy Plus Mini Kit with Qiagen Bacteria Protect RNA kit.  RNA samples were then treated with DNase (New England Biolabs) for 30 min at 37 °C. PGCGROWTHCONDITIONS	SRR3584193SRR3584194SRR3584195	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		Cell pellets were lysed and RNA collected using Qiagen 's RNeasy Plus Mini Kit with Qiagen Bacteria Protect RNA kit . RNA samples were then treated with DNase ( New England Biolabs ) for <Supp> 30 min </Supp> at <Temp> 37 °C </Temp> . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE81584	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GSM2157649	MG1655_2		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE81584/GSE81584.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cell pellets were lysed and RNA collected using Qiagen’s RNeasy Plus Mini Kit with Qiagen Bacteria Protect RNA kit.  RNA samples were then treated with DNase (New England Biolabs) for 30 min at 37 °C. PGCGROWTHCONDITIONS	SRR3584196SRR3584197SRR3584198	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		Cell pellets were lysed and RNA collected using Qiagen 's RNeasy Plus Mini Kit with Qiagen Bacteria Protect RNA kit . RNA samples were then treated with DNase ( New England Biolabs ) for <Supp> 30 min </Supp> at <Temp> 37 °C </Temp> . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE81584	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GSM2157650	MG1655_3		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE81584/GSE81584.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cell pellets were lysed and RNA collected using Qiagen’s RNeasy Plus Mini Kit with Qiagen Bacteria Protect RNA kit.  RNA samples were then treated with DNase (New England Biolabs) for 30 min at 37 °C. PGCGROWTHCONDITIONS	SRR3584199SRR3584200	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		Cell pellets were lysed and RNA collected using Qiagen 's RNeasy Plus Mini Kit with Qiagen Bacteria Protect RNA kit . RNA samples were then treated with DNase ( New England Biolabs ) for <Supp> 30 min </Supp> at <Temp> 37 °C </Temp> . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE81584	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GSM2157651	mfd_1		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE81584/GSE81584.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cell pellets were lysed and RNA collected using Qiagen’s RNeasy Plus Mini Kit with Qiagen Bacteria Protect RNA kit.  RNA samples were then treated with DNase (New England Biolabs) for 30 min at 37 °C. PGCGROWTHCONDITIONS	SRR3584201SRR3584202	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		Cell pellets were lysed and RNA collected using Qiagen 's RNeasy Plus Mini Kit with Qiagen Bacteria Protect RNA kit . RNA samples were then treated with DNase ( New England Biolabs ) for <Supp> 30 min </Supp> at <Temp> 37 °C </Temp> . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE81584	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GSM2157652	mfd_2		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE81584/GSE81584.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cell pellets were lysed and RNA collected using Qiagen’s RNeasy Plus Mini Kit with Qiagen Bacteria Protect RNA kit.  RNA samples were then treated with DNase (New England Biolabs) for 30 min at 37 °C. PGCGROWTHCONDITIONS	SRR3584203SRR3584204	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		Cell pellets were lysed and RNA collected using Qiagen 's RNeasy Plus Mini Kit with Qiagen Bacteria Protect RNA kit . RNA samples were then treated with DNase ( New England Biolabs ) for <Supp> 30 min </Supp> at <Temp> 37 °C </Temp> . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE81584	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GSM2157653	mfd_3		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE81584/GSE81584.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cell pellets were lysed and RNA collected using Qiagen’s RNeasy Plus Mini Kit with Qiagen Bacteria Protect RNA kit.  RNA samples were then treated with DNase (New England Biolabs) for 30 min at 37 °C. PGCGROWTHCONDITIONS	SRR3584205SRR3584206SRR3584207	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		Cell pellets were lysed and RNA collected using Qiagen 's RNeasy Plus Mini Kit with Qiagen Bacteria Protect RNA kit . RNA samples were then treated with DNase ( New England Biolabs ) for <Supp> 30 min </Supp> at <Temp> 37 °C </Temp> . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE81584	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GSM2157654	MG1655_vector_1		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE81584/GSE81584.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cell pellets were lysed and RNA collected using Qiagen’s RNeasy Plus Mini Kit with Qiagen Bacteria Protect RNA kit.  RNA samples were then treated with DNase (New England Biolabs) for 30 min at 37 °C. PGCGROWTHCONDITIONS	SRR3584208SRR3584209	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		Cell pellets were lysed and RNA collected using Qiagen 's RNeasy Plus Mini Kit with Qiagen Bacteria Protect RNA kit . RNA samples were then treated with DNase ( New England Biolabs ) for <Supp> 30 min </Supp> at <Temp> 37 °C </Temp> . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE81584	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GSM2157655	MG1655_vector_2		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE81584/GSE81584.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cell pellets were lysed and RNA collected using Qiagen’s RNeasy Plus Mini Kit with Qiagen Bacteria Protect RNA kit.  RNA samples were then treated with DNase (New England Biolabs) for 30 min at 37 °C. PGCGROWTHCONDITIONS	SRR3584210SRR3584211	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		Cell pellets were lysed and RNA collected using Qiagen 's RNeasy Plus Mini Kit with Qiagen Bacteria Protect RNA kit . RNA samples were then treated with DNase ( New England Biolabs ) for <Supp> 30 min </Supp> at <Temp> 37 °C </Temp> . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE81584	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GSM2157656	MFD++_1		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE81584/GSE81584.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cell pellets were lysed and RNA collected using Qiagen’s RNeasy Plus Mini Kit with Qiagen Bacteria Protect RNA kit.  RNA samples were then treated with DNase (New England Biolabs) for 30 min at 37 °C. PGCGROWTHCONDITIONS	SRR3584212SRR3584213SRR3584214	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		Cell pellets were lysed and RNA collected using Qiagen 's RNeasy Plus Mini Kit with Qiagen Bacteria Protect RNA kit . RNA samples were then treated with DNase ( New England Biolabs ) for <Supp> 30 min </Supp> at <Temp> 37 °C </Temp> . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE81584	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GSM2157657	MFD++_2		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE81584/GSE81584.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cell pellets were lysed and RNA collected using Qiagen’s RNeasy Plus Mini Kit with Qiagen Bacteria Protect RNA kit.  RNA samples were then treated with DNase (New England Biolabs) for 30 min at 37 °C. PGCGROWTHCONDITIONS	SRR3584215SRR3584216SRR3584217	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		RNA was extracted from two biological replicates ( 30 mL ) of each bacterial culture isolated at each time point . The 30 mL culture was aliquoted into three 15 mL tubes containing 5 mL of ice-cold EtOH/Phenol stop solution ( 5 % water-saturated phenol pH 4.2 [ Invitrogen ] in 100 % ethanol ) . Cells were collected by centrifugation ( 4,000 rpm , 5 min , 4 °C ) and the pellet suspended in 800 µL TE pH 8.0 supplemented with 0.5 mg/mL lysozyme . SDS ( 80 µL at 10 % ( w/v ) ) was added , samples mixed by inversion , and incubated ( 65 °C , 2 min ) , before the addition of <Supp> 88 µL 1 M </Supp> NaOAc ( pH 5.2 ) . Each sample was added to an equal volume ( 1mL ) of water-saturated phenol ( pH 4.2 , 65 °C ) and incubated ( 65 °C , 6 min ) . The solution was separated into layers by centrifugation ( 14,000 rpm , 10 min , 4 °C ) and the upper aqueous RNA containing layer removed and transferred into a fresh tube . RNA was cleaned by three extractions with phenol : <Gtype> CHCl3 : IAA </Gtype> ( 25:24:1 , pH 8.0 ) before being precipitated ( -80 °C , O/N ) following the addition of 1/10 volume of 3M NaOAc ( pH 5.2 ) and 2 volumes of ice cold 100 % EtOH . RNA was pelleted ( 14,000 rpm , 25 min , 4 °C ) , the supernatant removed and the pellet washed with 1 mL 75 % cold EtOH ( made with DEPC-treated water ) . RNA was pelleted ( 14,000 rpm , 5 min , 4 °C ) and air dried before suspension in 80 µL RNAse free water ( Invitrogen ) and treatment with TURBO DNAse ( Ambion ) according to the manufacturer 's instructions . Briefly , 0.1 V of 10 X Turbo DNAse buffer ( Ambion ) was added to the RNA solution . 1 µL of TURBO DNAse was added to the solution , which was then incubated ( 30 min , <Temp> 37 °C </Temp> ) . Following incubation , 0.1 V of DNase Inactivation Reagent ( Ambion ) was added and then incubated ( 5 min , RT ) with occasional mixing . RNA was isolated and transferred into a fresh microfuge tube . RNA quality tested using the the Agilent RNA 6000 Nano Kit ( Agilent Technologies ) and quality analysed using the Agilent 2100 Bioanalyzer ( Agilent Technologies ) . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE87071	The Escherichia coli nucleoid is shaped around replication and transcription [RNA-Seq]	GSM2321583	10J.0		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE87071/GSE87071.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	RNA was extracted from two biological replicates (30 mL) of each bacterial culture isolated at each time point. The 30 mL culture was aliquoted into three 15 mL tubes containing 5 mL of ice-cold EtOH/Phenol stop solution (5% water-saturated phenol pH 4.2 [Invitrogen] in 100% ethanol). Cells were collected by centrifugation (4,000 rpm, 5 min, 4°C) and the pellet suspended in 800 µL TE pH 8.0 supplemented with 0.5 mg/mL lysozyme. SDS (80 µL at 10% (w/v)) was added, samples mixed by inversion, and incubated (65°C, 2 min), before the addition of 88 µL 1 M NaOAc (pH 5.2). Each sample was added to an equal volume (1mL) of water-saturated phenol (pH 4.2, 65°C) and incubated (65°C, 6 min). The solution was separated into layers by centrifugation (14,000 rpm, 10 min, 4°C) and the upper aqueous RNA containing layer removed and transferred into a fresh tube.  RNA was cleaned by three extractions with phenol:CHCl3:IAA (25:24:1, pH 8.0) before being precipitated (-80°C, O/N) following the addition of 1/10 volume of 3M NaOAc (pH 5.2) and 2 volumes of ice cold 100% EtOH. RNA was pelleted (14,000 rpm, 25 min, 4°C), the supernatant removed and the pellet washed with 1 mL 75% cold EtOH (made with DEPC-treated water).   RNA was pelleted (14,000 rpm, 5 min, 4°C) and air dried before suspension in 80 µL RNAse free water (Invitrogen) and treatment with TURBO DNAse (Ambion) according to the manufacturer’s instructions. Briefly, 0.1 V of 10 X Turbo DNAse buffer (Ambion) was added to the RNA solution. 1 µL of TURBO DNAse was added to the solution, which was then incubated (30 min, 37 °C). Following incubation, 0.1 V of DNase Inactivation Reagent (Ambion) was added and then incubated (5 min, RT) with occasional mixing. RNA was isolated and transferred into a fresh microfuge tube.  RNA quality tested using the the Agilent RNA 6000 Nano Kit (Agilent Technologies) and quality analysed using the Agilent 2100 Bioanalyzer (Agilent Technologies). PGCGROWTHCONDITIONS	SRR4255368	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Synchronization was achieved by passaging cells through one or two rounds of stationary phase according to Cutler and Evans 1966 . Briefly : <Gtype> Individual </Gtype> colonies ( LB plate , <Temp> 37 °C </Temp> , 24 h ) were inoculated into M9 media and grown O/N ( <Temp> 37 °C </Temp> , 200 rpm ) . M9 media was inoculated to a final OD600 = 0.25 ( early-logarithmic phase ) . Cultures were grown ( <Temp> 37 °C </Temp> , 200 rpm ) and maintained in stationary phase ( OD600 1.8 ) for <Supp> approximately 2 hours </Supp> . An appropriate amount of each culture was used to inoculate pre-warmed ( <Temp> 37 °C </Temp> ) M9 media to a final OD600 = 0.25 ( approximate 7-fold dilution ) . Released cultures were grown ( <Temp> 37 °C </Temp> , 200 rpm ) and harvested ( time = 0 , 1 hr , or 2 hr ) for GCC and RNA isolation . Samples ( 1 mL ) were also taken for FACS analysis and fluorescence microscopy ( t = 0 , 1 hr , and 2 hr ) . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE87071	The Escherichia coli nucleoid is shaped around replication and transcription [RNA-Seq]	GSM2321583	10J.0		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE87071/GSE87071.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Synchronization was achieved by passaging cells through one or two rounds of stationary phase according to Cutler and Evans 1966. Briefly: Individual colonies (LB plate, 37°C, 24 h) were inoculated into M9 media and grown O/N (37°C, 200 rpm). M9 media was inoculated to a final OD600 = 0.25 (early-logarithmic phase). Cultures were grown (37°C, 200 rpm) and maintained in stationary phase (OD600 1.8) for approximately 2 hours. An appropriate amount of each culture was used to inoculate pre-warmed (37°C) M9 media to a final OD600 = 0.25 (approximate 7-fold dilution). Released cultures were grown (37°C, 200 rpm) and harvested (time = 0, 1 hr, or 2 hr) for GCC and RNA isolation. Samples (1 mL) were also taken for FACS analysis and fluorescence microscopy (t=0, 1 hr, and 2 hr). PGCGROWTHCONDITIONS	SRR4255368	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		RNA was extracted from two biological replicates ( 30 mL ) of each bacterial culture isolated at each time point . The 30 mL culture was aliquoted into three 15 mL tubes containing 5 mL of ice-cold EtOH/Phenol stop solution ( 5 % water-saturated phenol pH 4.2 [ Invitrogen ] in 100 % ethanol ) . Cells were collected by centrifugation ( 4,000 rpm , 5 min , 4 °C ) and the pellet suspended in 800 µL TE pH 8.0 supplemented with 0.5 mg/mL lysozyme . SDS ( 80 µL at 10 % ( w/v ) ) was added , samples mixed by inversion , and incubated ( 65 °C , 2 min ) , before the addition of <Supp> 88 µL 1 M </Supp> NaOAc ( pH 5.2 ) . Each sample was added to an equal volume ( 1mL ) of water-saturated phenol ( pH 4.2 , 65 °C ) and incubated ( 65 °C , 6 min ) . The solution was separated into layers by centrifugation ( 14,000 rpm , 10 min , 4 °C ) and the upper aqueous RNA containing layer removed and transferred into a fresh tube . RNA was cleaned by three extractions with phenol : <Gtype> CHCl3 : IAA </Gtype> ( 25:24:1 , pH 8.0 ) before being precipitated ( -80 °C , O/N ) following the addition of 1/10 volume of 3M NaOAc ( pH 5.2 ) and 2 volumes of ice cold 100 % EtOH . RNA was pelleted ( 14,000 rpm , 25 min , 4 °C ) , the supernatant removed and the pellet washed with 1 mL 75 % cold EtOH ( made with DEPC-treated water ) . RNA was pelleted ( 14,000 rpm , 5 min , 4 °C ) and air dried before suspension in 80 µL RNAse free water ( Invitrogen ) and treatment with TURBO DNAse ( Ambion ) according to the manufacturer 's instructions . Briefly , 0.1 V of 10 X Turbo DNAse buffer ( Ambion ) was added to the RNA solution . 1 µL of TURBO DNAse was added to the solution , which was then incubated ( 30 min , <Temp> 37 °C </Temp> ) . Following incubation , 0.1 V of DNase Inactivation Reagent ( Ambion ) was added and then incubated ( 5 min , RT ) with occasional mixing . RNA was isolated and transferred into a fresh microfuge tube . RNA quality tested using the the Agilent RNA 6000 Nano Kit ( Agilent Technologies ) and quality analysed using the Agilent 2100 Bioanalyzer ( Agilent Technologies ) . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE87071	The Escherichia coli nucleoid is shaped around replication and transcription [RNA-Seq]	GSM2321584	11K.60		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE87071/GSE87071.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	RNA was extracted from two biological replicates (30 mL) of each bacterial culture isolated at each time point. The 30 mL culture was aliquoted into three 15 mL tubes containing 5 mL of ice-cold EtOH/Phenol stop solution (5% water-saturated phenol pH 4.2 [Invitrogen] in 100% ethanol). Cells were collected by centrifugation (4,000 rpm, 5 min, 4°C) and the pellet suspended in 800 µL TE pH 8.0 supplemented with 0.5 mg/mL lysozyme. SDS (80 µL at 10% (w/v)) was added, samples mixed by inversion, and incubated (65°C, 2 min), before the addition of 88 µL 1 M NaOAc (pH 5.2). Each sample was added to an equal volume (1mL) of water-saturated phenol (pH 4.2, 65°C) and incubated (65°C, 6 min). The solution was separated into layers by centrifugation (14,000 rpm, 10 min, 4°C) and the upper aqueous RNA containing layer removed and transferred into a fresh tube.  RNA was cleaned by three extractions with phenol:CHCl3:IAA (25:24:1, pH 8.0) before being precipitated (-80°C, O/N) following the addition of 1/10 volume of 3M NaOAc (pH 5.2) and 2 volumes of ice cold 100% EtOH. RNA was pelleted (14,000 rpm, 25 min, 4°C), the supernatant removed and the pellet washed with 1 mL 75% cold EtOH (made with DEPC-treated water).   RNA was pelleted (14,000 rpm, 5 min, 4°C) and air dried before suspension in 80 µL RNAse free water (Invitrogen) and treatment with TURBO DNAse (Ambion) according to the manufacturer’s instructions. Briefly, 0.1 V of 10 X Turbo DNAse buffer (Ambion) was added to the RNA solution. 1 µL of TURBO DNAse was added to the solution, which was then incubated (30 min, 37 °C). Following incubation, 0.1 V of DNase Inactivation Reagent (Ambion) was added and then incubated (5 min, RT) with occasional mixing. RNA was isolated and transferred into a fresh microfuge tube.  RNA quality tested using the the Agilent RNA 6000 Nano Kit (Agilent Technologies) and quality analysed using the Agilent 2100 Bioanalyzer (Agilent Technologies). PGCGROWTHCONDITIONS	SRR4255369	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Synchronization was achieved by passaging cells through one or two rounds of stationary phase according to Cutler and Evans 1966 . Briefly : <Gtype> Individual </Gtype> colonies ( LB plate , <Temp> 37 °C </Temp> , 24 h ) were inoculated into M9 media and grown O/N ( <Temp> 37 °C </Temp> , 200 rpm ) . M9 media was inoculated to a final OD600 = 0.25 ( early-logarithmic phase ) . Cultures were grown ( <Temp> 37 °C </Temp> , 200 rpm ) and maintained in stationary phase ( OD600 1.8 ) for <Supp> approximately 2 hours </Supp> . An appropriate amount of each culture was used to inoculate pre-warmed ( <Temp> 37 °C </Temp> ) M9 media to a final OD600 = 0.25 ( approximate 7-fold dilution ) . Released cultures were grown ( <Temp> 37 °C </Temp> , 200 rpm ) and harvested ( time = 0 , 1 hr , or 2 hr ) for GCC and RNA isolation . Samples ( 1 mL ) were also taken for FACS analysis and fluorescence microscopy ( t = 0 , 1 hr , and 2 hr ) . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE87071	The Escherichia coli nucleoid is shaped around replication and transcription [RNA-Seq]	GSM2321584	11K.60		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE87071/GSE87071.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Synchronization was achieved by passaging cells through one or two rounds of stationary phase according to Cutler and Evans 1966. Briefly: Individual colonies (LB plate, 37°C, 24 h) were inoculated into M9 media and grown O/N (37°C, 200 rpm). M9 media was inoculated to a final OD600 = 0.25 (early-logarithmic phase). Cultures were grown (37°C, 200 rpm) and maintained in stationary phase (OD600 1.8) for approximately 2 hours. An appropriate amount of each culture was used to inoculate pre-warmed (37°C) M9 media to a final OD600 = 0.25 (approximate 7-fold dilution). Released cultures were grown (37°C, 200 rpm) and harvested (time = 0, 1 hr, or 2 hr) for GCC and RNA isolation. Samples (1 mL) were also taken for FACS analysis and fluorescence microscopy (t=0, 1 hr, and 2 hr). PGCGROWTHCONDITIONS	SRR4255369	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		RNA was extracted from two biological replicates ( 30 mL ) of each bacterial culture isolated at each time point . The 30 mL culture was aliquoted into three 15 mL tubes containing 5 mL of ice-cold EtOH/Phenol stop solution ( 5 % water-saturated phenol pH 4.2 [ Invitrogen ] in 100 % ethanol ) . Cells were collected by centrifugation ( 4,000 rpm , 5 min , 4 °C ) and the pellet suspended in 800 µL TE pH 8.0 supplemented with 0.5 mg/mL lysozyme . SDS ( 80 µL at 10 % ( w/v ) ) was added , samples mixed by inversion , and incubated ( 65 °C , 2 min ) , before the addition of <Supp> 88 µL 1 M </Supp> NaOAc ( pH 5.2 ) . Each sample was added to an equal volume ( 1mL ) of water-saturated phenol ( pH 4.2 , 65 °C ) and incubated ( 65 °C , 6 min ) . The solution was separated into layers by centrifugation ( 14,000 rpm , 10 min , 4 °C ) and the upper aqueous RNA containing layer removed and transferred into a fresh tube . RNA was cleaned by three extractions with phenol : <Gtype> CHCl3 : IAA </Gtype> ( 25:24:1 , pH 8.0 ) before being precipitated ( -80 °C , O/N ) following the addition of 1/10 volume of 3M NaOAc ( pH 5.2 ) and 2 volumes of ice cold 100 % EtOH . RNA was pelleted ( 14,000 rpm , 25 min , 4 °C ) , the supernatant removed and the pellet washed with 1 mL 75 % cold EtOH ( made with DEPC-treated water ) . RNA was pelleted ( 14,000 rpm , 5 min , 4 °C ) and air dried before suspension in 80 µL RNAse free water ( Invitrogen ) and treatment with TURBO DNAse ( Ambion ) according to the manufacturer 's instructions . Briefly , 0.1 V of 10 X Turbo DNAse buffer ( Ambion ) was added to the RNA solution . 1 µL of TURBO DNAse was added to the solution , which was then incubated ( 30 min , <Temp> 37 °C </Temp> ) . Following incubation , 0.1 V of DNase Inactivation Reagent ( Ambion ) was added and then incubated ( 5 min , RT ) with occasional mixing . RNA was isolated and transferred into a fresh microfuge tube . RNA quality tested using the the Agilent RNA 6000 Nano Kit ( Agilent Technologies ) and quality analysed using the Agilent 2100 Bioanalyzer ( Agilent Technologies ) . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE87071	The Escherichia coli nucleoid is shaped around replication and transcription [RNA-Seq]	GSM2321585	12L.120		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE87071/GSE87071.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	RNA was extracted from two biological replicates (30 mL) of each bacterial culture isolated at each time point. The 30 mL culture was aliquoted into three 15 mL tubes containing 5 mL of ice-cold EtOH/Phenol stop solution (5% water-saturated phenol pH 4.2 [Invitrogen] in 100% ethanol). Cells were collected by centrifugation (4,000 rpm, 5 min, 4°C) and the pellet suspended in 800 µL TE pH 8.0 supplemented with 0.5 mg/mL lysozyme. SDS (80 µL at 10% (w/v)) was added, samples mixed by inversion, and incubated (65°C, 2 min), before the addition of 88 µL 1 M NaOAc (pH 5.2). Each sample was added to an equal volume (1mL) of water-saturated phenol (pH 4.2, 65°C) and incubated (65°C, 6 min). The solution was separated into layers by centrifugation (14,000 rpm, 10 min, 4°C) and the upper aqueous RNA containing layer removed and transferred into a fresh tube.  RNA was cleaned by three extractions with phenol:CHCl3:IAA (25:24:1, pH 8.0) before being precipitated (-80°C, O/N) following the addition of 1/10 volume of 3M NaOAc (pH 5.2) and 2 volumes of ice cold 100% EtOH. RNA was pelleted (14,000 rpm, 25 min, 4°C), the supernatant removed and the pellet washed with 1 mL 75% cold EtOH (made with DEPC-treated water).   RNA was pelleted (14,000 rpm, 5 min, 4°C) and air dried before suspension in 80 µL RNAse free water (Invitrogen) and treatment with TURBO DNAse (Ambion) according to the manufacturer’s instructions. Briefly, 0.1 V of 10 X Turbo DNAse buffer (Ambion) was added to the RNA solution. 1 µL of TURBO DNAse was added to the solution, which was then incubated (30 min, 37 °C). Following incubation, 0.1 V of DNase Inactivation Reagent (Ambion) was added and then incubated (5 min, RT) with occasional mixing. RNA was isolated and transferred into a fresh microfuge tube.  RNA quality tested using the the Agilent RNA 6000 Nano Kit (Agilent Technologies) and quality analysed using the Agilent 2100 Bioanalyzer (Agilent Technologies). PGCGROWTHCONDITIONS	SRR4255370	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Synchronization was achieved by passaging cells through one or two rounds of stationary phase according to Cutler and Evans 1966 . Briefly : <Gtype> Individual </Gtype> colonies ( LB plate , <Temp> 37 °C </Temp> , 24 h ) were inoculated into M9 media and grown O/N ( <Temp> 37 °C </Temp> , 200 rpm ) . M9 media was inoculated to a final OD600 = 0.25 ( early-logarithmic phase ) . Cultures were grown ( <Temp> 37 °C </Temp> , 200 rpm ) and maintained in stationary phase ( OD600 1.8 ) for <Supp> approximately 2 hours </Supp> . An appropriate amount of each culture was used to inoculate pre-warmed ( <Temp> 37 °C </Temp> ) M9 media to a final OD600 = 0.25 ( approximate 7-fold dilution ) . Released cultures were grown ( <Temp> 37 °C </Temp> , 200 rpm ) and harvested ( time = 0 , 1 hr , or 2 hr ) for GCC and RNA isolation . Samples ( 1 mL ) were also taken for FACS analysis and fluorescence microscopy ( t = 0 , 1 hr , and 2 hr ) . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE87071	The Escherichia coli nucleoid is shaped around replication and transcription [RNA-Seq]	GSM2321585	12L.120		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE87071/GSE87071.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Synchronization was achieved by passaging cells through one or two rounds of stationary phase according to Cutler and Evans 1966. Briefly: Individual colonies (LB plate, 37°C, 24 h) were inoculated into M9 media and grown O/N (37°C, 200 rpm). M9 media was inoculated to a final OD600 = 0.25 (early-logarithmic phase). Cultures were grown (37°C, 200 rpm) and maintained in stationary phase (OD600 1.8) for approximately 2 hours. An appropriate amount of each culture was used to inoculate pre-warmed (37°C) M9 media to a final OD600 = 0.25 (approximate 7-fold dilution). Released cultures were grown (37°C, 200 rpm) and harvested (time = 0, 1 hr, or 2 hr) for GCC and RNA isolation. Samples (1 mL) were also taken for FACS analysis and fluorescence microscopy (t=0, 1 hr, and 2 hr). PGCGROWTHCONDITIONS	SRR4255370	MCO000003199	37 °C	Temperature	True
extract_protocol	35.7 C		RNA was extracted from two biological replicates ( 30 mL ) of each bacterial culture isolated at each time point . The 30 mL culture was aliquoted into three 15 mL tubes containing 5 mL of ice-cold EtOH/Phenol stop solution ( 5 % water-saturated phenol pH 4.2 [ Invitrogen ] in 100 % ethanol ) . Cells were collected by centrifugation ( 4,000 rpm , 5 min , 4 °C ) and the pellet suspended in 800 µL TE pH 8.0 supplemented with 0.5 mg/mL lysozyme . SDS ( 80 µL at 10 % ( w/v ) ) was added , samples mixed by inversion , and incubated ( 65 °C , 2 min ) , before the addition of <Supp> 88 µL 1 M </Supp> NaOAc ( pH 5.2 ) . Each sample was added to an equal volume ( 1mL ) of water-saturated phenol ( pH 4.2 , 65 °C ) and incubated ( 65 °C , 6 min ) . The solution was separated into layers by centrifugation ( 14,000 rpm , 10 min , 4 °C ) and the upper aqueous RNA containing layer removed and transferred into a fresh tube . RNA was cleaned by three extractions with phenol : <Gtype> CHCl3 : IAA </Gtype> ( 25:24:1 , pH 8.0 ) before being precipitated ( -80 °C , O/N ) following the addition of 1/10 volume of 3M NaOAc ( pH 5.2 ) and 2 volumes of ice cold 100 % EtOH . RNA was pelleted ( 14,000 rpm , 25 min , 4 °C ) , the supernatant removed and the pellet washed with 1 mL 75 % cold EtOH ( made with DEPC-treated water ) . RNA was pelleted ( 14,000 rpm , 5 min , 4 °C ) and air dried before suspension in 80 µL RNAse free water ( Invitrogen ) and treatment with TURBO DNAse ( Ambion ) according to the manufacturer 's instructions . Briefly , 0.1 V of 10 X Turbo DNAse buffer ( Ambion ) was added to the RNA solution . 1 µL of TURBO DNAse was added to the solution , which was then incubated ( 30 min , <Temp> 37 °C </Temp> ) . Following incubation , 0.1 V of DNase Inactivation Reagent ( Ambion ) was added and then incubated ( 5 min , RT ) with occasional mixing . RNA was isolated and transferred into a fresh microfuge tube . RNA quality tested using the the Agilent RNA 6000 Nano Kit ( Agilent Technologies ) and quality analysed using the Agilent 2100 Bioanalyzer ( Agilent Technologies ) . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE87071	The Escherichia coli nucleoid is shaped around replication and transcription [RNA-Seq]	GSM2321586	7G.0		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE87071/GSE87071.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	RNA was extracted from two biological replicates (30 mL) of each bacterial culture isolated at each time point. The 30 mL culture was aliquoted into three 15 mL tubes containing 5 mL of ice-cold EtOH/Phenol stop solution (5% water-saturated phenol pH 4.2 [Invitrogen] in 100% ethanol). Cells were collected by centrifugation (4,000 rpm, 5 min, 4°C) and the pellet suspended in 800 µL TE pH 8.0 supplemented with 0.5 mg/mL lysozyme. SDS (80 µL at 10% (w/v)) was added, samples mixed by inversion, and incubated (65°C, 2 min), before the addition of 88 µL 1 M NaOAc (pH 5.2). Each sample was added to an equal volume (1mL) of water-saturated phenol (pH 4.2, 65°C) and incubated (65°C, 6 min). The solution was separated into layers by centrifugation (14,000 rpm, 10 min, 4°C) and the upper aqueous RNA containing layer removed and transferred into a fresh tube.  RNA was cleaned by three extractions with phenol:CHCl3:IAA (25:24:1, pH 8.0) before being precipitated (-80°C, O/N) following the addition of 1/10 volume of 3M NaOAc (pH 5.2) and 2 volumes of ice cold 100% EtOH. RNA was pelleted (14,000 rpm, 25 min, 4°C), the supernatant removed and the pellet washed with 1 mL 75% cold EtOH (made with DEPC-treated water).   RNA was pelleted (14,000 rpm, 5 min, 4°C) and air dried before suspension in 80 µL RNAse free water (Invitrogen) and treatment with TURBO DNAse (Ambion) according to the manufacturer’s instructions. Briefly, 0.1 V of 10 X Turbo DNAse buffer (Ambion) was added to the RNA solution. 1 µL of TURBO DNAse was added to the solution, which was then incubated (30 min, 37 °C). Following incubation, 0.1 V of DNase Inactivation Reagent (Ambion) was added and then incubated (5 min, RT) with occasional mixing. RNA was isolated and transferred into a fresh microfuge tube.  RNA quality tested using the the Agilent RNA 6000 Nano Kit (Agilent Technologies) and quality analysed using the Agilent 2100 Bioanalyzer (Agilent Technologies). PGCGROWTHCONDITIONS	SRR4255371	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Synchronization was achieved by passaging cells through one or two rounds of stationary phase according to Cutler and Evans 1966 . Briefly : <Gtype> Individual </Gtype> colonies ( LB plate , <Temp> 37 °C </Temp> , 24 h ) were inoculated into M9 media and grown O/N ( <Temp> 37 °C </Temp> , 200 rpm ) . M9 media was inoculated to a final OD600 = 0.25 ( early-logarithmic phase ) . Cultures were grown ( <Temp> 37 °C </Temp> , 200 rpm ) and maintained in stationary phase ( OD600 1.8 ) for <Supp> approximately 2 hours </Supp> . An appropriate amount of each culture was used to inoculate pre-warmed ( <Temp> 37 °C </Temp> ) M9 media to a final OD600 = 0.25 ( approximate 7-fold dilution ) . Released cultures were grown ( <Temp> 37 °C </Temp> , 200 rpm ) and harvested ( time = 0 , 1 hr , or 2 hr ) for GCC and RNA isolation . Samples ( 1 mL ) were also taken for FACS analysis and fluorescence microscopy ( t = 0 , 1 hr , and 2 hr ) . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE87071	The Escherichia coli nucleoid is shaped around replication and transcription [RNA-Seq]	GSM2321586	7G.0		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE87071/GSE87071.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Synchronization was achieved by passaging cells through one or two rounds of stationary phase according to Cutler and Evans 1966. Briefly: Individual colonies (LB plate, 37°C, 24 h) were inoculated into M9 media and grown O/N (37°C, 200 rpm). M9 media was inoculated to a final OD600 = 0.25 (early-logarithmic phase). Cultures were grown (37°C, 200 rpm) and maintained in stationary phase (OD600 1.8) for approximately 2 hours. An appropriate amount of each culture was used to inoculate pre-warmed (37°C) M9 media to a final OD600 = 0.25 (approximate 7-fold dilution). Released cultures were grown (37°C, 200 rpm) and harvested (time = 0, 1 hr, or 2 hr) for GCC and RNA isolation. Samples (1 mL) were also taken for FACS analysis and fluorescence microscopy (t=0, 1 hr, and 2 hr). PGCGROWTHCONDITIONS	SRR4255371	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All strains were grown shaking at <Temp> 37 °C </Temp> in 200mL cultures of <Med> MOPS complete-glucose liquid media </Med> ( unless otherwise annotated ) in 1L flasks and cells were harvested at OD ( 420nm ) between 0.4 - 0.6 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE88725	Global analysis of translation termination in E. coli using release factor manipulations	GSM2344783	WT_exp1_mRNA	28301469	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88725/GSE88725.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All strains were grown shaking at 37°C  in 200mL cultures of MOPS complete-glucose liquid media (unless otherwise annotated) in 1L flasks and cells were harvested at OD(420nm) between 0.4 - 0.6 PGCGROWTHCONDITIONS	SRR4421263	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All strains were grown shaking at <Temp> 37 °C </Temp> in 200mL cultures of <Med> MOPS complete-glucose liquid media </Med> ( unless otherwise annotated ) in 1L flasks and cells were harvested at OD ( 420nm ) between 0.4 - 0.6 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE88725	Global analysis of translation termination in E. coli using release factor manipulations	GSM2344784	WT_exp2_mRNA	28301469	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88725/GSE88725.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All strains were grown shaking at 37°C  in 200mL cultures of MOPS complete-glucose liquid media (unless otherwise annotated) in 1L flasks and cells were harvested at OD(420nm) between 0.4 - 0.6 PGCGROWTHCONDITIONS	SRR4421264	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All strains were grown shaking at <Temp> 37 °C </Temp> in 200mL cultures of <Med> MOPS complete-glucose liquid media </Med> ( unless otherwise annotated ) in 1L flasks and cells were harvested at OD ( 420nm ) between 0.4 - 0.6 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE88725	Global analysis of translation termination in E. coli using release factor manipulations	GSM2344785	WT_exp3_mRNA	28301469	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88725/GSE88725.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All strains were grown shaking at 37°C  in 200mL cultures of MOPS complete-glucose liquid media (unless otherwise annotated) in 1L flasks and cells were harvested at OD(420nm) between 0.4 - 0.6 PGCGROWTHCONDITIONS	SRR4421265SRR4421266	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All strains were grown shaking at <Temp> 37 °C </Temp> in 200mL cultures of <Med> MOPS complete-glucose liquid media </Med> ( unless otherwise annotated ) in 1L flasks and cells were harvested at OD ( 420nm ) between 0.4 - 0.6 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE88725	Global analysis of translation termination in E. coli using release factor manipulations	GSM2344786	WT_exp4_mRNA	28301469	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88725/GSE88725.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All strains were grown shaking at 37°C  in 200mL cultures of MOPS complete-glucose liquid media (unless otherwise annotated) in 1L flasks and cells were harvested at OD(420nm) between 0.4 - 0.6 PGCGROWTHCONDITIONS	SRR4421267	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All strains were grown shaking at <Temp> 37 °C </Temp> in 200mL cultures of <Med> MOPS complete-glucose liquid media </Med> ( unless otherwise annotated ) in 1L flasks and cells were harvested at OD ( 420nm ) between 0.4 - 0.6 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE88725	Global analysis of translation termination in E. coli using release factor manipulations	GSM2344787	∆RF3_exp1_mRNA	28301469	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88725/GSE88725.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All strains were grown shaking at 37°C  in 200mL cultures of MOPS complete-glucose liquid media (unless otherwise annotated) in 1L flasks and cells were harvested at OD(420nm) between 0.4 - 0.6 PGCGROWTHCONDITIONS	SRR4421268	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All strains were grown shaking at <Temp> 37 °C </Temp> in 200mL cultures of <Med> MOPS complete-glucose liquid media </Med> ( unless otherwise annotated ) in 1L flasks and cells were harvested at OD ( 420nm ) between 0.4 - 0.6 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE88725	Global analysis of translation termination in E. coli using release factor manipulations	GSM2344788	∆RF3_exp3_mRNA	28301469	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88725/GSE88725.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All strains were grown shaking at 37°C  in 200mL cultures of MOPS complete-glucose liquid media (unless otherwise annotated) in 1L flasks and cells were harvested at OD(420nm) between 0.4 - 0.6 PGCGROWTHCONDITIONS	SRR4421269SRR4421270	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All strains were grown shaking at <Temp> 37 °C </Temp> in 200mL cultures of <Med> MOPS complete-glucose liquid media </Med> ( unless otherwise annotated ) in 1L flasks and cells were harvested at OD ( 420nm ) between 0.4 - 0.6 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE88725	Global analysis of translation termination in E. coli using release factor manipulations	GSM2344789	RF2*_exp1_mRNA	28301469	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88725/GSE88725.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All strains were grown shaking at 37°C  in 200mL cultures of MOPS complete-glucose liquid media (unless otherwise annotated) in 1L flasks and cells were harvested at OD(420nm) between 0.4 - 0.6 PGCGROWTHCONDITIONS	SRR4421271	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All strains were grown shaking at <Temp> 37 °C </Temp> in 200mL cultures of <Med> MOPS complete-glucose liquid media </Med> ( unless otherwise annotated ) in 1L flasks and cells were harvested at OD ( 420nm ) between 0.4 - 0.6 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE88725	Global analysis of translation termination in E. coli using release factor manipulations	GSM2344790	RF2*_exp3_mRNA	28301469	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88725/GSE88725.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All strains were grown shaking at 37°C  in 200mL cultures of MOPS complete-glucose liquid media (unless otherwise annotated) in 1L flasks and cells were harvested at OD(420nm) between 0.4 - 0.6 PGCGROWTHCONDITIONS	SRR4421272SRR4421273	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All strains were grown shaking at <Temp> 37 °C </Temp> in 200mL cultures of <Med> MOPS complete-glucose liquid media </Med> ( unless otherwise annotated ) in 1L flasks and cells were harvested at OD ( 420nm ) between 0.4 - 0.6 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE88725	Global analysis of translation termination in E. coli using release factor manipulations	GSM2344791	RF2*∆RF3_exp2_repA_mRNA	28301469	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88725/GSE88725.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All strains were grown shaking at 37°C  in 200mL cultures of MOPS complete-glucose liquid media (unless otherwise annotated) in 1L flasks and cells were harvested at OD(420nm) between 0.4 - 0.6 PGCGROWTHCONDITIONS	SRR4421274	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All strains were grown shaking at <Temp> 37 °C </Temp> in 200mL cultures of <Med> MOPS complete-glucose liquid media </Med> ( unless otherwise annotated ) in 1L flasks and cells were harvested at OD ( 420nm ) between 0.4 - 0.6 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE88725	Global analysis of translation termination in E. coli using release factor manipulations	GSM2344792	RF2*∆RF3_exp2_repB_mRNA	28301469	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88725/GSE88725.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All strains were grown shaking at 37°C  in 200mL cultures of MOPS complete-glucose liquid media (unless otherwise annotated) in 1L flasks and cells were harvested at OD(420nm) between 0.4 - 0.6 PGCGROWTHCONDITIONS	SRR4421275	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All strains were grown shaking at <Temp> 37 °C </Temp> in 200mL cultures of <Med> MOPS complete-glucose liquid media </Med> ( unless otherwise annotated ) in 1L flasks and cells were harvested at OD ( 420nm ) between 0.4 - 0.6 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE88725	Global analysis of translation termination in E. coli using release factor manipulations	GSM2344793	RF2*∆RF3_exp3_mRNA	28301469	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88725/GSE88725.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All strains were grown shaking at 37°C  in 200mL cultures of MOPS complete-glucose liquid media (unless otherwise annotated) in 1L flasks and cells were harvested at OD(420nm) between 0.4 - 0.6 PGCGROWTHCONDITIONS	SRR4421276SRR4421277	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All strains were grown shaking at <Temp> 37 °C </Temp> in 200mL cultures of <Med> MOPS complete-glucose liquid media </Med> ( unless otherwise annotated ) in 1L flasks and cells were harvested at OD ( 420nm ) between 0.4 - 0.6 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE88725	Global analysis of translation termination in E. coli using release factor manipulations	GSM2344794	RF2*∆RF3_exp4_repA_mRNA	28301469	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88725/GSE88725.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All strains were grown shaking at 37°C  in 200mL cultures of MOPS complete-glucose liquid media (unless otherwise annotated) in 1L flasks and cells were harvested at OD(420nm) between 0.4 - 0.6 PGCGROWTHCONDITIONS	SRR4421278	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All strains were grown shaking at <Temp> 37 °C </Temp> in 200mL cultures of <Med> MOPS complete-glucose liquid media </Med> ( unless otherwise annotated ) in 1L flasks and cells were harvested at OD ( 420nm ) between 0.4 - 0.6 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE88725	Global analysis of translation termination in E. coli using release factor manipulations	GSM2344795	RF2*∆RF3_exp4_repB_mRNA	28301469	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88725/GSE88725.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All strains were grown shaking at 37°C  in 200mL cultures of MOPS complete-glucose liquid media (unless otherwise annotated) in 1L flasks and cells were harvested at OD(420nm) between 0.4 - 0.6 PGCGROWTHCONDITIONS	SRR4421279	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All strains were grown shaking at <Temp> 37 °C </Temp> in 200mL cultures of <Med> MOPS complete-glucose liquid media </Med> ( unless otherwise annotated ) in 1L flasks and cells were harvested at OD ( 420nm ) between 0.4 - 0.6 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE88725	Global analysis of translation termination in E. coli using release factor manipulations	GSM2344809	WT_minimal_mRNA	28301469	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88725/GSE88725.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All strains were grown shaking at 37°C  in 200mL cultures of MOPS complete-glucose liquid media (unless otherwise annotated) in 1L flasks and cells were harvested at OD(420nm) between 0.4 - 0.6 PGCGROWTHCONDITIONS	SRR4421297	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		All strains were grown shaking at <Temp> 37 °C </Temp> in 200mL cultures of <Med> MOPS complete-glucose liquid media </Med> ( unless otherwise annotated ) in 1L flasks and cells were harvested at OD ( 420nm ) between 0.4 - 0.6 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE88725	Global analysis of translation termination in E. coli using release factor manipulations	GSM2344810	∆RF3_minimal_mRNA	28301469	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88725/GSE88725.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	All strains were grown shaking at 37°C  in 200mL cultures of MOPS complete-glucose liquid media (unless otherwise annotated) in 1L flasks and cells were harvested at OD(420nm) between 0.4 - 0.6 PGCGROWTHCONDITIONS	SRR4421298	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . For culture tube assays ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) , cells were diluted 658-fold ( 4.56 µL into 3 mL ) into EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE88835	Genetic circuit 0x58	GSM2349915	Tube state 1 (IPTG-/aTc-/Ara-)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR4427755	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . For culture tube assays ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) , cells were diluted 658-fold ( 4.56 µL into 3 mL ) into EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE88835	Genetic circuit 0x58	GSM2349916	Tube state 2 (IPTG+/aTc-/Ara-)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR4427756	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . For culture tube assays ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) , cells were diluted 658-fold ( 4.56 µL into 3 mL ) into EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE88835	Genetic circuit 0x58	GSM2349917	Tube state 3 (IPTG-/aTc+/Ara-)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR4427757	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . For culture tube assays ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) , cells were diluted 658-fold ( 4.56 µL into 3 mL ) into EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE88835	Genetic circuit 0x58	GSM2349918	Tube state 4 (IPTG+/aTc+/Ara-)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR4427758	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . For culture tube assays ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) , cells were diluted 658-fold ( 4.56 µL into 3 mL ) into EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE88835	Genetic circuit 0x58	GSM2349919	Tube state 5 (IPTG-/aTc-/Ara+)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR4427759	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . For culture tube assays ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) , cells were diluted 658-fold ( 4.56 µL into 3 mL ) into EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE88835	Genetic circuit 0x58	GSM2349920	Tube state 6 (IPTG+/aTc-/Ara+)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR4427760	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . For culture tube assays ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) , cells were diluted 658-fold ( 4.56 µL into 3 mL ) into EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE88835	Genetic circuit 0x58	GSM2349921	Tube state 7 (IPTG-/aTc+/Ara+)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR4427761	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . For culture tube assays ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) , cells were diluted 658-fold ( 4.56 µL into 3 mL ) into EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE88835	Genetic circuit 0x58	GSM2349922	Tube state 8 (IPTG+/aTc+/Ara+)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR4427762	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . For culture tube assays ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) , cells were diluted 658-fold ( 4.56 µL into 3 mL ) into EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE88835	Genetic circuit 0x58	GSM2349923	Flask state 1 (IPTG-/aTc-/Ara-)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR4427763	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . For culture tube assays ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) , cells were diluted 658-fold ( 4.56 µL into 3 mL ) into EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE88835	Genetic circuit 0x58	GSM2349924	Flask state 2 (IPTG+/aTc-/Ara-)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR4427764	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . For culture tube assays ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) , cells were diluted 658-fold ( 4.56 µL into 3 mL ) into EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE88835	Genetic circuit 0x58	GSM2349925	Flask state 3 (IPTG-/aTc+/Ara-)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR4427765	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . For culture tube assays ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) , cells were diluted 658-fold ( 4.56 µL into 3 mL ) into EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE88835	Genetic circuit 0x58	GSM2349926	Flask state 4 (IPTG+/aTc+/Ara-)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR4427766	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . For culture tube assays ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) , cells were diluted 658-fold ( 4.56 µL into 3 mL ) into EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE88835	Genetic circuit 0x58	GSM2349927	Flask state 5 (IPTG-/aTc-/Ara+)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR4427767	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . For culture tube assays ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) , cells were diluted 658-fold ( 4.56 µL into 3 mL ) into EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE88835	Genetic circuit 0x58	GSM2349928	Flask state 6 (IPTG+/aTc-/Ara+)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR4427768	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . For culture tube assays ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) , cells were diluted 658-fold ( 4.56 µL into 3 mL ) into EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE88835	Genetic circuit 0x58	GSM2349929	Flask state 7 (IPTG-/aTc+/Ara+)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR4427769	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . For culture tube assays ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) , cells were diluted 658-fold ( 4.56 µL into 3 mL ) into EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE88835	Genetic circuit 0x58	GSM2349930	Flask state 8 (IPTG+/aTc+/Ara+)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR4427770	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT and ΔompR were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . Then cells were treated with <Supp> 0.3 M of NaCl </Supp> at mid-log pahse for <Supp> 30 min </Supp> with agitation . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE88980	Revealing the genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles and unexpected importance of narU under osmotic stress in Escherichia coli K-12 MG1655 [RNA-seq]	GSM2356687	WT NaCl 1	28526842	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88980/GSE88980.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT and ΔompR were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 0.3 M of NaCl at mid-log pahse for 30 min with agitation. PGCGROWTHCONDITIONS	SRR4435464	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT and ΔompR were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . Then cells were treated with <Supp> 0.3 M of NaCl </Supp> at mid-log pahse for <Supp> 30 min </Supp> with agitation . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE88980	Revealing the genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles and unexpected importance of narU under osmotic stress in Escherichia coli K-12 MG1655 [RNA-seq]	GSM2356688	WT NaCl 2	28526842	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88980/GSE88980.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT and ΔompR were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 0.3 M of NaCl at mid-log pahse for 30 min with agitation. PGCGROWTHCONDITIONS	SRR4435465	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT and ΔompR were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . Then cells were treated with <Supp> 0.3 M of NaCl </Supp> at mid-log pahse for <Supp> 30 min </Supp> with agitation . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE88980	Revealing the genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles and unexpected importance of narU under osmotic stress in Escherichia coli K-12 MG1655 [RNA-seq]	GSM2356689	ΔompR NaCl 1	28526842	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88980/GSE88980.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT and ΔompR were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 0.3 M of NaCl at mid-log pahse for 30 min with agitation. PGCGROWTHCONDITIONS	SRR4435466	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K-12 MG1655 WT and ΔompR were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . Then cells were treated with <Supp> 0.3 M of NaCl </Supp> at mid-log pahse for <Supp> 30 min </Supp> with agitation . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE88980	Revealing the genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles and unexpected importance of narU under osmotic stress in Escherichia coli K-12 MG1655 [RNA-seq]	GSM2356690	ΔompR NaCl 2	28526842	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88980/GSE88980.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT and ΔompR were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 0.3 M of NaCl at mid-log pahse for 30 min with agitation. PGCGROWTHCONDITIONS	SRR4435467	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411669	chemostat STR-PFR culture STR 5min, rep1	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071589	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411670	chemostat STR-PFR culture STR 10min, rep1	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071590	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411671	chemostat STR-PFR culture STR 25min, rep1	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071591	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411672	chemostat STR-PFR culture STR 45min, rep1	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071592	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411673	chemostat STR-PFR culture STR 75min, rep1	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071593	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411674	chemostat STR-PFR culture STR 120min, rep1	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071594	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411675	chemostat STR-PFR culture STR 210min, rep1	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071595	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411676	chemostat STR-PFR culture STR 330min, rep1	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071596	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411677	chemostat STR-PFR culture STR 25h, rep1	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071597	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411678	chemostat STR-PFR culture STR 26h, rep1	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071598	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411679	chemostat STR-PFR culture STR 28h, rep1	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071599	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411680	chemostat STR culture STR  reference 1, rep1	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071600	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411681	chemostat STR culture STR  reference 2, rep1	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071601	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411682	chemostat STR culture STR  reference 3, rep1	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071602	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411683	chemostat STR-PFR culture PFR P5 5min, rep1	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071603	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411684	chemostat STR-PFR culture PFR P5 10min, rep1	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071604	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411685	chemostat STR-PFR culture PFR P5 25min, rep1	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071605	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411686	chemostat STR-PFR culture PFR P3 25min, rep1	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071606	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411687	chemostat STR-PFR culture PFR P1 25min, rep1	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071607	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411688	chemostat STR-PFR culture PFR P5 45min, rep1	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071608	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411689	chemostat STR-PFR culture PFR P5 120min, rep1	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071609	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411690	chemostat STR-PFR culture PFR P3 120min, rep1	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071610	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411691	chemostat STR-PFR culture PFR P1 120min, rep1	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071611	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411692	chemostat STR-PFR culture PFR P5 210min, rep1	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071612	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411693	chemostat STR-PFR culture PFR P5 25h, rep1	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071613	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411694	chemostat STR-PFR culture PFR P3 28h, rep1	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071614	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411695	chemostat STR-PFR culture PFR P5 28h, rep1	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071615	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411696	chemostat STR-PFR culture PFR P1 28h, rep1	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071616	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411697	chemostat STR-PFR culture STR 5min, rep2	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071617	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411698	chemostat STR-PFR culture STR 10min, rep2	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071618	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411699	chemostat STR-PFR culture STR 25min, rep2	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071619	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411700	chemostat STR-PFR culture STR 45min, rep2	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071620	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411701	chemostat STR-PFR culture STR 75min, rep2	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071621	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411702	chemostat STR-PFR culture STR 120min, rep2	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071622	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411703	chemostat STR-PFR culture STR 210min, rep2	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071623	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411704	chemostat STR-PFR culture STR 330min, rep2	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071624	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411705	chemostat STR-PFR culture STR 25h, rep2	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071625	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411706	chemostat STR-PFR culture STR 26h, rep2	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071626	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411707	chemostat STR-PFR culture STR 28h, rep2	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071627	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411708	chemostat STR culture STR reference 1 , rep2	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071628	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411709	chemostat STR culture STR reference 2 , rep2	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071629	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411710	chemostat STR culture STR reference 3 , rep2	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071630	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411711	chemostat STR-PFR culture PFR P5 5min, rep2	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071631	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411712	chemostat STR-PFR culture PFR P5 10min, rep2	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071632	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411713	chemostat STR-PFR culture PFR P5 25min, rep2	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071633	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411714	chemostat STR-PFR culture PFR P3 25min, rep2	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071634	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411715	chemostat STR-PFR culture PFR P1 25min, rep2	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071635	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411716	chemostat STR-PFR culture PFR P5 45min, rep2	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071636	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411717	chemostat STR-PFR culture PFR P5 75min, rep2	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071637	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411718	chemostat STR-PFR culture PFR P5 120min, rep2	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071638	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411719	chemostat STR-PFR culture PFR P3 120min, rep2	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071639	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411720	chemostat STR-PFR culture PFR P1 120min, rep2	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071640	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411721	chemostat STR-PFR culture PFR P5 210min, rep2	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071641	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411722	chemostat STR-PFR culture PFR P5 330min, rep2	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071642	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411723	chemostat STR-PFR culture PFR P5 25h, rep2	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071643	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411724	chemostat STR-PFR culture PFR P5 26h, rep2	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071644	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411725	chemostat STR-PFR culture PFR P5 28h, rep2	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071645	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411726	chemostat STR-PFR culture PFR P3 28h, rep2	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071646	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli K12 substrain W3110 was used in this study . Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR ( 3L ) with a recycle loop ( PFR ) in defined medium at pH7 and <Temp> 37 °C </Temp> . Bioreactor cultivations were carried out with a minimal medium containing ( per liter ) 19.0 g glucose , 1.0 g NaH2PO4 . · 2 H2O , 2.6 g K2HPO4 , 3.8 g ( NH4 ) 2SO4 , and a trace element solution ( 0.11 g Na3C6H5O7 , 0.00835 g FeCl3 · 6 H2O , 0.00009 g ZnSO4 · 7 H2O , 0.00005 g MnSO4 · H2O , 0.0008 g CuSO4 · 5 H2O , 0.00009 g CoCl2 · 6 H2O , 0.0044 g CaCl2 · 2 H2O , 0.1 g MgSO4 · 7 H2O ) . The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate . First , a reference steady state ( µ = 0.2 h − 1 ) was established in the STR and sampled three times during a 16 h period following establishment of the steady state . Then , the PFR was added and samples for RNA-sequencing were aquired . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE90743	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GSM2411727	chemostat STR-PFR culture PFR P1 28h, rep2	2844739128702020	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 substrain W3110 was used in this study. Bioreactor cultivations were performed using a two-compartment bioreactor system consisting of an STR (3L) with a recycle loop (PFR)  in defined medium at pH7 and 37°C. Bioreactor cultivations were carried out with a minimal medium containing (per liter) 19.0 g glucose, 1.0 g NaH2PO4.· 2 H2O, 2.6 g K2HPO4, 3.8 g (NH4)2SO4, and a trace element solution (0.11 g Na3C6H5O7, 0.00835 g FeCl3· 6 H2O, 0.00009 g ZnSO4· 7 H2O, 0.00005 g MnSO4· H2O, 0.0008 g CuSO4· 5 H2O, 0.00009 g CoCl2· 6 H2O, 0.0044 g CaCl2· 2 H2O, 0.1 g MgSO4· 7 H2O). The STR-PFR was operated as a chemostat with ammonia as the growth-limiting substrate. First, a reference steady state (µ=0.2 h−1) was established in the STR and sampled three times during a 16 h period following establishment of the steady state. Then, the PFR was added and samples for RNA-sequencing were aquired. PGCGROWTHCONDITIONS	SRR5071647	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli TolC cells were grown o/n in LB medium at <Temp> 37 °C </Temp> and 200 rpm . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE93125	Transcriptomal changes of Escherichia coli TolC grown with the biofilm inhibitor Carolacton	GSM2445135	Eco_TolC_0min_A	28959742	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE93125/GSE93125.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS	SRR5143857	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli TolC cells were grown o/n in LB medium at <Temp> 37 °C </Temp> and 200 rpm . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE93125	Transcriptomal changes of Escherichia coli TolC grown with the biofilm inhibitor Carolacton	GSM2445138	Eco_TolC_0min_B	28959742	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE93125/GSE93125.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS	SRR5143858	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli TolC cells were grown o/n in LB medium at <Temp> 37 °C </Temp> and 200 rpm . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE93125	Transcriptomal changes of Escherichia coli TolC grown with the biofilm inhibitor Carolacton	GSM2445140	Eco_TolC_5min_control_A	28959742	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE93125/GSE93125.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS	SRR5143859	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli TolC cells were grown o/n in LB medium at <Temp> 37 °C </Temp> and 200 rpm . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE93125	Transcriptomal changes of Escherichia coli TolC grown with the biofilm inhibitor Carolacton	GSM2445142	Eco_TolC_5min_control_B	28959742	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE93125/GSE93125.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS	SRR5143860	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli TolC cells were grown o/n in LB medium at <Temp> 37 °C </Temp> and 200 rpm . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE93125	Transcriptomal changes of Escherichia coli TolC grown with the biofilm inhibitor Carolacton	GSM2445144	Eco_TolC_5min_Carolacton_A	28959742	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE93125/GSE93125.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS	SRR5143861	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli TolC cells were grown o/n in LB medium at <Temp> 37 °C </Temp> and 200 rpm . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE93125	Transcriptomal changes of Escherichia coli TolC grown with the biofilm inhibitor Carolacton	GSM2445145	Eco_TolC_5min_Carolacton_B	28959742	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE93125/GSE93125.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS	SRR5143862	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli TolC cells were grown o/n in LB medium at <Temp> 37 °C </Temp> and 200 rpm . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE93125	Transcriptomal changes of Escherichia coli TolC grown with the biofilm inhibitor Carolacton	GSM2445147	Eco_TolC_15min_control_A	28959742	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE93125/GSE93125.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS	SRR5143863	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli TolC cells were grown o/n in LB medium at <Temp> 37 °C </Temp> and 200 rpm . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE93125	Transcriptomal changes of Escherichia coli TolC grown with the biofilm inhibitor Carolacton	GSM2445149	Eco_TolC_15min_control_B	28959742	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE93125/GSE93125.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS	SRR5143864	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli TolC cells were grown o/n in LB medium at <Temp> 37 °C </Temp> and 200 rpm . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE93125	Transcriptomal changes of Escherichia coli TolC grown with the biofilm inhibitor Carolacton	GSM2445151	Eco_TolC_15min_Carolacton_A	28959742	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE93125/GSE93125.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS	SRR5143865	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli TolC cells were grown o/n in LB medium at <Temp> 37 °C </Temp> and 200 rpm . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE93125	Transcriptomal changes of Escherichia coli TolC grown with the biofilm inhibitor Carolacton	GSM2445153	Eco_TolC_15min_Carolacton_B	28959742	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE93125/GSE93125.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS	SRR5143866	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli TolC cells were grown o/n in LB medium at <Temp> 37 °C </Temp> and 200 rpm . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE93125	Transcriptomal changes of Escherichia coli TolC grown with the biofilm inhibitor Carolacton	GSM2445155	Eco_TolC_30min_control_A	28959742	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE93125/GSE93125.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS	SRR5143868	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli TolC cells were grown o/n in LB medium at <Temp> 37 °C </Temp> and 200 rpm . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE93125	Transcriptomal changes of Escherichia coli TolC grown with the biofilm inhibitor Carolacton	GSM2445157	Eco_TolC_30min_control_B	28959742	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE93125/GSE93125.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS	SRR5143869	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli TolC cells were grown o/n in LB medium at <Temp> 37 °C </Temp> and 200 rpm . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE93125	Transcriptomal changes of Escherichia coli TolC grown with the biofilm inhibitor Carolacton	GSM2445159	Eco_TolC_30min_Carolacton_A	28959742	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE93125/GSE93125.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS	SRR5143870	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		E. coli TolC cells were grown o/n in LB medium at <Temp> 37 °C </Temp> and 200 rpm . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE93125	Transcriptomal changes of Escherichia coli TolC grown with the biofilm inhibitor Carolacton	GSM2445161	Eco_TolC_30min_Carolacton_B	28959742	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE93125/GSE93125.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS	SRR5143871	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		LB medium , 180 rpm shaking , at <Temp> 37 °C </Temp> , between exponential and <Phase> stationary phase </Phase> 	GPL23073	GPL23073: Illumina MiSeq (Escherichia coli O157:H7 str. EDL933)	GSE94984	Differentiation of ncRNAs from small mRNAs in Escherichia coli O157:H7 EDL933 (EHEC) by combined RNAseq and RIBOseq – ryhB encodes the regulatory RNA RyhB and a peptide, RyhP	GSM2493797	EHEC in LB Experiment 2 [RNA-Seq]	28245801	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE94984/GSE94984.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	LB medium, 180 rpm shaking, at 37°C, between exponential and stationary phase PGCGROWTHCONDITIONS	SRR5266619	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516609	1A_MG_t0	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304286	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516610	2A_MG_t10	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304287	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516611	3A_MG_t30	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304288	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516612	4A_MG_t60	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304289	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516613	5A_MG+Hg_t10	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304290	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516614	6A_MG+Hg_t30	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304291	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516615	7A_MG+Hg_t60	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304292	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516616	8A_MG+PMA_t10	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304293	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516617	9A_MG+PMA_t30	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304294	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516618	10A_MG+PMA_t60	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304295	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516619	1B_MG_t0	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304296	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516620	2B_MG_t10	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304297	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516621	3B_MG_t30	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304298	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516622	4B_MG_t60	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304299	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516623	5B_MG+Hg_t10	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304300	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516624	6B_MG+Hg_t30	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304301	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516625	7B_MG+Hg_t60	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304302	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516626	8B_MG+PMA_t10	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304303	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516627	9B_MG+PMA_t30	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304304	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516628	10B_MG+PMA_t60	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304305	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516629	1C_MG_t0	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304306	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516630	2C_MG_t10	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304307	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516631	3C_MG_t30	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304308	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516632	4C_MG_t60	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304309	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516633	5C_MG+Hg_t10	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304310	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516634	6C_MG+Hg_t30	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304311	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516635	7C_MG+Hg_t60	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304312	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516636	8C_MG+PMA_t10	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304313	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516637	9C_MG+PMA_t30	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304314	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516638	10C_MG+PMA_t60	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304315	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . Cells were diluted 658-fold ( 4.56 µL into 3 mL ) into culture tubes ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) containing EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE98890	Genetic circuit 0x58 replicates and modified	GSM2757255	0x58 replicate 2 state 1 (IPTG-/aTc-/Ara-)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR5985582	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . Cells were diluted 658-fold ( 4.56 µL into 3 mL ) into culture tubes ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) containing EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE98890	Genetic circuit 0x58 replicates and modified	GSM2757256	0x58 replicate 2 state 2 (IPTG+/aTc-/Ara-)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR5985583	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . Cells were diluted 658-fold ( 4.56 µL into 3 mL ) into culture tubes ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) containing EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE98890	Genetic circuit 0x58 replicates and modified	GSM2757257	0x58 replicate 2 state 3 (IPTG-/aTc+/Ara-)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR5985584	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . Cells were diluted 658-fold ( 4.56 µL into 3 mL ) into culture tubes ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) containing EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE98890	Genetic circuit 0x58 replicates and modified	GSM2757258	0x58 replicate 2 state 4 (IPTG+/aTc+/Ara-)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR5985585	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . Cells were diluted 658-fold ( 4.56 µL into 3 mL ) into culture tubes ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) containing EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE98890	Genetic circuit 0x58 replicates and modified	GSM2757259	0x58 replicate 2 state 5 (IPTG-/aTc-/Ara+)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR5985586	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . Cells were diluted 658-fold ( 4.56 µL into 3 mL ) into culture tubes ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) containing EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE98890	Genetic circuit 0x58 replicates and modified	GSM2757260	0x58 replicate 2 state 6 (IPTG+/aTc-/Ara+)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR5985587	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . Cells were diluted 658-fold ( 4.56 µL into 3 mL ) into culture tubes ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) containing EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE98890	Genetic circuit 0x58 replicates and modified	GSM2757261	0x58 replicate 2 state 7 (IPTG-/aTc+/Ara+)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR5985588	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . Cells were diluted 658-fold ( 4.56 µL into 3 mL ) into culture tubes ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) containing EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE98890	Genetic circuit 0x58 replicates and modified	GSM2757262	0x58 replicate 2 state 8 (IPTG+/aTc+/Ara+)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR5985589	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . Cells were diluted 658-fold ( 4.56 µL into 3 mL ) into culture tubes ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) containing EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE98890	Genetic circuit 0x58 replicates and modified	GSM2757263	0x58 replicate 3 state 1 (IPTG-/aTc-/Ara-)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR5985590	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . Cells were diluted 658-fold ( 4.56 µL into 3 mL ) into culture tubes ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) containing EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE98890	Genetic circuit 0x58 replicates and modified	GSM2757264	0x58 replicate 3 state 2 (IPTG+/aTc-/Ara-)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR5985591	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . Cells were diluted 658-fold ( 4.56 µL into 3 mL ) into culture tubes ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) containing EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE98890	Genetic circuit 0x58 replicates and modified	GSM2757265	0x58 replicate 3 state 3 (IPTG-/aTc+/Ara-)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR5985592	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . Cells were diluted 658-fold ( 4.56 µL into 3 mL ) into culture tubes ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) containing EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE98890	Genetic circuit 0x58 replicates and modified	GSM2757266	0x58 replicate 3 state 4 (IPTG+/aTc+/Ara-)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR5985593	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . Cells were diluted 658-fold ( 4.56 µL into 3 mL ) into culture tubes ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) containing EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE98890	Genetic circuit 0x58 replicates and modified	GSM2757267	0x58 replicate 3 state 5 (IPTG-/aTc-/Ara+)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR5985594	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . Cells were diluted 658-fold ( 4.56 µL into 3 mL ) into culture tubes ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) containing EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE98890	Genetic circuit 0x58 replicates and modified	GSM2757268	0x58 replicate 3 state 6 (IPTG+/aTc-/Ara+)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR5985595	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . Cells were diluted 658-fold ( 4.56 µL into 3 mL ) into culture tubes ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) containing EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE98890	Genetic circuit 0x58 replicates and modified	GSM2757269	0x58 replicate 3 state 7 (IPTG-/aTc+/Ara+)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR5985596	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . Cells were diluted 658-fold ( 4.56 µL into 3 mL ) into culture tubes ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) containing EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE98890	Genetic circuit 0x58 replicates and modified	GSM2757270	0x58 replicate 3 state 8 (IPTG+/aTc+/Ara+)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR5985597	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . Cells were diluted 658-fold ( 4.56 µL into 3 mL ) into culture tubes ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) containing EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE98890	Genetic circuit 0x58 replicates and modified	GSM2757272	Control pAN1201 replicate 1 (IPTG-/aTc-/Ara-)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR5985599	MCO000003199	37 °C	Temperature	True
growth_protocol	35.7 C		Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . Cells were diluted 658-fold ( 4.56 µL into 3 mL ) into culture tubes ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) containing EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE98890	Genetic circuit 0x58 replicates and modified	GSM2757273	Control pAN1201 replicate 2 (IPTG-/aTc-/Ara-)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR5985600	MCO000003199	37 °C	Temperature	True
treatment_protocol	iptg		Starting from single colonies , the following cultures were set up in triplicate for overnight incubation : GJ13507 , GJ13531 , and GJ13533 in glucose-minimal A ; and GJ13519 also in 0.2 % glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG , with the exception of the cultures of GJ13507 whose supplementation with <Supp> IPTG was </Supp> at 3 μM . The overnight-grown cultures were each subcultured into 20 ml <Med> of fresh medium </Med> of the same composition , with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder , and grown to an A600 of 0.4 to 0.45 , before the cells were harvested for making the RNA preparations 	GPL24020	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	GSE103937	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GSM2786596	WT glucose_replicate1	29474582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Starting from single colonies, the following cultures were set up in triplicate for overnight incubation: GJ13507, GJ13531, and GJ13533 in glucose-minimal A; and GJ13519 also in 0.2% glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG, with the exception of the cultures of GJ13507 whose supplementation with IPTG was at 3 μM. The overnight-grown cultures were each subcultured into 20 ml of fresh medium of the same composition, with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder, and grown to an A600 of 0.4 to 0.45, before the cells were harvested for making the RNA preparations PGCGROWTHCONDITIONS	SRR6048166	MCO000002105	IPTG was	Medium supplement	True
treatment_protocol	iptg		Starting from single colonies , the following cultures were set up in triplicate for overnight incubation : GJ13507 , GJ13531 , and GJ13533 in glucose-minimal A ; and GJ13519 also in 0.2 % glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG , with the exception of the cultures of GJ13507 whose supplementation with <Supp> IPTG was </Supp> at 3 μM . The overnight-grown cultures were each subcultured into 20 ml <Med> of fresh medium </Med> of the same composition , with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder , and grown to an A600 of 0.4 to 0.45 , before the cells were harvested for making the RNA preparations 	GPL24020	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	GSE103937	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GSM2786597	WT glucose_replicate2	29474582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Starting from single colonies, the following cultures were set up in triplicate for overnight incubation: GJ13507, GJ13531, and GJ13533 in glucose-minimal A; and GJ13519 also in 0.2% glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG, with the exception of the cultures of GJ13507 whose supplementation with IPTG was at 3 μM. The overnight-grown cultures were each subcultured into 20 ml of fresh medium of the same composition, with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder, and grown to an A600 of 0.4 to 0.45, before the cells were harvested for making the RNA preparations PGCGROWTHCONDITIONS	SRR6048167	MCO000002105	IPTG was	Medium supplement	True
treatment_protocol	iptg		Starting from single colonies , the following cultures were set up in triplicate for overnight incubation : GJ13507 , GJ13531 , and GJ13533 in glucose-minimal A ; and GJ13519 also in 0.2 % glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG , with the exception of the cultures of GJ13507 whose supplementation with <Supp> IPTG was </Supp> at 3 μM . The overnight-grown cultures were each subcultured into 20 ml <Med> of fresh medium </Med> of the same composition , with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder , and grown to an A600 of 0.4 to 0.45 , before the cells were harvested for making the RNA preparations 	GPL24020	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	GSE103937	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GSM2786598	WT glucose_replicate3	29474582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Starting from single colonies, the following cultures were set up in triplicate for overnight incubation: GJ13507, GJ13531, and GJ13533 in glucose-minimal A; and GJ13519 also in 0.2% glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG, with the exception of the cultures of GJ13507 whose supplementation with IPTG was at 3 μM. The overnight-grown cultures were each subcultured into 20 ml of fresh medium of the same composition, with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder, and grown to an A600 of 0.4 to 0.45, before the cells were harvested for making the RNA preparations PGCGROWTHCONDITIONS	SRR6048168	MCO000002105	IPTG was	Medium supplement	True
treatment_protocol	iptg		Starting from single colonies , the following cultures were set up in triplicate for overnight incubation : GJ13507 , GJ13531 , and GJ13533 in glucose-minimal A ; and GJ13519 also in 0.2 % glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG , with the exception of the cultures of GJ13507 whose supplementation with <Supp> IPTG was </Supp> at 3 μM . The overnight-grown cultures were each subcultured into 20 ml <Med> of fresh medium </Med> of the same composition , with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder , and grown to an A600 of 0.4 to 0.45 , before the cells were harvested for making the RNA preparations 	GPL24020	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	GSE103937	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GSM2786599	WT_glycerol_replicate1	29474582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Starting from single colonies, the following cultures were set up in triplicate for overnight incubation: GJ13507, GJ13531, and GJ13533 in glucose-minimal A; and GJ13519 also in 0.2% glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG, with the exception of the cultures of GJ13507 whose supplementation with IPTG was at 3 μM. The overnight-grown cultures were each subcultured into 20 ml of fresh medium of the same composition, with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder, and grown to an A600 of 0.4 to 0.45, before the cells were harvested for making the RNA preparations PGCGROWTHCONDITIONS	SRR6048169	MCO000002105	IPTG was	Medium supplement	True
treatment_protocol	iptg		Starting from single colonies , the following cultures were set up in triplicate for overnight incubation : GJ13507 , GJ13531 , and GJ13533 in glucose-minimal A ; and GJ13519 also in 0.2 % glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG , with the exception of the cultures of GJ13507 whose supplementation with <Supp> IPTG was </Supp> at 3 μM . The overnight-grown cultures were each subcultured into 20 ml <Med> of fresh medium </Med> of the same composition , with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder , and grown to an A600 of 0.4 to 0.45 , before the cells were harvested for making the RNA preparations 	GPL24020	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	GSE103937	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GSM2786600	WT_glycerol_replicate2	29474582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Starting from single colonies, the following cultures were set up in triplicate for overnight incubation: GJ13507, GJ13531, and GJ13533 in glucose-minimal A; and GJ13519 also in 0.2% glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG, with the exception of the cultures of GJ13507 whose supplementation with IPTG was at 3 μM. The overnight-grown cultures were each subcultured into 20 ml of fresh medium of the same composition, with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder, and grown to an A600 of 0.4 to 0.45, before the cells were harvested for making the RNA preparations PGCGROWTHCONDITIONS	SRR6048170	MCO000002105	IPTG was	Medium supplement	True
treatment_protocol	iptg		Starting from single colonies , the following cultures were set up in triplicate for overnight incubation : GJ13507 , GJ13531 , and GJ13533 in glucose-minimal A ; and GJ13519 also in 0.2 % glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG , with the exception of the cultures of GJ13507 whose supplementation with <Supp> IPTG was </Supp> at 3 μM . The overnight-grown cultures were each subcultured into 20 ml <Med> of fresh medium </Med> of the same composition , with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder , and grown to an A600 of 0.4 to 0.45 , before the cells were harvested for making the RNA preparations 	GPL24020	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	GSE103937	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GSM2786601	WT_glycerol_replicate3	29474582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Starting from single colonies, the following cultures were set up in triplicate for overnight incubation: GJ13507, GJ13531, and GJ13533 in glucose-minimal A; and GJ13519 also in 0.2% glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG, with the exception of the cultures of GJ13507 whose supplementation with IPTG was at 3 μM. The overnight-grown cultures were each subcultured into 20 ml of fresh medium of the same composition, with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder, and grown to an A600 of 0.4 to 0.45, before the cells were harvested for making the RNA preparations PGCGROWTHCONDITIONS	SRR6048171	MCO000002105	IPTG was	Medium supplement	True
treatment_protocol	iptg		Starting from single colonies , the following cultures were set up in triplicate for overnight incubation : GJ13507 , GJ13531 , and GJ13533 in glucose-minimal A ; and GJ13519 also in 0.2 % glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG , with the exception of the cultures of GJ13507 whose supplementation with <Supp> IPTG was </Supp> at 3 μM . The overnight-grown cultures were each subcultured into 20 ml <Med> of fresh medium </Med> of the same composition , with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder , and grown to an A600 of 0.4 to 0.45 , before the cells were harvested for making the RNA preparations 	GPL24020	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	GSE103937	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GSM2786602	WT UvsW_replicate1	29474582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Starting from single colonies, the following cultures were set up in triplicate for overnight incubation: GJ13507, GJ13531, and GJ13533 in glucose-minimal A; and GJ13519 also in 0.2% glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG, with the exception of the cultures of GJ13507 whose supplementation with IPTG was at 3 μM. The overnight-grown cultures were each subcultured into 20 ml of fresh medium of the same composition, with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder, and grown to an A600 of 0.4 to 0.45, before the cells were harvested for making the RNA preparations PGCGROWTHCONDITIONS	SRR6048172	MCO000002105	IPTG was	Medium supplement	True
treatment_protocol	iptg		Starting from single colonies , the following cultures were set up in triplicate for overnight incubation : GJ13507 , GJ13531 , and GJ13533 in glucose-minimal A ; and GJ13519 also in 0.2 % glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG , with the exception of the cultures of GJ13507 whose supplementation with <Supp> IPTG was </Supp> at 3 μM . The overnight-grown cultures were each subcultured into 20 ml <Med> of fresh medium </Med> of the same composition , with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder , and grown to an A600 of 0.4 to 0.45 , before the cells were harvested for making the RNA preparations 	GPL24020	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	GSE103937	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GSM2786603	WT UvsW_replicate2	29474582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Starting from single colonies, the following cultures were set up in triplicate for overnight incubation: GJ13507, GJ13531, and GJ13533 in glucose-minimal A; and GJ13519 also in 0.2% glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG, with the exception of the cultures of GJ13507 whose supplementation with IPTG was at 3 μM. The overnight-grown cultures were each subcultured into 20 ml of fresh medium of the same composition, with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder, and grown to an A600 of 0.4 to 0.45, before the cells were harvested for making the RNA preparations PGCGROWTHCONDITIONS	SRR6048173	MCO000002105	IPTG was	Medium supplement	True
treatment_protocol	iptg		Starting from single colonies , the following cultures were set up in triplicate for overnight incubation : GJ13507 , GJ13531 , and GJ13533 in glucose-minimal A ; and GJ13519 also in 0.2 % glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG , with the exception of the cultures of GJ13507 whose supplementation with <Supp> IPTG was </Supp> at 3 μM . The overnight-grown cultures were each subcultured into 20 ml <Med> of fresh medium </Med> of the same composition , with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder , and grown to an A600 of 0.4 to 0.45 , before the cells were harvested for making the RNA preparations 	GPL24020	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	GSE103937	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GSM2786604	WT UvsW_replicate3	29474582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Starting from single colonies, the following cultures were set up in triplicate for overnight incubation: GJ13507, GJ13531, and GJ13533 in glucose-minimal A; and GJ13519 also in 0.2% glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG, with the exception of the cultures of GJ13507 whose supplementation with IPTG was at 3 μM. The overnight-grown cultures were each subcultured into 20 ml of fresh medium of the same composition, with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder, and grown to an A600 of 0.4 to 0.45, before the cells were harvested for making the RNA preparations PGCGROWTHCONDITIONS	SRR6048174	MCO000002105	IPTG was	Medium supplement	True
treatment_protocol	iptg		Starting from single colonies , the following cultures were set up in triplicate for overnight incubation : GJ13507 , GJ13531 , and GJ13533 in glucose-minimal A ; and GJ13519 also in 0.2 % glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG , with the exception of the cultures of GJ13507 whose supplementation with <Supp> IPTG was </Supp> at 3 μM . The overnight-grown cultures were each subcultured into 20 ml <Med> of fresh medium </Med> of the same composition , with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder , and grown to an A600 of 0.4 to 0.45 , before the cells were harvested for making the RNA preparations 	GPL24020	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	GSE103937	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GSM2786605	∆rho UvsW_replicate1	29474582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Starting from single colonies, the following cultures were set up in triplicate for overnight incubation: GJ13507, GJ13531, and GJ13533 in glucose-minimal A; and GJ13519 also in 0.2% glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG, with the exception of the cultures of GJ13507 whose supplementation with IPTG was at 3 μM. The overnight-grown cultures were each subcultured into 20 ml of fresh medium of the same composition, with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder, and grown to an A600 of 0.4 to 0.45, before the cells were harvested for making the RNA preparations PGCGROWTHCONDITIONS	SRR6048175	MCO000002105	IPTG was	Medium supplement	True
treatment_protocol	iptg		Starting from single colonies , the following cultures were set up in triplicate for overnight incubation : GJ13507 , GJ13531 , and GJ13533 in glucose-minimal A ; and GJ13519 also in 0.2 % glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG , with the exception of the cultures of GJ13507 whose supplementation with <Supp> IPTG was </Supp> at 3 μM . The overnight-grown cultures were each subcultured into 20 ml <Med> of fresh medium </Med> of the same composition , with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder , and grown to an A600 of 0.4 to 0.45 , before the cells were harvested for making the RNA preparations 	GPL24020	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	GSE103937	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GSM2786606	∆rho UvsW_replicate2	29474582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Starting from single colonies, the following cultures were set up in triplicate for overnight incubation: GJ13507, GJ13531, and GJ13533 in glucose-minimal A; and GJ13519 also in 0.2% glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG, with the exception of the cultures of GJ13507 whose supplementation with IPTG was at 3 μM. The overnight-grown cultures were each subcultured into 20 ml of fresh medium of the same composition, with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder, and grown to an A600 of 0.4 to 0.45, before the cells were harvested for making the RNA preparations PGCGROWTHCONDITIONS	SRR6048176	MCO000002105	IPTG was	Medium supplement	True
treatment_protocol	iptg		Starting from single colonies , the following cultures were set up in triplicate for overnight incubation : GJ13507 , GJ13531 , and GJ13533 in glucose-minimal A ; and GJ13519 also in 0.2 % glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG , with the exception of the cultures of GJ13507 whose supplementation with <Supp> IPTG was </Supp> at 3 μM . The overnight-grown cultures were each subcultured into 20 ml <Med> of fresh medium </Med> of the same composition , with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder , and grown to an A600 of 0.4 to 0.45 , before the cells were harvested for making the RNA preparations 	GPL24020	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	GSE103937	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GSM2786607	∆rho UvsW_replicate3	29474582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Starting from single colonies, the following cultures were set up in triplicate for overnight incubation: GJ13507, GJ13531, and GJ13533 in glucose-minimal A; and GJ13519 also in 0.2% glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG, with the exception of the cultures of GJ13507 whose supplementation with IPTG was at 3 μM. The overnight-grown cultures were each subcultured into 20 ml of fresh medium of the same composition, with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder, and grown to an A600 of 0.4 to 0.45, before the cells were harvested for making the RNA preparations PGCGROWTHCONDITIONS	SRR6048177	MCO000002105	IPTG was	Medium supplement	True
treatment_protocol	iptg		Starting from single colonies , the following cultures were set up in triplicate for overnight incubation : GJ13507 , GJ13531 , and GJ13533 in glucose-minimal A ; and GJ13519 also in 0.2 % glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG , with the exception of the cultures of GJ13507 whose supplementation with <Supp> IPTG was </Supp> at 3 μM . The overnight-grown cultures were each subcultured into 20 ml <Med> of fresh medium </Med> of the same composition , with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder , and grown to an A600 of 0.4 to 0.45 , before the cells were harvested for making the RNA preparations 	GPL24020	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	GSE103937	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GSM2786608	∆nusG UvsW_replicate1	29474582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Starting from single colonies, the following cultures were set up in triplicate for overnight incubation: GJ13507, GJ13531, and GJ13533 in glucose-minimal A; and GJ13519 also in 0.2% glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG, with the exception of the cultures of GJ13507 whose supplementation with IPTG was at 3 μM. The overnight-grown cultures were each subcultured into 20 ml of fresh medium of the same composition, with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder, and grown to an A600 of 0.4 to 0.45, before the cells were harvested for making the RNA preparations PGCGROWTHCONDITIONS	SRR6048178	MCO000002105	IPTG was	Medium supplement	True
treatment_protocol	iptg		Starting from single colonies , the following cultures were set up in triplicate for overnight incubation : GJ13507 , GJ13531 , and GJ13533 in glucose-minimal A ; and GJ13519 also in 0.2 % glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG , with the exception of the cultures of GJ13507 whose supplementation with <Supp> IPTG was </Supp> at 3 μM . The overnight-grown cultures were each subcultured into 20 ml <Med> of fresh medium </Med> of the same composition , with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder , and grown to an A600 of 0.4 to 0.45 , before the cells were harvested for making the RNA preparations 	GPL24020	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	GSE103937	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GSM2786609	∆nusG UvsW_replicate2	29474582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Starting from single colonies, the following cultures were set up in triplicate for overnight incubation: GJ13507, GJ13531, and GJ13533 in glucose-minimal A; and GJ13519 also in 0.2% glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG, with the exception of the cultures of GJ13507 whose supplementation with IPTG was at 3 μM. The overnight-grown cultures were each subcultured into 20 ml of fresh medium of the same composition, with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder, and grown to an A600 of 0.4 to 0.45, before the cells were harvested for making the RNA preparations PGCGROWTHCONDITIONS	SRR6048179	MCO000002105	IPTG was	Medium supplement	True
treatment_protocol	iptg		Starting from single colonies , the following cultures were set up in triplicate for overnight incubation : GJ13507 , GJ13531 , and GJ13533 in glucose-minimal A ; and GJ13519 also in 0.2 % glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG , with the exception of the cultures of GJ13507 whose supplementation with <Supp> IPTG was </Supp> at 3 μM . The overnight-grown cultures were each subcultured into 20 ml <Med> of fresh medium </Med> of the same composition , with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder , and grown to an A600 of 0.4 to 0.45 , before the cells were harvested for making the RNA preparations 	GPL24020	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	GSE103937	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GSM2786610	∆nusG UvsW_replicate3	29474582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Starting from single colonies, the following cultures were set up in triplicate for overnight incubation: GJ13507, GJ13531, and GJ13533 in glucose-minimal A; and GJ13519 also in 0.2% glycerol-minimal A. All the cultures were supplemented with 200 μM IPTG, with the exception of the cultures of GJ13507 whose supplementation with IPTG was at 3 μM. The overnight-grown cultures were each subcultured into 20 ml of fresh medium of the same composition, with an inoculum of 1:50 for GJ13507 and GJ13531 and of 1:100 for the remainder, and grown to an A600 of 0.4 to 0.45, before the cells were harvested for making the RNA preparations PGCGROWTHCONDITIONS	SRR6048180	MCO000002105	IPTG was	Medium supplement	True
characteristics	exponential phase		growth phase : <Anti> Mid </Anti> <Phase> exponential </Phase> 	GPL21222-GPL21726	GPL21222: Illumina NextSeq 500 (Escherichia coli). GPL21726: Ion Torrent Proton (Escherichia coli)	GSE104504	Crosstalk between global regulators CRP and FIS in E. coli.	GSM2802560	fis.rep1.me	29205228	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE104504/GSE104504.soft.gz	100	79	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth phase: Mid exponential PGCGROWTHCONDITIONS	SRR6125551	MCO000002864	exponential	Growth phase	True
characteristics	exponential phase		growth phase : <Anti> Mid </Anti> <Phase> exponential </Phase> 	GPL21222-GPL21726	GPL21222: Illumina NextSeq 500 (Escherichia coli). GPL21726: Ion Torrent Proton (Escherichia coli)	GSE104504	Crosstalk between global regulators CRP and FIS in E. coli.	GSM2802561	fis.rep2.me	29205228	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE104504/GSE104504.soft.gz	100	79	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth phase: Mid exponential PGCGROWTHCONDITIONS	SRR6125552	MCO000002864	exponential	Growth phase	True
characteristics	exponential phase		growth phase : <Anti> Mid </Anti> <Phase> exponential </Phase> 	GPL21222-GPL21726	GPL21222: Illumina NextSeq 500 (Escherichia coli). GPL21726: Ion Torrent Proton (Escherichia coli)	GSE104504	Crosstalk between global regulators CRP and FIS in E. coli.	GSM2802565	cya.rep2.me	29205228	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE104504/GSE104504.soft.gz	100	79	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth phase: Mid exponential PGCGROWTHCONDITIONS	SRR6125556	MCO000002864	exponential	Growth phase	True
characteristics	exponential phase		growth phase : <Anti> Mid </Anti> <Phase> exponential </Phase> 	GPL21222-GPL21726	GPL21222: Illumina NextSeq 500 (Escherichia coli). GPL21726: Ion Torrent Proton (Escherichia coli)	GSE104504	Crosstalk between global regulators CRP and FIS in E. coli.	GSM2802566	wt.rep1.me	29205228	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE104504/GSE104504.soft.gz	100	79	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth phase: Mid exponential PGCGROWTHCONDITIONS	SRR6125557	MCO000002864	exponential	Growth phase	True
characteristics	exponential phase		growth phase : <Anti> Mid </Anti> <Phase> exponential </Phase> 	GPL21222-GPL21726	GPL21222: Illumina NextSeq 500 (Escherichia coli). GPL21726: Ion Torrent Proton (Escherichia coli)	GSE104504	Crosstalk between global regulators CRP and FIS in E. coli.	GSM2802567	wt.rep2.me	29205228	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE104504/GSE104504.soft.gz	100	79	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth phase: Mid exponential PGCGROWTHCONDITIONS	SRR6125558	MCO000002864	exponential	Growth phase	True
characteristics	exponential phase		growth phase : <Phase> exponential </Phase> 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331409	LB 0.4 B1 TEX neg L1 GA	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	79	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth phase: exponential PGCGROWTHCONDITIONS	SRR1173965	MCO000002864	exponential	Growth phase	True
characteristics	exponential phase		growth phase : <Phase> exponential </Phase> 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331410	LB 0.4 B1 TEX pos L1 GA	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	79	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth phase: exponential PGCGROWTHCONDITIONS	SRR1173966	MCO000002864	exponential	Growth phase	True
characteristics	exponential phase		growth phase : <Phase> exponential </Phase> 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331411	LB 0.4 B2 TEX neg L1 HS1	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	79	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth phase: exponential PGCGROWTHCONDITIONS	SRR1173967	MCO000002864	exponential	Growth phase	True
characteristics	exponential phase		growth phase : <Phase> exponential </Phase> 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331412	LB 0.4 B2 TEX neg L1 HS2	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	79	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth phase: exponential PGCGROWTHCONDITIONS	SRR1173968	MCO000002864	exponential	Growth phase	True
characteristics	exponential phase		growth phase : <Phase> exponential </Phase> 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331413	LB 0.4 B2 TEX pos L1 HS1	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	79	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth phase: exponential PGCGROWTHCONDITIONS	SRR1173969	MCO000002864	exponential	Growth phase	True
characteristics	exponential phase		growth phase : <Phase> exponential </Phase> 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331414	LB 0.4 B2 TEX pos L1 HS2	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	79	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth phase: exponential PGCGROWTHCONDITIONS	SRR1173970	MCO000002864	exponential	Growth phase	True
characteristics	exponential phase		growth phase : <Phase> exponential </Phase> 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331426	M63 0.4 B1 TEX pos L1 GA	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	79	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth phase: exponential PGCGROWTHCONDITIONS	SRR1173982	MCO000002864	exponential	Growth phase	True
characteristics	exponential phase		growth phase : <Phase> exponential </Phase> 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331427	M63 0.4 B2 TEX neg L1 HS1	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	79	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth phase: exponential PGCGROWTHCONDITIONS	SRR1173983	MCO000002864	exponential	Growth phase	True
characteristics	exponential phase		growth phase : <Phase> exponential </Phase> 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331428	M63 0.4 B2 TEX neg L1 HS2	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	79	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth phase: exponential PGCGROWTHCONDITIONS	SRR1173984	MCO000002864	exponential	Growth phase	True
characteristics	exponential phase		growth phase : <Phase> exponential </Phase> 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331429	M63 0.4 B2 TEX pos L1 HS1	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	79	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth phase: exponential PGCGROWTHCONDITIONS	SRR1173985	MCO000002864	exponential	Growth phase	True
characteristics	exponential phase		growth phase : <Phase> exponential </Phase> 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331430	M63 0.4 B2 TEX pos L1 HS2	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	79	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth phase: exponential PGCGROWTHCONDITIONS	SRR1173986	MCO000002864	exponential	Growth phase	True
characteristics	30.0 C		growth condition : <Supp> MM + 0.12 % casaminoacids +0.4 % glucose </Supp> at <Temp> 30 °C </Temp> 	GPL15010-GPL21117	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21117: Illumina NextSeq 500 (Escherichia coli str. K-12 substr. MG1655)	GSE107301	Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins	GSM2870440	RNA-seq of E. coli wt cells in stationary phase 30°C (30h)	29358050	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107301/GSE107301.soft.gz	100	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth condition: MM + 0.12% casaminoacids +0.4% glucose at 30°C PGCGROWTHCONDITIONS	SRR6354578	MCO000002695	30 °C	Temperature	True
characteristics	30.0 C		growth condition : <Supp> MM + 0.12 % casaminoacids +0.4 % glucose </Supp> at <Temp> 30 °C </Temp> 	GPL15010-GPL21117	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21117: Illumina NextSeq 500 (Escherichia coli str. K-12 substr. MG1655)	GSE107301	Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins	GSM2870441	RNA-seq of E. coli wt cells in stationary phase 30°C (30h) -Replicate 1	29358050	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107301/GSE107301.soft.gz	100	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth condition: MM + 0.12% casaminoacids +0.4% glucose at 30°C PGCGROWTHCONDITIONS	SRR6354579	MCO000002695	30 °C	Temperature	True
growth_protocol	30.0 C		E. coli [ K-12 MG1655 strain ( <Gversion> U00096 .2 </Gversion> ) ] was grown overnight at <Temp> 30 °C </Temp> in LB medium . The resulting culture was diluted 500-fold in fresh LB medium and grown at 30 °C for 3.5 hours such that O.D. at 600 nm became 0.30-0.35 . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE34449	Digital RNA Sequencing Minimizes Sequence-Dependent Bias and Amplification Noise with Optimized Single Molecule Barcodes	GSM849370	E_coli_transcriptome_1	22232676	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE34449/GSE34449.soft.gz	100	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli [K-12 MG1655 strain (U00096.2)] was grown overnight at 30 °C in LB medium.  The resulting culture was diluted 500-fold in fresh LB medium and grown at 30 °C for 3.5 hours such that O.D. at 600 nm became 0.30-0.35. PGCGROWTHCONDITIONS	SRR389819	MCO000002695	30 °C	Temperature	True
growth_protocol	30.0 C		E. coli [ K-12 MG1655 strain ( <Gversion> U00096 .2 </Gversion> ) ] was grown overnight at <Temp> 30 °C </Temp> in LB medium . The resulting culture was diluted 500-fold in fresh LB medium and grown at 30 °C for 3.5 hours such that O.D. at 600 nm became 0.30-0.35 . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE34449	Digital RNA Sequencing Minimizes Sequence-Dependent Bias and Amplification Noise with Optimized Single Molecule Barcodes	GSM849371	E_coli_transcriptome_2	22232676	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE34449/GSE34449.soft.gz	100	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli [K-12 MG1655 strain (U00096.2)] was grown overnight at 30 °C in LB medium.  The resulting culture was diluted 500-fold in fresh LB medium and grown at 30 °C for 3.5 hours such that O.D. at 600 nm became 0.30-0.35. PGCGROWTHCONDITIONS	SRR389820	MCO000002695	30 °C	Temperature	True
growth_protocol	M9 minimal medium		Experiments were performed at <Temp> 37 °C </Temp> and followed three steps : seed culture , pre-culture and experimental culture . In the seed culture the cells were grown overnight in Luria Broth , then diluted 1:100 in either <Med> M9 minimal media </Med> with glycerol or glucose for the pre-cultures . Finally , the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm ( OD600 ) of 0.05 . Cultures were harvested at mid-exponential phase , cells were immediately spun down and cell pellets stored at -80 °C until processed . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914313	CF104.3.3_y2	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS	SRR6449107	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		Experiments were performed at <Temp> 37 °C </Temp> and followed three steps : seed culture , pre-culture and experimental culture . In the seed culture the cells were grown overnight in Luria Broth , then diluted 1:100 in either <Med> M9 minimal media </Med> with glycerol or glucose for the pre-cultures . Finally , the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm ( OD600 ) of 0.05 . Cultures were harvested at mid-exponential phase , cells were immediately spun down and cell pellets stored at -80 °C until processed . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914315	CF108.4B_y3	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS	SRR6449109	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		Experiments were performed at <Temp> 37 °C </Temp> and followed three steps : seed culture , pre-culture and experimental culture . In the seed culture the cells were grown overnight in Luria Broth , then diluted 1:100 in either <Med> M9 minimal media </Med> with glycerol or glucose for the pre-cultures . Finally , the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm ( OD600 ) of 0.05 . Cultures were harvested at mid-exponential phase , cells were immediately spun down and cell pellets stored at -80 °C until processed . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914317	CON206.3A_y1	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS	SRR6449111	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		Experiments were performed at <Temp> 37 °C </Temp> and followed three steps : seed culture , pre-culture and experimental culture . In the seed culture the cells were grown overnight in Luria Broth , then diluted 1:100 in either <Med> M9 minimal media </Med> with glycerol or glucose for the pre-cultures . Finally , the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm ( OD600 ) of 0.05 . Cultures were harvested at mid-exponential phase , cells were immediately spun down and cell pellets stored at -80 °C until processed . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914318	CON206.3A_y2	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS	SRR6449112	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		Experiments were performed at <Temp> 37 °C </Temp> and followed three steps : seed culture , pre-culture and experimental culture . In the seed culture the cells were grown overnight in Luria Broth , then diluted 1:100 in either <Med> M9 minimal media </Med> with glycerol or glucose for the pre-cultures . Finally , the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm ( OD600 ) of 0.05 . Cultures were harvested at mid-exponential phase , cells were immediately spun down and cell pellets stored at -80 °C until processed . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914319	CON208.3A_y2	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS	SRR6449113	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		Experiments were performed at <Temp> 37 °C </Temp> and followed three steps : seed culture , pre-culture and experimental culture . In the seed culture the cells were grown overnight in Luria Broth , then diluted 1:100 in either <Med> M9 minimal media </Med> with glycerol or glucose for the pre-cultures . Finally , the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm ( OD600 ) of 0.05 . Cultures were harvested at mid-exponential phase , cells were immediately spun down and cell pellets stored at -80 °C until processed . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914320	CON208.3A_y6	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS	SRR6449114	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		Experiments were performed at <Temp> 37 °C </Temp> and followed three steps : seed culture , pre-culture and experimental culture . In the seed culture the cells were grown overnight in Luria Broth , then diluted 1:100 in either <Med> M9 minimal media </Med> with glycerol or glucose for the pre-cultures . Finally , the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm ( OD600 ) of 0.05 . Cultures were harvested at mid-exponential phase , cells were immediately spun down and cell pellets stored at -80 °C until processed . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914321	CF104.3.3_u1	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS	SRR6449115	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		Experiments were performed at <Temp> 37 °C </Temp> and followed three steps : seed culture , pre-culture and experimental culture . In the seed culture the cells were grown overnight in Luria Broth , then diluted 1:100 in either <Med> M9 minimal media </Med> with glycerol or glucose for the pre-cultures . Finally , the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm ( OD600 ) of 0.05 . Cultures were harvested at mid-exponential phase , cells were immediately spun down and cell pellets stored at -80 °C until processed . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914322	CF104.3.3_u7	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS	SRR6449116	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		Experiments were performed at <Temp> 37 °C </Temp> and followed three steps : seed culture , pre-culture and experimental culture . In the seed culture the cells were grown overnight in Luria Broth , then diluted 1:100 in either <Med> M9 minimal media </Med> with glycerol or glucose for the pre-cultures . Finally , the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm ( OD600 ) of 0.05 . Cultures were harvested at mid-exponential phase , cells were immediately spun down and cell pellets stored at -80 °C until processed . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914323	CF108.4B_u1	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS	SRR6449117	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		Experiments were performed at <Temp> 37 °C </Temp> and followed three steps : seed culture , pre-culture and experimental culture . In the seed culture the cells were grown overnight in Luria Broth , then diluted 1:100 in either <Med> M9 minimal media </Med> with glycerol or glucose for the pre-cultures . Finally , the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm ( OD600 ) of 0.05 . Cultures were harvested at mid-exponential phase , cells were immediately spun down and cell pellets stored at -80 °C until processed . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914324	CF108.4B_u2	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS	SRR6449118	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		Experiments were performed at <Temp> 37 °C </Temp> and followed three steps : seed culture , pre-culture and experimental culture . In the seed culture the cells were grown overnight in Luria Broth , then diluted 1:100 in either <Med> M9 minimal media </Med> with glycerol or glucose for the pre-cultures . Finally , the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm ( OD600 ) of 0.05 . Cultures were harvested at mid-exponential phase , cells were immediately spun down and cell pellets stored at -80 °C until processed . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914325	CON206.3A_u1	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS	SRR6449119	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		Experiments were performed at <Temp> 37 °C </Temp> and followed three steps : seed culture , pre-culture and experimental culture . In the seed culture the cells were grown overnight in Luria Broth , then diluted 1:100 in either <Med> M9 minimal media </Med> with glycerol or glucose for the pre-cultures . Finally , the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm ( OD600 ) of 0.05 . Cultures were harvested at mid-exponential phase , cells were immediately spun down and cell pellets stored at -80 °C until processed . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914326	CON206.3A_u2	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS	SRR6449120	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		Experiments were performed at <Temp> 37 °C </Temp> and followed three steps : seed culture , pre-culture and experimental culture . In the seed culture the cells were grown overnight in Luria Broth , then diluted 1:100 in either <Med> M9 minimal media </Med> with glycerol or glucose for the pre-cultures . Finally , the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm ( OD600 ) of 0.05 . Cultures were harvested at mid-exponential phase , cells were immediately spun down and cell pellets stored at -80 °C until processed . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914327	CON208.3A_u1	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS	SRR6449121	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		Experiments were performed at <Temp> 37 °C </Temp> and followed three steps : seed culture , pre-culture and experimental culture . In the seed culture the cells were grown overnight in Luria Broth , then diluted 1:100 in either <Med> M9 minimal media </Med> with glycerol or glucose for the pre-cultures . Finally , the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm ( OD600 ) of 0.05 . Cultures were harvested at mid-exponential phase , cells were immediately spun down and cell pellets stored at -80 °C until processed . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE108846	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GSM2914328	CON208.3A_u8	29378945	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Experiments were performed at 37°C and followed three steps: seed culture, pre-culture and experimental culture. In the seed culture the cells were grown overnight in Luria Broth, then diluted 1:100 in either M9 minimal media with glycerol or glucose for the pre-cultures. Finally, the experimental cultures were started from the overnight grown pre-cultures containing the same carbon source at a normalized optical density at 600 nm (OD600) of 0.05. Cultures were harvested at mid-exponential phase, cells were immediately spun down and cell pellets stored at -80°C until processed. PGCGROWTHCONDITIONS	SRR6449122	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		glycerol stocks of E. coli strains were inoculated into 0.2 % ( w/v ) glucose M9 minimal media . <Med> M9 minimal media </Med> was also supplemented with 1 ml trace element solution ( 100X ) , excluding MG _ no _ te _ 1 and MG _ no _ te _ 2 . The culture was incubated at <Temp> 37 ℃ </Temp> overnight with agitation , and then was used to inoculate the fresh <Med> media </Med> . The fresh culture was incubated at 37 ℃ with agitation to the <Phase> mid-log phase </Phase> ( OD600 ≈ 0.5 ) . 10mM glutamate was added to the media MG _ glu _ 1 and MG _ glu _ 2 . 	GPL17024-GPL17439-GPL18995-GPL25769	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	GSE122211	Expression profiling of E. coli K-12 MG1655	GSM3461156	MG_no_te_1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	glycerol stocks of E. coli strains were inoculated into 0.2%(w/v) glucose M9 minimal media. M9 minimal media was also supplemented with 1 ml trace element solution (100X), excluding MG_no_te_1 and MG_no_te_2. The culture was incubated at 37 ℃ overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37 ℃ with agitation to the mid-log phase (OD600 ≈ 0.5). 10mM glutamate was added to the media MG_glu_1 and MG_glu_2. PGCGROWTHCONDITIONS	SRR8164476	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / 0.2 % glucose w/o trace elements 	GPL17024-GPL17439-GPL18995-GPL25769	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	GSE122211	Expression profiling of E. coli K-12 MG1655	GSM3461156	MG_no_te_1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 0.2% glucose w/o trace elements PGCGROWTHCONDITIONS	SRR8164476	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		glycerol stocks of E. coli strains were inoculated into 0.2 % ( w/v ) glucose M9 minimal media . <Med> M9 minimal media </Med> was also supplemented with 1 ml trace element solution ( 100X ) , excluding MG _ no _ te _ 1 and MG _ no _ te _ 2 . The culture was incubated at <Temp> 37 ℃ </Temp> overnight with agitation , and then was used to inoculate the fresh <Med> media </Med> . The fresh culture was incubated at 37 ℃ with agitation to the <Phase> mid-log phase </Phase> ( OD600 ≈ 0.5 ) . 10mM glutamate was added to the media MG _ glu _ 1 and MG _ glu _ 2 . 	GPL17024-GPL17439-GPL18995-GPL25769	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	GSE122211	Expression profiling of E. coli K-12 MG1655	GSM3461157	MG_no_te_2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	glycerol stocks of E. coli strains were inoculated into 0.2%(w/v) glucose M9 minimal media. M9 minimal media was also supplemented with 1 ml trace element solution (100X), excluding MG_no_te_1 and MG_no_te_2. The culture was incubated at 37 ℃ overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37 ℃ with agitation to the mid-log phase (OD600 ≈ 0.5). 10mM glutamate was added to the media MG_glu_1 and MG_glu_2. PGCGROWTHCONDITIONS	SRR8164477	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / 0.2 % glucose w/o trace elements 	GPL17024-GPL17439-GPL18995-GPL25769	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	GSE122211	Expression profiling of E. coli K-12 MG1655	GSM3461157	MG_no_te_2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 0.2% glucose w/o trace elements PGCGROWTHCONDITIONS	SRR8164477	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		glycerol stocks of E. coli strains were inoculated into 0.2 % ( w/v ) glucose M9 minimal media . <Med> M9 minimal media </Med> was also supplemented with 1 ml trace element solution ( 100X ) , excluding MG _ no _ te _ 1 and MG _ no _ te _ 2 . The culture was incubated at <Temp> 37 ℃ </Temp> overnight with agitation , and then was used to inoculate the fresh <Med> media </Med> . The fresh culture was incubated at 37 ℃ with agitation to the <Phase> mid-log phase </Phase> ( OD600 ≈ 0.5 ) . 10mM glutamate was added to the media MG _ glu _ 1 and MG _ glu _ 2 . 	GPL17024-GPL17439-GPL18995-GPL25769	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	GSE122211	Expression profiling of E. coli K-12 MG1655	GSM3461164	MG_glu_1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	glycerol stocks of E. coli strains were inoculated into 0.2%(w/v) glucose M9 minimal media. M9 minimal media was also supplemented with 1 ml trace element solution (100X), excluding MG_no_te_1 and MG_no_te_2. The culture was incubated at 37 ℃ overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37 ℃ with agitation to the mid-log phase (OD600 ≈ 0.5). 10mM glutamate was added to the media MG_glu_1 and MG_glu_2. PGCGROWTHCONDITIONS	SRR8164484	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 0.2 % glucose </Supp> and 10mM glutamate 	GPL17024-GPL17439-GPL18995-GPL25769	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	GSE122211	Expression profiling of E. coli K-12 MG1655	GSM3461164	MG_glu_1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 0.2% glucose and 10mM glutamate PGCGROWTHCONDITIONS	SRR8164484	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		glycerol stocks of E. coli strains were inoculated into 0.2 % ( w/v ) glucose M9 minimal media . <Med> M9 minimal media </Med> was also supplemented with 1 ml trace element solution ( 100X ) , excluding MG _ no _ te _ 1 and MG _ no _ te _ 2 . The culture was incubated at <Temp> 37 ℃ </Temp> overnight with agitation , and then was used to inoculate the fresh <Med> media </Med> . The fresh culture was incubated at 37 ℃ with agitation to the <Phase> mid-log phase </Phase> ( OD600 ≈ 0.5 ) . 10mM glutamate was added to the media MG _ glu _ 1 and MG _ glu _ 2 . 	GPL17024-GPL17439-GPL18995-GPL25769	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	GSE122211	Expression profiling of E. coli K-12 MG1655	GSM3461165	MG_glu_2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	glycerol stocks of E. coli strains were inoculated into 0.2%(w/v) glucose M9 minimal media. M9 minimal media was also supplemented with 1 ml trace element solution (100X), excluding MG_no_te_1 and MG_no_te_2. The culture was incubated at 37 ℃ overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37 ℃ with agitation to the mid-log phase (OD600 ≈ 0.5). 10mM glutamate was added to the media MG_glu_1 and MG_glu_2. PGCGROWTHCONDITIONS	SRR8164485	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 0.2 % glucose </Supp> and 10mM glutamate 	GPL17024-GPL17439-GPL18995-GPL25769	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	GSE122211	Expression profiling of E. coli K-12 MG1655	GSM3461165	MG_glu_2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 0.2% glucose and 10mM glutamate PGCGROWTHCONDITIONS	SRR8164485	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		glycerol stocks of E. coli strains were inoculated into 0.2 % ( w/v ) glucose M9 minimal media . <Med> M9 minimal media </Med> was also supplemented with 1 ml trace element solution ( 100X ) , excluding MG _ no _ te _ 1 and MG _ no _ te _ 2 . The culture was incubated at <Temp> 37 ℃ </Temp> overnight with agitation , and then was used to inoculate the fresh <Med> media </Med> . The fresh culture was incubated at 37 ℃ with agitation to the <Phase> mid-log phase </Phase> ( OD600 ≈ 0.5 ) . 10mM glutamate was added to the media MG _ glu _ 1 and MG _ glu _ 2 . 	GPL17024-GPL17439-GPL18995-GPL25769	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	GSE122211	Expression profiling of E. coli K-12 MG1655	GSM3461166	MG_glc	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	glycerol stocks of E. coli strains were inoculated into 0.2%(w/v) glucose M9 minimal media. M9 minimal media was also supplemented with 1 ml trace element solution (100X), excluding MG_no_te_1 and MG_no_te_2. The culture was incubated at 37 ℃ overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37 ℃ with agitation to the mid-log phase (OD600 ≈ 0.5). 10mM glutamate was added to the media MG_glu_1 and MG_glu_2. PGCGROWTHCONDITIONS	SRR8164486	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 0.2 % glucose </Supp> 	GPL17024-GPL17439-GPL18995-GPL25769	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	GSE122211	Expression profiling of E. coli K-12 MG1655	GSM3461166	MG_glc	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 0.2% glucose PGCGROWTHCONDITIONS	SRR8164486	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463565	wt_glc__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	SRR8173227	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463566	wt_glc__2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	SRR8173228	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463567	wt_glc__3	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	SRR8173229	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463568	wt_glc__4	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	SRR8173230	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / 4g/L D-sorbitol 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463569	arg_sbt__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L D-sorbitol PGCGROWTHCONDITIONS	SRR8173231	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / 4g/L D-sorbitol 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463570	arg_sbt__2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L D-sorbitol PGCGROWTHCONDITIONS	SRR8173232	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / 4g/L D-ribose 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463571	cytd_rib__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L D-ribose PGCGROWTHCONDITIONS	SRR8173233	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / 4g/L D-ribose 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463572	cytd_rib__2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L D-ribose PGCGROWTHCONDITIONS	SRR8173234	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463573	gth__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	SRR8173235	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463574	gth__2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	SRR8173236	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / 4g/L glucarate 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463575	leu_glcr__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucarate PGCGROWTHCONDITIONS	SRR8173237	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / 4g/L glucarate 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463576	leu_glcr__2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucarate PGCGROWTHCONDITIONS	SRR8173238	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463577	met_glc__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	SRR8173239	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463578	met_glc__2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	SRR8173240	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Air> anaerobic </Air> <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463579	no3_anaero__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: anaerobic M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	SRR8173241	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Air> anaerobic </Air> <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463580	no3_anaero__2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: anaerobic M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	SRR8173242	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / 4g/L N-acetylglucosamine 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463581	phe_acgam__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L N-acetylglucosamine PGCGROWTHCONDITIONS	SRR8173243	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / 4g/L N-acetylglucosamine 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463582	phe_acgam__2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L N-acetylglucosamine PGCGROWTHCONDITIONS	SRR8173244	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / 4g/L galactose 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463583	thm_gal__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L galactose PGCGROWTHCONDITIONS	SRR8173245	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / 4g/L galactose 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463584	thm_gal__2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L galactose PGCGROWTHCONDITIONS	SRR8173246	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / 4g/L D-gluconate 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463585	tyr_glcn__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L D-gluconate PGCGROWTHCONDITIONS	SRR8173247	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / 4g/L D-gluconate 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463586	tyr_glcn__2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L D-gluconate PGCGROWTHCONDITIONS	SRR8173248	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3854833	wt_glc_5__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	SRR9204648	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3854834	wt_glc_6__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	SRR9204649	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose and 1 mM cytidine </Supp> 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3854835	bw_delpurR_cytd__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 2g/L glucose and 1 mM cytidine PGCGROWTHCONDITIONS	SRR9204650	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose and 1 mM cytidine </Supp> 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3854836	bw_delpurR_cytd__2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 2g/L glucose and 1 mM cytidine PGCGROWTHCONDITIONS	SRR9204651	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> and 100 mg/L adenine 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3854837	ade_glc__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 2g/L glucose and 100 mg/L adenine PGCGROWTHCONDITIONS	SRR9204652	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> and 100 mg/L adenine 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3854838	ade_glc__2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 2g/L glucose and 100 mg/L adenine PGCGROWTHCONDITIONS	SRR9204653	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE122296	Expression profiling of multiple Escherichia coli strains on glucose minimal media	GSM3463601	MG1655_1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122296/GSE122296.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	SRR8173221	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE122296	Expression profiling of multiple Escherichia coli strains on glucose minimal media	GSM3463602	MG1655_2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122296/GSE122296.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	SRR8173222	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT , Δfis and Δhns were grown in Luria-Bertani ( LB ) broth and agar ( 15g/l ) . Where needed , kanamycin was used at final concentration of 50µg/ml . For RNA extraction , E. coli cultures were grown to mid-exponential growth phase <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with 40 % ( w/v ) glucose . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE123554	Reconstruction of transcriptional regulatory networks of Fis and H-NS in Escherichia coli from genome wide data analysis	GSM3507068	delta-fis rep1		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE123554/GSE123554.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, Δfis and Δhns were grown in Luria-Bertani (LB) broth and agar (15g/l). Where needed, kanamycin was used at final concentration of 50µg/ml. For RNA extraction, E. coli cultures were grown to mid-exponential growth phase aerobically at 37°C in M9 minimal media supplemented with 40% (w/v) glucose. PGCGROWTHCONDITIONS	SRR8309841	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT , Δfis and Δhns were grown in Luria-Bertani ( LB ) broth and agar ( 15g/l ) . Where needed , kanamycin was used at final concentration of 50µg/ml . For RNA extraction , E. coli cultures were grown to mid-exponential growth phase <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with 40 % ( w/v ) glucose . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE123554	Reconstruction of transcriptional regulatory networks of Fis and H-NS in Escherichia coli from genome wide data analysis	GSM3507069	delta-fis rep2		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE123554/GSE123554.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, Δfis and Δhns were grown in Luria-Bertani (LB) broth and agar (15g/l). Where needed, kanamycin was used at final concentration of 50µg/ml. For RNA extraction, E. coli cultures were grown to mid-exponential growth phase aerobically at 37°C in M9 minimal media supplemented with 40% (w/v) glucose. PGCGROWTHCONDITIONS	SRR8309842	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT , Δfis and Δhns were grown in Luria-Bertani ( LB ) broth and agar ( 15g/l ) . Where needed , kanamycin was used at final concentration of 50µg/ml . For RNA extraction , E. coli cultures were grown to mid-exponential growth phase <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with 40 % ( w/v ) glucose . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE123554	Reconstruction of transcriptional regulatory networks of Fis and H-NS in Escherichia coli from genome wide data analysis	GSM3507070	delta-hns rep1		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE123554/GSE123554.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, Δfis and Δhns were grown in Luria-Bertani (LB) broth and agar (15g/l). Where needed, kanamycin was used at final concentration of 50µg/ml. For RNA extraction, E. coli cultures were grown to mid-exponential growth phase aerobically at 37°C in M9 minimal media supplemented with 40% (w/v) glucose. PGCGROWTHCONDITIONS	SRR8309843	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT , Δfis and Δhns were grown in Luria-Bertani ( LB ) broth and agar ( 15g/l ) . Where needed , kanamycin was used at final concentration of 50µg/ml . For RNA extraction , E. coli cultures were grown to mid-exponential growth phase <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with 40 % ( w/v ) glucose . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE123554	Reconstruction of transcriptional regulatory networks of Fis and H-NS in Escherichia coli from genome wide data analysis	GSM3507071	delta-hns rep2		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE123554/GSE123554.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, Δfis and Δhns were grown in Luria-Bertani (LB) broth and agar (15g/l). Where needed, kanamycin was used at final concentration of 50µg/ml. For RNA extraction, E. coli cultures were grown to mid-exponential growth phase aerobically at 37°C in M9 minimal media supplemented with 40% (w/v) glucose. PGCGROWTHCONDITIONS	SRR8309844	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013462	WT_1	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919224	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013463	WT_2	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919225	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013464	WT_H2O2_1	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919226	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013465	WT_H2O2_2	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919227	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013466	GMOS_1	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919228	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013467	GMOS_2	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919229	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013468	GMOS_H2O2_1	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919230	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013470	EC ALE-1_1	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919232	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013471	EC ALE-1_2	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919233	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013472	EC ALE-1_H2O2_1	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919234	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013473	EC ALE-1_H2O2_2	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919235	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013474	EC ALE-2_1	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919236	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013475	EC ALE-2_2	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919237	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013476	EC ALE-2_H2O2_1	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919238	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013477	EC ALE-2_H2O2_2	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919239	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013478	EC ALE-3_1	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919240	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013479	EC ALE-3_2	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919241	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013480	EC ALE-3_H2O2_1	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919242	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013481	EC ALE-3_H2O2_2	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919243	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013482	EC ALE-4_1	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919244	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013483	EC ALE-4_2	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919245	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013484	EC ALE-4_H2O2_1	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919246	MCO000002526	M9 minimal media	Medium	True
characteristics	M9 minimal medium		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013485	EC ALE-4_H2O2_2	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919247	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174823	Mid log_wildtype_glc minimal media_aerobic rep1	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922260	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174824	Mid log_wildtype_glc minimal media_aerobic rep2	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922261	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174825	Mid log_wildtype_glc minimal media_aerobic rep3	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922262	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174826	Mid log_wildtype_glc minimal media + adenine_aerobic	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922263	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174827	Mid log_wildtype_glc minimal media + L-tryptophan_aerobic	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922264	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174828	Mid log_wildtype_glc minimal media_anaerobic rep1	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922265	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174829	Mid log_wildtype_glc minimal media_anaerobic rep2	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922266	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174830	Mid log_wildtype_glc minimal media_anaerobic rep3	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922267	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174831	Mid log_nac KO_glc minimal media_aerobic	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922268	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174832	Mid log_nac KO_glc minimal media + adenine_aerobic	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922269	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174833	Mid log_cra KO_glc minimal media_aerobic	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922270	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174834	Mid log_cra KO_glc minimal media + L-tryptophan_aerobic	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922271	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174835	Mid log_mntR KO_glc minimal media_aerobic	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922272	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174836	Mid log_mntR KO_glc minimal media_anaerobic	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922273	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT and Δfur were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . For iron treated cells , 0.1 mM of FeCl2 were treated from the beginning of culture , and for DPD treated cells , <Supp> 0.2 mM of DPD </Supp> were added at early-log phase and continued to culture for additional <Supp> 2h </Supp> . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE54900	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GSM1326347	WT with Fe 1 (RNA-seq)	25222563	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT and Δfur were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. PGCGROWTHCONDITIONS	SRR1168133	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT and Δfur were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . For iron treated cells , 0.1 mM of FeCl2 were treated from the beginning of culture , and for DPD treated cells , <Supp> 0.2 mM of DPD </Supp> were added at early-log phase and continued to culture for additional <Supp> 2h </Supp> . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE54900	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GSM1326348	WT with Fe 2 (RNA-seq)	25222563	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT and Δfur were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. PGCGROWTHCONDITIONS	SRR1168134	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT and Δfur were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . For iron treated cells , 0.1 mM of FeCl2 were treated from the beginning of culture , and for DPD treated cells , <Supp> 0.2 mM of DPD </Supp> were added at early-log phase and continued to culture for additional <Supp> 2h </Supp> . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE54900	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GSM1326349	WT with DPD 1 (RNA-seq)	25222563	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT and Δfur were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. PGCGROWTHCONDITIONS	SRR1168135	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT and Δfur were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . For iron treated cells , 0.1 mM of FeCl2 were treated from the beginning of culture , and for DPD treated cells , <Supp> 0.2 mM of DPD </Supp> were added at early-log phase and continued to culture for additional <Supp> 2h </Supp> . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE54900	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GSM1326350	WT with DPD 2 (RNA-seq)	25222563	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT and Δfur were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. PGCGROWTHCONDITIONS	SRR1168136	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT and Δfur were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . For iron treated cells , 0.1 mM of FeCl2 were treated from the beginning of culture , and for DPD treated cells , <Supp> 0.2 mM of DPD </Supp> were added at early-log phase and continued to culture for additional <Supp> 2h </Supp> . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE54900	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GSM1326351	Δfur with Fe 1 (RNA-seq)	25222563	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT and Δfur were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. PGCGROWTHCONDITIONS	SRR1168137	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT and Δfur were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . For iron treated cells , 0.1 mM of FeCl2 were treated from the beginning of culture , and for DPD treated cells , <Supp> 0.2 mM of DPD </Supp> were added at early-log phase and continued to culture for additional <Supp> 2h </Supp> . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE54900	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GSM1326352	Δfur with Fe 2 (RNA-seq)	25222563	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT and Δfur were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. PGCGROWTHCONDITIONS	SRR1168138	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT and Δfur were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . For iron treated cells , 0.1 mM of FeCl2 were treated from the beginning of culture , and for DPD treated cells , <Supp> 0.2 mM of DPD </Supp> were added at early-log phase and continued to culture for additional <Supp> 2h </Supp> . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE54900	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GSM1326353	Δfur with DPD 1 (RNA-seq)	25222563	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT and Δfur were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. PGCGROWTHCONDITIONS	SRR1168139	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT and Δfur were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . For iron treated cells , 0.1 mM of FeCl2 were treated from the beginning of culture , and for DPD treated cells , <Supp> 0.2 mM of DPD </Supp> were added at early-log phase and continued to culture for additional <Supp> 2h </Supp> . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE54900	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GSM1326354	Δfur with DPD 2 (RNA-seq)	25222563	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT and Δfur were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. For iron treated cells, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, 0.2mM of DPD were added at early-log phase and continued to culture for additional 2h. PGCGROWTHCONDITIONS	SRR1168140	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT , and Δcra were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> , fructose and acetate . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602347	WT glucose 1	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, and Δcra were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS	SRR1787590	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT , and Δcra were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> , fructose and acetate . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602348	WT glucose 2	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, and Δcra were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS	SRR1787591	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT , and Δcra were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> , fructose and acetate . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602349	WT fructose 1	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, and Δcra were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS	SRR1787592	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT , and Δcra were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> , fructose and acetate . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602350	WT fructose 2	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, and Δcra were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS	SRR1787593	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT , and Δcra were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> , fructose and acetate . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602351	WT acetate 1	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, and Δcra were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS	SRR1787594	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT , and Δcra were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> , fructose and acetate . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602352	WT acetate 2	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, and Δcra were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS	SRR1787595	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT , and Δcra were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> , fructose and acetate . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602353	Δcra glucose 1	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, and Δcra were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS	SRR1787596	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT , and Δcra were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> , fructose and acetate . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602354	Δcra glucose 2	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, and Δcra were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS	SRR1787597	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT , and Δcra were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> , fructose and acetate . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602355	Δcra fructose 1	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, and Δcra were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS	SRR1787598	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT , and Δcra were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> , fructose and acetate . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602356	Δcra fructose 2	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, and Δcra were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS	SRR1787599	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT , and Δcra were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> , fructose and acetate . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602357	Δcra acetate 1	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, and Δcra were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS	SRR1787600	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT , and Δcra were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> , fructose and acetate . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602358	Δcra acetate 2	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, and Δcra were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose, fructose and acetate. PGCGROWTHCONDITIONS	SRR1787601	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT , ΔoxyR , ΔsoxR , and ΔsoxS were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65711	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GSM1603386	WT PQ 1	26279566	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, ΔoxyR, ΔsoxR, and ΔsoxS were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation. PGCGROWTHCONDITIONS	SRR1796598	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT , ΔoxyR , ΔsoxR , and ΔsoxS were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65711	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GSM1603387	WT PQ 2	26279566	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, ΔoxyR, ΔsoxR, and ΔsoxS were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation. PGCGROWTHCONDITIONS	SRR1796599	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT , ΔoxyR , ΔsoxR , and ΔsoxS were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65711	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GSM1603388	ΔoxyR PQ 1	26279566	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, ΔoxyR, ΔsoxR, and ΔsoxS were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation. PGCGROWTHCONDITIONS	SRR1796600	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT , ΔoxyR , ΔsoxR , and ΔsoxS were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65711	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GSM1603389	ΔoxyR PQ 2	26279566	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, ΔoxyR, ΔsoxR, and ΔsoxS were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation. PGCGROWTHCONDITIONS	SRR1796601	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT , ΔoxyR , ΔsoxR , and ΔsoxS were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65711	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GSM1603391	ΔsoxR PQ 2	26279566	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, ΔoxyR, ΔsoxR, and ΔsoxS were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation. PGCGROWTHCONDITIONS	SRR1796603	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT , ΔoxyR , ΔsoxR , and ΔsoxS were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65711	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GSM1603392	ΔsoxS PQ 1	26279566	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, ΔoxyR, ΔsoxR, and ΔsoxS were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation. PGCGROWTHCONDITIONS	SRR1796604	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT , ΔoxyR , ΔsoxR , and ΔsoxS were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65711	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GSM1603393	ΔsoxS PQ 2	26279566	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, ΔoxyR, ΔsoxR, and ΔsoxS were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation. PGCGROWTHCONDITIONS	SRR1796605	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT , gadE , gadW and gadX mutant cells were grown to <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) <Air> aerobically </Air> ( <Agit> 250 rpm </Agit> ) at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> at <pH> pH 5.5 </pH> . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623160	WT pH5.5 1	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5. PGCGROWTHCONDITIONS	SRR1824557	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT , gadE , gadW and gadX mutant cells were grown to <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) <Air> aerobically </Air> ( <Agit> 250 rpm </Agit> ) at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> at <pH> pH 5.5 </pH> . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623161	WT pH5.5 2	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5. PGCGROWTHCONDITIONS	SRR1824558	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT , gadE , gadW and gadX mutant cells were grown to <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) <Air> aerobically </Air> ( <Agit> 250 rpm </Agit> ) at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> at <pH> pH 5.5 </pH> . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623162	ΔgadE pH5.5 1	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5. PGCGROWTHCONDITIONS	SRR1824559	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT , gadE , gadW and gadX mutant cells were grown to <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) <Air> aerobically </Air> ( <Agit> 250 rpm </Agit> ) at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> at <pH> pH 5.5 </pH> . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623163	ΔgadE pH5.5 2	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5. PGCGROWTHCONDITIONS	SRR1824560	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT , gadE , gadW and gadX mutant cells were grown to <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) <Air> aerobically </Air> ( <Agit> 250 rpm </Agit> ) at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> at <pH> pH 5.5 </pH> . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623164	ΔgadW pH5.5 1	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5. PGCGROWTHCONDITIONS	SRR1824561	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT , gadE , gadW and gadX mutant cells were grown to <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) <Air> aerobically </Air> ( <Agit> 250 rpm </Agit> ) at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> at <pH> pH 5.5 </pH> . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623165	ΔgadW pH5.5 2	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5. PGCGROWTHCONDITIONS	SRR1824562	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT , gadE , gadW and gadX mutant cells were grown to <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) <Air> aerobically </Air> ( <Agit> 250 rpm </Agit> ) at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> at <pH> pH 5.5 </pH> . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623166	ΔgadX pH5.5 1	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5. PGCGROWTHCONDITIONS	SRR1824563	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT , gadE , gadW and gadX mutant cells were grown to <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) <Air> aerobically </Air> ( <Agit> 250 rpm </Agit> ) at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> at <pH> pH 5.5 </pH> . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623167	ΔgadX pH5.5 2	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5. PGCGROWTHCONDITIONS	SRR1824564	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		Escherichia coli strains E.coli C ( DSMZ 4860 ) , E. coli Crooks ( DSMZ 1576 ) , E. coli DH5α ( DSMZ 6897 ) E. coli W ( DSMZ 1116 ) , E. coli W3110 ( DSMZ 5911 ) were obtained from DSMZ-German Collection of Microorganism and Cell Cultures ; E. coli BL21 ( DE3 ) was purchased as competent cells from Agilent ( Agilent Technologies Inc. , USA ) , E. coli K-12 MG1655 ( ATCC 700926 ) . All strains were cultured in <Med> M9 minimal medium </Med> ( 1 ) containing Na2HPO4 x 7H2O ( 6.8 g ) , KH2PO4 ( 3 g ) , NaCl ( 0.5 g ) , NH4Cl ( 1 g ) , MgSO4 ( 2 mmol ) , CaCl2 ( 0.1 mmol ) , trace elements , Wolf 's vitamin solution ( 2 ) and glucose ( 2 g L-1 ) . Anoxic <Med> M9 minimal media </Med> with <Supp> glucose </Supp> was obtained by flushing solution with oxygen free nitrogen ( 95 % ) . Overnight cultures from single colonies of each of seven E. coli strains were diluted to a starting optical density ( OD600 ) of 0.01 . Cultures were grown in 250 ml flasks or 300 ml oxygen-free sealed bottles containing 50 ml <Med> glucose-M9 minimal media </Med> in a shaking incubator at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> . 	GPL14548-GPL15010-GPL21530-GPL21531-GPL21532-GPL21533-GPL21534	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21530: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. W3110). GPL21531: Illumina HiSeq 2000 (Escherichia coli W). GPL21532: Illumina HiSeq 2000 (Escherichia coli C). GPL21533: Illumina HiSeq 2000 (Escherichia coli BL21). GPL21534: Illumina HiSeq 2000 (Escherichia coli DH5[alpha])	GSE78756	Quantifying variation within the bacterial species E. coli	GSM2075722	Crooks_aero	27667363	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE78756/GSE78756.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Escherichia coli strains E.coli C (DSMZ 4860), E. coli Crooks (DSMZ 1576), E. coli DH5α (DSMZ 6897) E. coli W (DSMZ 1116), E. coli W3110 (DSMZ 5911) were obtained from DSMZ-German Collection of Microorganism and Cell Cultures; E. coli BL21 (DE3) was purchased as competent cells from Agilent (Agilent Technologies Inc., USA), E. coli K-12 MG1655 (ATCC 700926). All strains were cultured in M9 minimal medium (1) containing Na2HPO4 x 7H2O (6.8 g), KH2PO4 (3 g), NaCl (0.5 g), NH4Cl (1 g), MgSO4 (2 mmol), CaCl2 (0.1 mmol), trace elements, Wolf’s vitamin solution (2) and glucose (2 g L-1). Anoxic M9 minimal media with glucose was obtained by flushing solution with oxygen free nitrogen (95%). Overnight cultures from single colonies of each of seven E. coli strains were diluted to a starting optical density (OD600) of 0.01. Cultures were grown in 250 ml flasks or 300 ml oxygen-free sealed bottles containing 50 ml glucose-M9 minimal media in a shaking incubator at 37°C and 250 rpm. PGCGROWTHCONDITIONS	SRR3194453	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		Escherichia coli strains E.coli C ( DSMZ 4860 ) , E. coli Crooks ( DSMZ 1576 ) , E. coli DH5α ( DSMZ 6897 ) E. coli W ( DSMZ 1116 ) , E. coli W3110 ( DSMZ 5911 ) were obtained from DSMZ-German Collection of Microorganism and Cell Cultures ; E. coli BL21 ( DE3 ) was purchased as competent cells from Agilent ( Agilent Technologies Inc. , USA ) , E. coli K-12 MG1655 ( ATCC 700926 ) . All strains were cultured in <Med> M9 minimal medium </Med> ( 1 ) containing Na2HPO4 x 7H2O ( 6.8 g ) , KH2PO4 ( 3 g ) , NaCl ( 0.5 g ) , NH4Cl ( 1 g ) , MgSO4 ( 2 mmol ) , CaCl2 ( 0.1 mmol ) , trace elements , Wolf 's vitamin solution ( 2 ) and glucose ( 2 g L-1 ) . Anoxic <Med> M9 minimal media </Med> with <Supp> glucose </Supp> was obtained by flushing solution with oxygen free nitrogen ( 95 % ) . Overnight cultures from single colonies of each of seven E. coli strains were diluted to a starting optical density ( OD600 ) of 0.01 . Cultures were grown in 250 ml flasks or 300 ml oxygen-free sealed bottles containing 50 ml <Med> glucose-M9 minimal media </Med> in a shaking incubator at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> . 	GPL14548-GPL15010-GPL21530-GPL21531-GPL21532-GPL21533-GPL21534	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21530: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. W3110). GPL21531: Illumina HiSeq 2000 (Escherichia coli W). GPL21532: Illumina HiSeq 2000 (Escherichia coli C). GPL21533: Illumina HiSeq 2000 (Escherichia coli BL21). GPL21534: Illumina HiSeq 2000 (Escherichia coli DH5[alpha])	GSE78756	Quantifying variation within the bacterial species E. coli	GSM2075723	Crooks_anaero	27667363	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE78756/GSE78756.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Escherichia coli strains E.coli C (DSMZ 4860), E. coli Crooks (DSMZ 1576), E. coli DH5α (DSMZ 6897) E. coli W (DSMZ 1116), E. coli W3110 (DSMZ 5911) were obtained from DSMZ-German Collection of Microorganism and Cell Cultures; E. coli BL21 (DE3) was purchased as competent cells from Agilent (Agilent Technologies Inc., USA), E. coli K-12 MG1655 (ATCC 700926). All strains were cultured in M9 minimal medium (1) containing Na2HPO4 x 7H2O (6.8 g), KH2PO4 (3 g), NaCl (0.5 g), NH4Cl (1 g), MgSO4 (2 mmol), CaCl2 (0.1 mmol), trace elements, Wolf’s vitamin solution (2) and glucose (2 g L-1). Anoxic M9 minimal media with glucose was obtained by flushing solution with oxygen free nitrogen (95%). Overnight cultures from single colonies of each of seven E. coli strains were diluted to a starting optical density (OD600) of 0.01. Cultures were grown in 250 ml flasks or 300 ml oxygen-free sealed bottles containing 50 ml glucose-M9 minimal media in a shaking incubator at 37°C and 250 rpm. PGCGROWTHCONDITIONS	SRR3194455SRR3194456	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT and ΔompR were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . Then cells were treated with <Supp> 0.3 M of NaCl </Supp> at mid-log pahse for <Supp> 30 min </Supp> with agitation . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE88980	Revealing the genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles and unexpected importance of narU under osmotic stress in Escherichia coli K-12 MG1655 [RNA-seq]	GSM2356687	WT NaCl 1	28526842	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88980/GSE88980.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT and ΔompR were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 0.3 M of NaCl at mid-log pahse for 30 min with agitation. PGCGROWTHCONDITIONS	SRR4435464	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT and ΔompR were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . Then cells were treated with <Supp> 0.3 M of NaCl </Supp> at mid-log pahse for <Supp> 30 min </Supp> with agitation . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE88980	Revealing the genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles and unexpected importance of narU under osmotic stress in Escherichia coli K-12 MG1655 [RNA-seq]	GSM2356688	WT NaCl 2	28526842	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88980/GSE88980.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT and ΔompR were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 0.3 M of NaCl at mid-log pahse for 30 min with agitation. PGCGROWTHCONDITIONS	SRR4435465	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT and ΔompR were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . Then cells were treated with <Supp> 0.3 M of NaCl </Supp> at mid-log pahse for <Supp> 30 min </Supp> with agitation . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE88980	Revealing the genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles and unexpected importance of narU under osmotic stress in Escherichia coli K-12 MG1655 [RNA-seq]	GSM2356689	ΔompR NaCl 1	28526842	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88980/GSE88980.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT and ΔompR were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 0.3 M of NaCl at mid-log pahse for 30 min with agitation. PGCGROWTHCONDITIONS	SRR4435466	MCO000002526	M9 minimal media	Medium	True
growth_protocol	M9 minimal medium		E. coli K-12 MG1655 WT and ΔompR were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . Then cells were treated with <Supp> 0.3 M of NaCl </Supp> at mid-log pahse for <Supp> 30 min </Supp> with agitation . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE88980	Revealing the genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles and unexpected importance of narU under osmotic stress in Escherichia coli K-12 MG1655 [RNA-seq]	GSM2356690	ΔompR NaCl 2	28526842	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88980/GSE88980.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT and ΔompR were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 0.3 M of NaCl at mid-log pahse for 30 min with agitation. PGCGROWTHCONDITIONS	SRR4435467	MCO000002526	M9 minimal media	Medium	True
characteristics	mid log phase		phase : <Phase> mid-log phase </Phase> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE111094	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GSM3022135	WT rep1	33149261	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	phase: mid-log phase PGCGROWTHCONDITIONS	SRR6781997	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		phase : <Phase> mid-log phase </Phase> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE111094	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GSM3022136	WT rep2	33149261	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	phase: mid-log phase PGCGROWTHCONDITIONS	SRR6781998	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		phase : <Phase> mid-log phase </Phase> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE111094	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GSM3022137	yafC-KO rep1	33149261	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	phase: mid-log phase PGCGROWTHCONDITIONS	SRR6781999	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		phase : <Phase> mid-log phase </Phase> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE111094	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GSM3022138	yafC-KO rep2	33149261	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	phase: mid-log phase PGCGROWTHCONDITIONS	SRR6782000	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		phase : <Phase> mid-log phase </Phase> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE111094	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GSM3022139	yeiE-KO rep1	33149261	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	phase: mid-log phase PGCGROWTHCONDITIONS	SRR6782001	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		phase : <Phase> mid-log phase </Phase> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE111094	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GSM3022140	yeiE-KO rep2	33149261	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	phase: mid-log phase PGCGROWTHCONDITIONS	SRR6782002	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		phase : <Phase> mid-log phase </Phase> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE111094	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GSM3022141	yiaJ-KO rep1	33149261	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	phase: mid-log phase PGCGROWTHCONDITIONS	SRR6782003	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		phase : <Phase> mid-log phase </Phase> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE111094	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GSM3022142	yiaJ-KO rep2	33149261	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	phase: mid-log phase PGCGROWTHCONDITIONS	SRR6782004	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		phase : <Phase> mid-log phase </Phase> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE111094	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GSM3022143	yieP-KO rep1	33149261	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	phase: mid-log phase PGCGROWTHCONDITIONS	SRR6782005	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		phase : <Phase> mid-log phase </Phase> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE111094	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GSM3022144	yieP-KO rep2	33149261	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	phase: mid-log phase PGCGROWTHCONDITIONS	SRR6782006	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		phase : <Phase> mid-log phase </Phase> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE111094	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GSM3108934	WT-low-ph rep1	33149261	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	phase: mid-log phase PGCGROWTHCONDITIONS	SRR7057985	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		phase : <Phase> mid-log phase </Phase> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE111094	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GSM3108935	WT-low-ph rep2	33149261	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	phase: mid-log phase PGCGROWTHCONDITIONS	SRR7057986	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		phase : <Phase> mid-log phase </Phase> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE111094	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GSM3108936	WT-high-ph rep1	33149261	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	phase: mid-log phase PGCGROWTHCONDITIONS	SRR7057987	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		phase : <Phase> mid-log phase </Phase> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE111094	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GSM3108937	WT-high-ph rep2	33149261	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	phase: mid-log phase PGCGROWTHCONDITIONS	SRR7057988	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		phase : <Phase> mid-log phase </Phase> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE111094	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GSM3108938	ybaO-KO rep1	33149261	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	phase: mid-log phase PGCGROWTHCONDITIONS	SRR7057989	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		phase : <Phase> mid-log phase </Phase> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE111094	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GSM3108939	ybaO-KO rep2	33149261	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	phase: mid-log phase PGCGROWTHCONDITIONS	SRR7057990	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		phase : <Phase> mid-log phase </Phase> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE111094	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GSM3108940	ybaQ-KO rep1	33149261	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	phase: mid-log phase PGCGROWTHCONDITIONS	SRR7057991	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		phase : <Phase> mid-log phase </Phase> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE111094	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GSM3108941	ybaQ-KO rep2	33149261	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	phase: mid-log phase PGCGROWTHCONDITIONS	SRR7057992	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		phase : <Phase> mid-log phase </Phase> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE111094	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GSM3108942	ybiH-KO rep1	33149261	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	phase: mid-log phase PGCGROWTHCONDITIONS	SRR7057993	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		phase : <Phase> mid-log phase </Phase> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE111094	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GSM3108943	ybiH-KO rep2	33149261	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	phase: mid-log phase PGCGROWTHCONDITIONS	SRR7057994	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		phase : <Phase> mid-log phase </Phase> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE111094	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GSM3108944	ydcI-KO-low-ph rep1	33149261	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	phase: mid-log phase PGCGROWTHCONDITIONS	SRR7057995	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		phase : <Phase> mid-log phase </Phase> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE111094	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GSM3108945	ydcI-KO-low-ph rep2	33149261	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	phase: mid-log phase PGCGROWTHCONDITIONS	SRR7057996	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		phase : <Phase> mid-log phase </Phase> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE111094	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GSM3108946	ydcI-KO-high-ph rep1	33149261	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	phase: mid-log phase PGCGROWTHCONDITIONS	SRR7057997	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		phase : <Phase> mid-log phase </Phase> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE111094	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GSM3108947	ydcI-KO-high-ph rep2	33149261	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	phase: mid-log phase PGCGROWTHCONDITIONS	SRR7057998	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		phase : <Phase> mid-log phase </Phase> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE111094	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GSM3108948	yddM-KO rep1	33149261	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	phase: mid-log phase PGCGROWTHCONDITIONS	SRR7057999	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		phase : <Phase> mid-log phase </Phase> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE111094	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GSM3108949	yddM-KO rep2	33149261	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	phase: mid-log phase PGCGROWTHCONDITIONS	SRR7058000	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		phase : <Phase> mid-log phase </Phase> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE111094	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GSM3108950	yheO-KO rep1	33149261	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	phase: mid-log phase PGCGROWTHCONDITIONS	SRR7058001	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		phase : <Phase> mid-log phase </Phase> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE111094	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GSM3108951	yheO-KO rep2	33149261	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	phase: mid-log phase PGCGROWTHCONDITIONS	SRR7058002	MCO000002872	mid-log phase	Growth phase	True
growth_protocol	mid log phase		glycerol stocks of E. coli strains were inoculated into M9 minimal media with <Supp> 2g/L glucose </Supp> , supplemented with 1 ml trace element solution ( 100X ) . The culture was incubated at 37C overnight with agitation , and then was used to inoculate the fresh <Med> media </Med> . The fresh culture was incubated at 37C with agitation to the <Phase> mid-log phase </Phase> ( OD600 ≈ 0.5 ) . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE122296	Expression profiling of multiple Escherichia coli strains on glucose minimal media	GSM3463601	MG1655_1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122296/GSE122296.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	glycerol stocks of E. coli strains were inoculated into M9 minimal media with 2g/L glucose, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5). PGCGROWTHCONDITIONS	SRR8173221	MCO000002872	mid-log phase	Growth phase	True
growth_protocol	mid log phase		glycerol stocks of E. coli strains were inoculated into M9 minimal media with <Supp> 2g/L glucose </Supp> , supplemented with 1 ml trace element solution ( 100X ) . The culture was incubated at 37C overnight with agitation , and then was used to inoculate the fresh <Med> media </Med> . The fresh culture was incubated at 37C with agitation to the <Phase> mid-log phase </Phase> ( OD600 ≈ 0.5 ) . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE122296	Expression profiling of multiple Escherichia coli strains on glucose minimal media	GSM3463602	MG1655_2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122296/GSE122296.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	glycerol stocks of E. coli strains were inoculated into M9 minimal media with 2g/L glucose, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5). PGCGROWTHCONDITIONS	SRR8173222	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		growth stage : <Phase> mid-log phase </Phase> 	GPL10328	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	GSE33671	Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo	GSM832606	DSP1_AP	22153074	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE33671/GSE33671.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	growth stage: mid-log phase PGCGROWTHCONDITIONS	SRR364363	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		growth stage : <Phase> mid-log phase </Phase> 	GPL10328	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	GSE33671	Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo	GSM832607	DSP1_Total	22153074	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE33671/GSE33671.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	growth stage: mid-log phase PGCGROWTHCONDITIONS	SRR364364	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		growth stage : <Phase> mid-log phase </Phase> 	GPL10328	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	GSE33671	Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo	GSM832608	DSP2_AP	22153074	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE33671/GSE33671.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	growth stage: mid-log phase PGCGROWTHCONDITIONS	SRR364365	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		growth stage : <Phase> mid-log phase </Phase> 	GPL10328	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	GSE33671	Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo	GSM832609	DSP2_Total	22153074	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE33671/GSE33671.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	growth stage: mid-log phase PGCGROWTHCONDITIONS	SRR364366	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		growth stage : <Phase> mid-log phase </Phase> 	GPL10328	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	GSE33671	Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo	GSM832610	DSP3_AP	22153074	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE33671/GSE33671.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	growth stage: mid-log phase PGCGROWTHCONDITIONS	SRR364367	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		growth stage : <Phase> mid-log phase </Phase> 	GPL10328	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	GSE33671	Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo	GSM832611	DSP3_Total	22153074	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE33671/GSE33671.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	growth stage: mid-log phase PGCGROWTHCONDITIONS	SRR364368	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		growth stage : <Phase> mid-log phase </Phase> 	GPL10328	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	GSE33671	Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo	GSM832612	EDC1_AP	22153074	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE33671/GSE33671.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	growth stage: mid-log phase PGCGROWTHCONDITIONS	SRR364369	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		growth stage : <Phase> mid-log phase </Phase> 	GPL10328	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	GSE33671	Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo	GSM832613	EDC1_Total	22153074	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE33671/GSE33671.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	growth stage: mid-log phase PGCGROWTHCONDITIONS	SRR364370	MCO000002872	mid-log phase	Growth phase	True
growth_protocol	mid log phase		E. coli MC4100 strain was cultured at <Temp> 37 °C </Temp> to <Phase> mid-log phase </Phase> ( OD600 ~ 0.4 ) in <Med> LB media </Med> 	GPL14548-GPL18945	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	GSE63817	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GSM1558078	LB mRNA	26495981	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE63817/GSE63817.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media PGCGROWTHCONDITIONS	SRR1692165	MCO000002872	mid-log phase	Growth phase	True
growth_protocol	mid log phase		E. coli MC4100 strain was cultured at <Temp> 37 °C </Temp> to <Phase> mid-log phase </Phase> ( OD600 ~ 0.4 ) in <Med> LB media </Med> 	GPL14548-GPL18945	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	GSE63817	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GSM1558079	LB RPF	26495981	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE63817/GSE63817.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media PGCGROWTHCONDITIONS	SRR1692166	MCO000002872	mid-log phase	Growth phase	True
growth_protocol	mid log phase		E. coli MC4100 strain was cultured at <Temp> 37 °C </Temp> to <Phase> mid-log phase </Phase> ( OD600 ~ 0.4 ) in <Med> LB media </Med> 	GPL14548-GPL18945	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	GSE63817	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GSM1558080	LB mRNA technical replicate	26495981	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE63817/GSE63817.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media PGCGROWTHCONDITIONS	SRR1692167	MCO000002872	mid-log phase	Growth phase	True
growth_protocol	mid log phase		E. coli MC4100 strain was cultured at <Temp> 37 °C </Temp> to <Phase> mid-log phase </Phase> ( OD600 ~ 0.4 ) in <Med> LB media </Med> 	GPL14548-GPL18945	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	GSE63817	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GSM1558081	LB RPF biological replicate	26495981	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE63817/GSE63817.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media PGCGROWTHCONDITIONS	SRR1692168	MCO000002872	mid-log phase	Growth phase	True
growth_protocol	mid log phase		E. coli MC4100 strain was cultured at <Temp> 37 °C </Temp> to <Phase> mid-log phase </Phase> ( OD600 ~ 0.4 ) in <Med> LB media </Med> 	GPL14548-GPL18945	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	GSE63817	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GSM1558082	LB mRNA biological replicate	26495981	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE63817/GSE63817.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media PGCGROWTHCONDITIONS	SRR1692169	MCO000002872	mid-log phase	Growth phase	True
growth_protocol	mid log phase		E. coli MC4100 strain was cultured at <Temp> 37 °C </Temp> to <Phase> mid-log phase </Phase> ( OD600 ~ 0.4 ) in <Med> LB media </Med> 	GPL14548-GPL18945	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	GSE63817	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GSM1558086	AT1 biological replicate	26495981	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE63817/GSE63817.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media PGCGROWTHCONDITIONS	SRR1692173	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		growth phase : <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623160	WT pH5.5 1	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	growth phase: mid-log phase (OD600 = 0.3) PGCGROWTHCONDITIONS	SRR1824557	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		growth phase : <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623161	WT pH5.5 2	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	growth phase: mid-log phase (OD600 = 0.3) PGCGROWTHCONDITIONS	SRR1824558	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		growth phase : <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623162	ΔgadE pH5.5 1	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	growth phase: mid-log phase (OD600 = 0.3) PGCGROWTHCONDITIONS	SRR1824559	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		growth phase : <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623163	ΔgadE pH5.5 2	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	growth phase: mid-log phase (OD600 = 0.3) PGCGROWTHCONDITIONS	SRR1824560	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		growth phase : <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623164	ΔgadW pH5.5 1	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	growth phase: mid-log phase (OD600 = 0.3) PGCGROWTHCONDITIONS	SRR1824561	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		growth phase : <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623165	ΔgadW pH5.5 2	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	growth phase: mid-log phase (OD600 = 0.3) PGCGROWTHCONDITIONS	SRR1824562	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		growth phase : <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623166	ΔgadX pH5.5 1	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	growth phase: mid-log phase (OD600 = 0.3) PGCGROWTHCONDITIONS	SRR1824563	MCO000002872	mid-log phase	Growth phase	True
characteristics	mid log phase		growth phase : <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623167	ΔgadX pH5.5 2	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	growth phase: mid-log phase (OD600 = 0.3) PGCGROWTHCONDITIONS	SRR1824564	MCO000002872	mid-log phase	Growth phase	True
data_processing	Escherichia coli BW25113		Genome _ build : <Gtype> E.coli K12 BW25113 </Gtype> 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE114262	RNA-seq Analyzes Transcriptomes of dnaB-Ts and dnaB-Ts ΔahpC at Both Permissive and Non-permissive Temperature	GSM3138597	dnaB-Ts ΔahpC_30°C	30948634	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE114262/GSE114262.soft.gz	80	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Genome_build: E.coli K12 BW25113 PGCGROWTHCONDITIONS	SRR7140738	MCO000002505	E.coli K12 BW25113	Genetic background	True
data_processing	Escherichia coli BW25113		Genome _ build : <Gtype> E.coli K12 BW25113 </Gtype> 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE114262	RNA-seq Analyzes Transcriptomes of dnaB-Ts and dnaB-Ts ΔahpC at Both Permissive and Non-permissive Temperature	GSM3138598	dnaB-Ts_42°C	30948634	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE114262/GSE114262.soft.gz	80	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Genome_build: E.coli K12 BW25113 PGCGROWTHCONDITIONS	SRR7140739	MCO000002505	E.coli K12 BW25113	Genetic background	True
data_processing	Escherichia coli BW25113		Genome _ build : <Gtype> E.coli K12 BW25113 </Gtype> 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE114262	RNA-seq Analyzes Transcriptomes of dnaB-Ts and dnaB-Ts ΔahpC at Both Permissive and Non-permissive Temperature	GSM3138599	dnaB-Ts ΔahpC_42°C	30948634	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE114262/GSE114262.soft.gz	80	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Genome_build: E.coli K12 BW25113 PGCGROWTHCONDITIONS	SRR7140740	MCO000002505	E.coli K12 BW25113	Genetic background	True
growth_protocol	synH medium		Overnight cultures of the dnaB-Ts single mutant ( strain 2429 ) and the dnaB-Ts ΔahpC double mutant ( strain 3780 ) were diluted 100-fold into fresh <Med> SB medium </Med> ( 3.2 % peptone , 2 % yeast extract and 1 % NaCl ) , and they were then grown at 30 °C to early-log phase ( OD600 = 0.15 ) . Next these log-phase cultures were diluted 20-fold into 200 ml pre-warmed , fresh SB medium , and they were grown at 30 °C for another 60 min . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE114262	RNA-seq Analyzes Transcriptomes of dnaB-Ts and dnaB-Ts ΔahpC at Both Permissive and Non-permissive Temperature	GSM3138597	dnaB-Ts ΔahpC_30°C	30948634	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE114262/GSE114262.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Overnight cultures of the dnaB-Ts single mutant (strain 2429) and the dnaB-Ts ΔahpC double mutant (strain 3780) were diluted 100-fold into fresh SB medium (3.2% peptone, 2% yeast extract and 1% NaCl), and they were then grown at 30 °C to early-log phase (OD600 = 0.15).  Next these log-phase cultures were diluted 20-fold into 200 ml pre-warmed, fresh SB medium, and they were grown at 30 °C for another 60 min. PGCGROWTHCONDITIONS	SRR7140738	MCO000003163	SB medium	Medium	True
growth_protocol	synH medium		Overnight cultures of the dnaB-Ts single mutant ( strain 2429 ) and the dnaB-Ts ΔahpC double mutant ( strain 3780 ) were diluted 100-fold into fresh <Med> SB medium </Med> ( 3.2 % peptone , 2 % yeast extract and 1 % NaCl ) , and they were then grown at 30 °C to early-log phase ( OD600 = 0.15 ) . Next these log-phase cultures were diluted 20-fold into 200 ml pre-warmed , fresh SB medium , and they were grown at 30 °C for another 60 min . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE114262	RNA-seq Analyzes Transcriptomes of dnaB-Ts and dnaB-Ts ΔahpC at Both Permissive and Non-permissive Temperature	GSM3138598	dnaB-Ts_42°C	30948634	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE114262/GSE114262.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Overnight cultures of the dnaB-Ts single mutant (strain 2429) and the dnaB-Ts ΔahpC double mutant (strain 3780) were diluted 100-fold into fresh SB medium (3.2% peptone, 2% yeast extract and 1% NaCl), and they were then grown at 30 °C to early-log phase (OD600 = 0.15).  Next these log-phase cultures were diluted 20-fold into 200 ml pre-warmed, fresh SB medium, and they were grown at 30 °C for another 60 min. PGCGROWTHCONDITIONS	SRR7140739	MCO000003163	SB medium	Medium	True
growth_protocol	synH medium		Overnight cultures of the dnaB-Ts single mutant ( strain 2429 ) and the dnaB-Ts ΔahpC double mutant ( strain 3780 ) were diluted 100-fold into fresh <Med> SB medium </Med> ( 3.2 % peptone , 2 % yeast extract and 1 % NaCl ) , and they were then grown at 30 °C to early-log phase ( OD600 = 0.15 ) . Next these log-phase cultures were diluted 20-fold into 200 ml pre-warmed , fresh SB medium , and they were grown at 30 °C for another 60 min . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE114262	RNA-seq Analyzes Transcriptomes of dnaB-Ts and dnaB-Ts ΔahpC at Both Permissive and Non-permissive Temperature	GSM3138599	dnaB-Ts ΔahpC_42°C	30948634	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE114262/GSE114262.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Overnight cultures of the dnaB-Ts single mutant (strain 2429) and the dnaB-Ts ΔahpC double mutant (strain 3780) were diluted 100-fold into fresh SB medium (3.2% peptone, 2% yeast extract and 1% NaCl), and they were then grown at 30 °C to early-log phase (OD600 = 0.15).  Next these log-phase cultures were diluted 20-fold into 200 ml pre-warmed, fresh SB medium, and they were grown at 30 °C for another 60 min. PGCGROWTHCONDITIONS	SRR7140740	MCO000003163	SB medium	Medium	True
characteristics	wild type		plasmid : <Gtype> pLCenvZ , pPCB ( wild type ) </Gtype> 	GPL25346	GPL25346: HiSeq X Ten (Escherichia coli)	GSE117326	Gene expression profiles in E. coli under different frequency signals	GSM3291044	envz600		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117326/GSE117326.soft.gz	100	58	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	plasmid: pLCenvZ, pPCB (wild type) PGCGROWTHCONDITIONS	SRR7537397	MCO000002470	pLCenvZ , pPCB ( wild type )	Genetic background	True
characteristics	wild type		plasmid : <Gtype> pLCenvZ , pPCB ( wild type ) </Gtype> 	GPL25346	GPL25346: HiSeq X Ten (Escherichia coli)	GSE117326	Gene expression profiles in E. coli under different frequency signals	GSM3291045	envz900		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117326/GSE117326.soft.gz	100	58	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	plasmid: pLCenvZ, pPCB (wild type) PGCGROWTHCONDITIONS	SRR7537398	MCO000002470	pLCenvZ , pPCB ( wild type )	Genetic background	True
characteristics	wild type		plasmid : <Gtype> pLCenvZ , pPCB ( wild type ) </Gtype> 	GPL25346	GPL25346: HiSeq X Ten (Escherichia coli)	GSE117326	Gene expression profiles in E. coli under different frequency signals	GSM3291049	envz3600		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117326/GSE117326.soft.gz	100	58	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	plasmid: pLCenvZ, pPCB (wild type) PGCGROWTHCONDITIONS	SRR7537402	MCO000002470	pLCenvZ , pPCB ( wild type )	Genetic background	True
growth_protocol	LB medium		Escherichia coli K-12 MG1655 were cultured in <Med> LB media </Med> ( 10 g/L tryptone , 5 g/L yeast extract , 10 g/L NaCl , pH 7.4 ) under aerobic conditions at <Temp> 37 °C </Temp> . The temperature-sensitive RNase E mutant E.coli strain [ rne-3071 ( ts ) ] was cultured in <Med> LB media </Med> at 28 °C for normal culture and shift to 44 °C to deactive RNase E activity . 	GPL16085-GPL21222	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE117737	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GSM3566393	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 4	31308523	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	82	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Escherichia coli K-12 MG1655 were cultured in LB media (10 g/L tryptone, 5 g/L yeast extract, 10 g/L NaCl, pH 7.4) under aerobic conditions at 37 °C. The temperature-sensitive RNase E mutant E.coli strain [rne-3071(ts)] was cultured in LB media at 28 °C  for normal culture and shift to 44 °C to deactive RNase E activity. PGCGROWTHCONDITIONS	SRR8449235	MCO000002533	LB media	Medium	True
treatment_protocol	LB medium		<Gtype> Wild type </Gtype> E. coli , pnp knoctout , rnb knoctout and rnr knoct out strains were cultured in <Med> LB media </Med> at <Temp> 37 °C </Temp> , RNA samples and ChIP-seq samples were collected when the growth stage of indicated cells reached to log phase or stationary phase . rne-3071 ( ts ) mutation strain was cultured in <Med> LB media </Med> at 28 °C to retain the RNase E activity or shifted to 44 °C in water bath for 30 minutes to deactivate RNase E . In order to <Gtype> inactive the rho activity , the wild type ( WT ) Wild type </Gtype> E. coli was cultured in <Med> LB media </Med> with 50 μg/ml bicyclomycin at <Temp> 37 °C </Temp> for 15 min at indicated growth condition . 	GPL16085-GPL21222	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE117737	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GSM3566393	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 4	31308523	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	82	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Wild type E. coli, pnp knoctout, rnb knoctout and rnr knoct out strains were cultured in LB media at 37 °C, RNA samples and ChIP-seq samples were collected when the growth stage of indicated cells reached to log phase or stationary phase.  rne-3071(ts) mutation strain was cultured in LB media at 28 °C to retain the RNase E activity or shifted to 44 °C in water bath for 30 minutes to deactivate RNase E. In order to inactive the rho activity, the wild type (WT) Wild type E. coli was cultured in LB media with 50 μg/ml bicyclomycin at 37 °C for 15 min at indicated growth condition. PGCGROWTHCONDITIONS	SRR8449235	MCO000002533	LB media	Medium	True
growth_protocol	LB medium		Escherichia coli K-12 MG1655 were cultured in <Med> LB media </Med> ( 10 g/L tryptone , 5 g/L yeast extract , 10 g/L NaCl , pH 7.4 ) under aerobic conditions at <Temp> 37 °C </Temp> . The temperature-sensitive RNase E mutant E.coli strain [ rne-3071 ( ts ) ] was cultured in <Med> LB media </Med> at 28 °C for normal culture and shift to 44 °C to deactive RNase E activity . 	GPL16085-GPL21222	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE117737	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GSM3566394	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 5	31308523	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	82	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Escherichia coli K-12 MG1655 were cultured in LB media (10 g/L tryptone, 5 g/L yeast extract, 10 g/L NaCl, pH 7.4) under aerobic conditions at 37 °C. The temperature-sensitive RNase E mutant E.coli strain [rne-3071(ts)] was cultured in LB media at 28 °C  for normal culture and shift to 44 °C to deactive RNase E activity. PGCGROWTHCONDITIONS	SRR8449236	MCO000002533	LB media	Medium	True
treatment_protocol	LB medium		<Gtype> Wild type </Gtype> E. coli , pnp knoctout , rnb knoctout and rnr knoct out strains were cultured in <Med> LB media </Med> at <Temp> 37 °C </Temp> , RNA samples and ChIP-seq samples were collected when the growth stage of indicated cells reached to log phase or stationary phase . rne-3071 ( ts ) mutation strain was cultured in <Med> LB media </Med> at 28 °C to retain the RNase E activity or shifted to 44 °C in water bath for 30 minutes to deactivate RNase E . In order to <Gtype> inactive the rho activity , the wild type ( WT ) Wild type </Gtype> E. coli was cultured in <Med> LB media </Med> with 50 μg/ml bicyclomycin at <Temp> 37 °C </Temp> for 15 min at indicated growth condition . 	GPL16085-GPL21222	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE117737	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GSM3566394	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 5	31308523	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	82	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Wild type E. coli, pnp knoctout, rnb knoctout and rnr knoct out strains were cultured in LB media at 37 °C, RNA samples and ChIP-seq samples were collected when the growth stage of indicated cells reached to log phase or stationary phase.  rne-3071(ts) mutation strain was cultured in LB media at 28 °C to retain the RNase E activity or shifted to 44 °C in water bath for 30 minutes to deactivate RNase E. In order to inactive the rho activity, the wild type (WT) Wild type E. coli was cultured in LB media with 50 μg/ml bicyclomycin at 37 °C for 15 min at indicated growth condition. PGCGROWTHCONDITIONS	SRR8449236	MCO000002533	LB media	Medium	True
growth_protocol	LB medium		Escherichia coli K-12 MG1655 were cultured in <Med> LB media </Med> ( 10 g/L tryptone , 5 g/L yeast extract , 10 g/L NaCl , pH 7.4 ) under aerobic conditions at <Temp> 37 °C </Temp> . The temperature-sensitive RNase E mutant E.coli strain [ rne-3071 ( ts ) ] was cultured in <Med> LB media </Med> at 28 °C for normal culture and shift to 44 °C to deactive RNase E activity . 	GPL16085-GPL21222	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE117737	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GSM3566395	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 6	31308523	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	82	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Escherichia coli K-12 MG1655 were cultured in LB media (10 g/L tryptone, 5 g/L yeast extract, 10 g/L NaCl, pH 7.4) under aerobic conditions at 37 °C. The temperature-sensitive RNase E mutant E.coli strain [rne-3071(ts)] was cultured in LB media at 28 °C  for normal culture and shift to 44 °C to deactive RNase E activity. PGCGROWTHCONDITIONS	SRR8449237	MCO000002533	LB media	Medium	True
treatment_protocol	LB medium		<Gtype> Wild type </Gtype> E. coli , pnp knoctout , rnb knoctout and rnr knoct out strains were cultured in <Med> LB media </Med> at <Temp> 37 °C </Temp> , RNA samples and ChIP-seq samples were collected when the growth stage of indicated cells reached to log phase or stationary phase . rne-3071 ( ts ) mutation strain was cultured in <Med> LB media </Med> at 28 °C to retain the RNase E activity or shifted to 44 °C in water bath for 30 minutes to deactivate RNase E . In order to <Gtype> inactive the rho activity , the wild type ( WT ) Wild type </Gtype> E. coli was cultured in <Med> LB media </Med> with 50 μg/ml bicyclomycin at <Temp> 37 °C </Temp> for 15 min at indicated growth condition . 	GPL16085-GPL21222	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE117737	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GSM3566395	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 6	31308523	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	82	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Wild type E. coli, pnp knoctout, rnb knoctout and rnr knoct out strains were cultured in LB media at 37 °C, RNA samples and ChIP-seq samples were collected when the growth stage of indicated cells reached to log phase or stationary phase.  rne-3071(ts) mutation strain was cultured in LB media at 28 °C to retain the RNase E activity or shifted to 44 °C in water bath for 30 minutes to deactivate RNase E. In order to inactive the rho activity, the wild type (WT) Wild type E. coli was cultured in LB media with 50 μg/ml bicyclomycin at 37 °C for 15 min at indicated growth condition. PGCGROWTHCONDITIONS	SRR8449237	MCO000002533	LB media	Medium	True
growth_protocol	LB medium		Escherichia coli K-12 MG1655 were cultured in <Med> LB media </Med> ( 10 g/L tryptone , 5 g/L yeast extract , 10 g/L NaCl , pH 7.4 ) under aerobic conditions at <Temp> 37 °C </Temp> . The temperature-sensitive RNase E mutant E.coli strain [ rne-3071 ( ts ) ] was cultured in <Med> LB media </Med> at 28 °C for normal culture and shift to 44 °C to deactive RNase E activity . 	GPL16085-GPL21222	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE117737	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GSM3566396	RNA-seq WT log phase related to total SEnd-seq WT stationary phase rep4	31308523	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	82	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Escherichia coli K-12 MG1655 were cultured in LB media (10 g/L tryptone, 5 g/L yeast extract, 10 g/L NaCl, pH 7.4) under aerobic conditions at 37 °C. The temperature-sensitive RNase E mutant E.coli strain [rne-3071(ts)] was cultured in LB media at 28 °C  for normal culture and shift to 44 °C to deactive RNase E activity. PGCGROWTHCONDITIONS	SRR8449238	MCO000002533	LB media	Medium	True
treatment_protocol	LB medium		<Gtype> Wild type </Gtype> E. coli , pnp knoctout , rnb knoctout and rnr knoct out strains were cultured in <Med> LB media </Med> at <Temp> 37 °C </Temp> , RNA samples and ChIP-seq samples were collected when the growth stage of indicated cells reached to log phase or stationary phase . rne-3071 ( ts ) mutation strain was cultured in <Med> LB media </Med> at 28 °C to retain the RNase E activity or shifted to 44 °C in water bath for 30 minutes to deactivate RNase E . In order to <Gtype> inactive the rho activity , the wild type ( WT ) Wild type </Gtype> E. coli was cultured in <Med> LB media </Med> with 50 μg/ml bicyclomycin at <Temp> 37 °C </Temp> for 15 min at indicated growth condition . 	GPL16085-GPL21222	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE117737	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GSM3566396	RNA-seq WT log phase related to total SEnd-seq WT stationary phase rep4	31308523	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	82	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Wild type E. coli, pnp knoctout, rnb knoctout and rnr knoct out strains were cultured in LB media at 37 °C, RNA samples and ChIP-seq samples were collected when the growth stage of indicated cells reached to log phase or stationary phase.  rne-3071(ts) mutation strain was cultured in LB media at 28 °C to retain the RNase E activity or shifted to 44 °C in water bath for 30 minutes to deactivate RNase E. In order to inactive the rho activity, the wild type (WT) Wild type E. coli was cultured in LB media with 50 μg/ml bicyclomycin at 37 °C for 15 min at indicated growth condition. PGCGROWTHCONDITIONS	SRR8449238	MCO000002533	LB media	Medium	True
extract_protocol	LB medium		From the cells cultured in <Med> LB media </Med> at 37 ℃ , total RNA was extracted using RNAsnapTM method , followed by the ethanol precipitation . rRNA was removed using ribo-zeroTM magnetic kit for bacteria in accordance with manufacturer 's instruction ( Epicentre ) . rRNA removal was confirmed using ExperionTM system . Subsequently , 4 µg of the purified RNA was fragmented to sizes of ~ 300 bp using RNA fragmentation reagent ( Ambion , Grand Island , NY ) . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE67218	Transcriptional expression level of E. coli at 37 ℃ in LB media	GSM1642593	RNA-seq 37C LB rep1		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE67218/GSE67218.soft.gz	82	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	From the cells cultured in LB media at 37 ℃, total RNA was extracted using RNAsnapTM method, followed by the ethanol precipitation. rRNA was removed using ribo-zeroTM magnetic kit for bacteria in accordance with manufacturer’s instruction (Epicentre). rRNA removal was confirmed using ExperionTM system. Subsequently, 4 µg of the purified RNA was fragmented to sizes of ~300 bp using RNA fragmentation reagent (Ambion, Grand Island, NY). PGCGROWTHCONDITIONS	SRR1927169	MCO000002533	LB media	Medium	True
extract_protocol	LB medium		From the cells cultured in <Med> LB media </Med> at 37 ℃ , total RNA was extracted using RNAsnapTM method , followed by the ethanol precipitation . rRNA was removed using ribo-zeroTM magnetic kit for bacteria in accordance with manufacturer 's instruction ( Epicentre ) . rRNA removal was confirmed using ExperionTM system . Subsequently , 4 µg of the purified RNA was fragmented to sizes of ~ 300 bp using RNA fragmentation reagent ( Ambion , Grand Island , NY ) . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE67218	Transcriptional expression level of E. coli at 37 ℃ in LB media	GSM1642594	RNA-seq 37C LB rep2		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE67218/GSE67218.soft.gz	82	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	From the cells cultured in LB media at 37 ℃, total RNA was extracted using RNAsnapTM method, followed by the ethanol precipitation. rRNA was removed using ribo-zeroTM magnetic kit for bacteria in accordance with manufacturer’s instruction (Epicentre). rRNA removal was confirmed using ExperionTM system. Subsequently, 4 µg of the purified RNA was fragmented to sizes of ~300 bp using RNA fragmentation reagent (Ambion, Grand Island, NY). PGCGROWTHCONDITIONS	SRR1927170	MCO000002533	LB media	Medium	True
treatment_protocol	wild type		<Gtype> Wild type </Gtype> E. coli , pnp knoctout , rnb knoctout and rnr knoct out strains were cultured in <Med> LB media </Med> at <Temp> 37 °C </Temp> , RNA samples and ChIP-seq samples were collected when the growth stage of indicated cells reached to log phase or stationary phase . rne-3071 ( ts ) mutation strain was cultured in <Med> LB media </Med> at 28 °C to retain the RNase E activity or shifted to 44 °C in water bath for 30 minutes to deactivate RNase E . In order to <Gtype> inactive the rho activity , the wild type ( WT ) Wild type </Gtype> E. coli was cultured in <Med> LB media </Med> with 50 μg/ml bicyclomycin at <Temp> 37 °C </Temp> for 15 min at indicated growth condition . 	GPL16085-GPL21222	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE117737	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GSM3566393	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 4	31308523	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Wild type E. coli, pnp knoctout, rnb knoctout and rnr knoct out strains were cultured in LB media at 37 °C, RNA samples and ChIP-seq samples were collected when the growth stage of indicated cells reached to log phase or stationary phase.  rne-3071(ts) mutation strain was cultured in LB media at 28 °C to retain the RNase E activity or shifted to 44 °C in water bath for 30 minutes to deactivate RNase E. In order to inactive the rho activity, the wild type (WT) Wild type E. coli was cultured in LB media with 50 μg/ml bicyclomycin at 37 °C for 15 min at indicated growth condition. PGCGROWTHCONDITIONS	SRR8449235	MCO000002470	Wild type	Genetic background	True
treatment_protocol	wild type		<Gtype> Wild type </Gtype> E. coli , pnp knoctout , rnb knoctout and rnr knoct out strains were cultured in <Med> LB media </Med> at <Temp> 37 °C </Temp> , RNA samples and ChIP-seq samples were collected when the growth stage of indicated cells reached to log phase or stationary phase . rne-3071 ( ts ) mutation strain was cultured in <Med> LB media </Med> at 28 °C to retain the RNase E activity or shifted to 44 °C in water bath for 30 minutes to deactivate RNase E . In order to <Gtype> inactive the rho activity , the wild type ( WT ) Wild type </Gtype> E. coli was cultured in <Med> LB media </Med> with 50 μg/ml bicyclomycin at <Temp> 37 °C </Temp> for 15 min at indicated growth condition . 	GPL16085-GPL21222	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE117737	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GSM3566394	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 5	31308523	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Wild type E. coli, pnp knoctout, rnb knoctout and rnr knoct out strains were cultured in LB media at 37 °C, RNA samples and ChIP-seq samples were collected when the growth stage of indicated cells reached to log phase or stationary phase.  rne-3071(ts) mutation strain was cultured in LB media at 28 °C to retain the RNase E activity or shifted to 44 °C in water bath for 30 minutes to deactivate RNase E. In order to inactive the rho activity, the wild type (WT) Wild type E. coli was cultured in LB media with 50 μg/ml bicyclomycin at 37 °C for 15 min at indicated growth condition. PGCGROWTHCONDITIONS	SRR8449236	MCO000002470	Wild type	Genetic background	True
treatment_protocol	wild type		<Gtype> Wild type </Gtype> E. coli , pnp knoctout , rnb knoctout and rnr knoct out strains were cultured in <Med> LB media </Med> at <Temp> 37 °C </Temp> , RNA samples and ChIP-seq samples were collected when the growth stage of indicated cells reached to log phase or stationary phase . rne-3071 ( ts ) mutation strain was cultured in <Med> LB media </Med> at 28 °C to retain the RNase E activity or shifted to 44 °C in water bath for 30 minutes to deactivate RNase E . In order to <Gtype> inactive the rho activity , the wild type ( WT ) Wild type </Gtype> E. coli was cultured in <Med> LB media </Med> with 50 μg/ml bicyclomycin at <Temp> 37 °C </Temp> for 15 min at indicated growth condition . 	GPL16085-GPL21222	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE117737	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GSM3566395	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 6	31308523	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Wild type E. coli, pnp knoctout, rnb knoctout and rnr knoct out strains were cultured in LB media at 37 °C, RNA samples and ChIP-seq samples were collected when the growth stage of indicated cells reached to log phase or stationary phase.  rne-3071(ts) mutation strain was cultured in LB media at 28 °C to retain the RNase E activity or shifted to 44 °C in water bath for 30 minutes to deactivate RNase E. In order to inactive the rho activity, the wild type (WT) Wild type E. coli was cultured in LB media with 50 μg/ml bicyclomycin at 37 °C for 15 min at indicated growth condition. PGCGROWTHCONDITIONS	SRR8449237	MCO000002470	Wild type	Genetic background	True
treatment_protocol	wild type		<Gtype> Wild type </Gtype> E. coli , pnp knoctout , rnb knoctout and rnr knoct out strains were cultured in <Med> LB media </Med> at <Temp> 37 °C </Temp> , RNA samples and ChIP-seq samples were collected when the growth stage of indicated cells reached to log phase or stationary phase . rne-3071 ( ts ) mutation strain was cultured in <Med> LB media </Med> at 28 °C to retain the RNase E activity or shifted to 44 °C in water bath for 30 minutes to deactivate RNase E . In order to <Gtype> inactive the rho activity , the wild type ( WT ) Wild type </Gtype> E. coli was cultured in <Med> LB media </Med> with 50 μg/ml bicyclomycin at <Temp> 37 °C </Temp> for 15 min at indicated growth condition . 	GPL16085-GPL21222	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE117737	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GSM3566396	RNA-seq WT log phase related to total SEnd-seq WT stationary phase rep4	31308523	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Wild type E. coli, pnp knoctout, rnb knoctout and rnr knoct out strains were cultured in LB media at 37 °C, RNA samples and ChIP-seq samples were collected when the growth stage of indicated cells reached to log phase or stationary phase.  rne-3071(ts) mutation strain was cultured in LB media at 28 °C to retain the RNase E activity or shifted to 44 °C in water bath for 30 minutes to deactivate RNase E. In order to inactive the rho activity, the wild type (WT) Wild type E. coli was cultured in LB media with 50 μg/ml bicyclomycin at 37 °C for 15 min at indicated growth condition. PGCGROWTHCONDITIONS	SRR8449238	MCO000002470	Wild type	Genetic background	True
growth_protocol	wild type		<Gtype> Wild type </Gtype> E. coli K-12 ( strain BW38038 ) and BW39452 ( ΔrpoS ) cultures were grown on <Med> MOPS glucose minimal medium </Med> with <Supp> 0.2 % glucose </Supp> as sole carbon source at <Temp> 37 °C </Temp> , pH was initially 7.4 , and the agitation speed was 500 rpm . Culture samples were harvested during logarithmic growth and following entry into stationary phase for the WT and rpoS mutant . OD600 measurements were made on a Beckman Coulter DU 800 spectrophotometer . Samples were harvested directly into ice-cold RNAlater at a 1:1 dilution to protect RNA from degradation and cells then were pelleted by centrifugation at 8000rpm for 10 minutes . Cell pellets were stored at -80 °C in an equal volume of RNAlater prior to RNA extraction . 	GPL18814	GPL18814: Illumina HiSeq 2000 (Escherichia coli BW38028)	GSE58556	RNA sequencing based analysis of the bacterial transcriptome	GSM1413874	WT_glucose_log	25483350	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE58556/GSE58556.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Wild type E. coli K-12 (strain BW38038) and BW39452(ΔrpoS) cultures were grown on MOPS glucose minimal medium with 0.2% glucose as sole carbon source at 37°C, pH was initially 7.4,  and the agitation speed was 500 rpm. Culture samples were harvested during logarithmic growth and  following entry into stationary phase for the WT and rpoS mutant. OD600 measurements were made on a Beckman Coulter DU 800 spectrophotometer. Samples were harvested directly into ice-cold RNAlater at a 1:1 dilution to protect RNA from degradation and cells then were pelleted by centrifugation at 8000rpm for 10 minutes. Cell pellets were stored at -80°C in an equal volume of RNAlater prior to RNA extraction. PGCGROWTHCONDITIONS	SRR1411272	MCO000002470	Wild type	Genetic background	True
growth_protocol	37.0 C		glycerol stocks of E. coli strains were inoculated into 0.2 % ( w/v ) glucose M9 minimal media . <Med> M9 minimal media </Med> was also supplemented with 1 ml trace element solution ( 100X ) , excluding MG _ no _ te _ 1 and MG _ no _ te _ 2 . The culture was incubated at <Temp> 37 ℃ </Temp> overnight with agitation , and then was used to inoculate the fresh <Med> media </Med> . The fresh culture was incubated at 37 ℃ with agitation to the <Phase> mid-log phase </Phase> ( OD600 ≈ 0.5 ) . 10mM glutamate was added to the media MG _ glu _ 1 and MG _ glu _ 2 . 	GPL17024-GPL17439-GPL18995-GPL25769	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	GSE122211	Expression profiling of E. coli K-12 MG1655	GSM3461156	MG_no_te_1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	100	50	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	glycerol stocks of E. coli strains were inoculated into 0.2%(w/v) glucose M9 minimal media. M9 minimal media was also supplemented with 1 ml trace element solution (100X), excluding MG_no_te_1 and MG_no_te_2. The culture was incubated at 37 ℃ overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37 ℃ with agitation to the mid-log phase (OD600 ≈ 0.5). 10mM glutamate was added to the media MG_glu_1 and MG_glu_2. PGCGROWTHCONDITIONS	SRR8164476	MCO000002697	37 ℃	Temperature	True
growth_protocol	37.0 C		glycerol stocks of E. coli strains were inoculated into 0.2 % ( w/v ) glucose M9 minimal media . <Med> M9 minimal media </Med> was also supplemented with 1 ml trace element solution ( 100X ) , excluding MG _ no _ te _ 1 and MG _ no _ te _ 2 . The culture was incubated at <Temp> 37 ℃ </Temp> overnight with agitation , and then was used to inoculate the fresh <Med> media </Med> . The fresh culture was incubated at 37 ℃ with agitation to the <Phase> mid-log phase </Phase> ( OD600 ≈ 0.5 ) . 10mM glutamate was added to the media MG _ glu _ 1 and MG _ glu _ 2 . 	GPL17024-GPL17439-GPL18995-GPL25769	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	GSE122211	Expression profiling of E. coli K-12 MG1655	GSM3461157	MG_no_te_2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	100	50	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	glycerol stocks of E. coli strains were inoculated into 0.2%(w/v) glucose M9 minimal media. M9 minimal media was also supplemented with 1 ml trace element solution (100X), excluding MG_no_te_1 and MG_no_te_2. The culture was incubated at 37 ℃ overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37 ℃ with agitation to the mid-log phase (OD600 ≈ 0.5). 10mM glutamate was added to the media MG_glu_1 and MG_glu_2. PGCGROWTHCONDITIONS	SRR8164477	MCO000002697	37 ℃	Temperature	True
growth_protocol	37.0 C		glycerol stocks of E. coli strains were inoculated into 0.2 % ( w/v ) glucose M9 minimal media . <Med> M9 minimal media </Med> was also supplemented with 1 ml trace element solution ( 100X ) , excluding MG _ no _ te _ 1 and MG _ no _ te _ 2 . The culture was incubated at <Temp> 37 ℃ </Temp> overnight with agitation , and then was used to inoculate the fresh <Med> media </Med> . The fresh culture was incubated at 37 ℃ with agitation to the <Phase> mid-log phase </Phase> ( OD600 ≈ 0.5 ) . 10mM glutamate was added to the media MG _ glu _ 1 and MG _ glu _ 2 . 	GPL17024-GPL17439-GPL18995-GPL25769	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	GSE122211	Expression profiling of E. coli K-12 MG1655	GSM3461164	MG_glu_1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	100	50	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	glycerol stocks of E. coli strains were inoculated into 0.2%(w/v) glucose M9 minimal media. M9 minimal media was also supplemented with 1 ml trace element solution (100X), excluding MG_no_te_1 and MG_no_te_2. The culture was incubated at 37 ℃ overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37 ℃ with agitation to the mid-log phase (OD600 ≈ 0.5). 10mM glutamate was added to the media MG_glu_1 and MG_glu_2. PGCGROWTHCONDITIONS	SRR8164484	MCO000002697	37 ℃	Temperature	True
growth_protocol	37.0 C		glycerol stocks of E. coli strains were inoculated into 0.2 % ( w/v ) glucose M9 minimal media . <Med> M9 minimal media </Med> was also supplemented with 1 ml trace element solution ( 100X ) , excluding MG _ no _ te _ 1 and MG _ no _ te _ 2 . The culture was incubated at <Temp> 37 ℃ </Temp> overnight with agitation , and then was used to inoculate the fresh <Med> media </Med> . The fresh culture was incubated at 37 ℃ with agitation to the <Phase> mid-log phase </Phase> ( OD600 ≈ 0.5 ) . 10mM glutamate was added to the media MG _ glu _ 1 and MG _ glu _ 2 . 	GPL17024-GPL17439-GPL18995-GPL25769	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	GSE122211	Expression profiling of E. coli K-12 MG1655	GSM3461165	MG_glu_2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	100	50	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	glycerol stocks of E. coli strains were inoculated into 0.2%(w/v) glucose M9 minimal media. M9 minimal media was also supplemented with 1 ml trace element solution (100X), excluding MG_no_te_1 and MG_no_te_2. The culture was incubated at 37 ℃ overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37 ℃ with agitation to the mid-log phase (OD600 ≈ 0.5). 10mM glutamate was added to the media MG_glu_1 and MG_glu_2. PGCGROWTHCONDITIONS	SRR8164485	MCO000002697	37 ℃	Temperature	True
growth_protocol	37.0 C		glycerol stocks of E. coli strains were inoculated into 0.2 % ( w/v ) glucose M9 minimal media . <Med> M9 minimal media </Med> was also supplemented with 1 ml trace element solution ( 100X ) , excluding MG _ no _ te _ 1 and MG _ no _ te _ 2 . The culture was incubated at <Temp> 37 ℃ </Temp> overnight with agitation , and then was used to inoculate the fresh <Med> media </Med> . The fresh culture was incubated at 37 ℃ with agitation to the <Phase> mid-log phase </Phase> ( OD600 ≈ 0.5 ) . 10mM glutamate was added to the media MG _ glu _ 1 and MG _ glu _ 2 . 	GPL17024-GPL17439-GPL18995-GPL25769	GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655). GPL18995: Illumina MiSeq (Escherichia coli BW25113). GPL25769: Illumina Genome Analyzer IIx (Escherichia coli BW25113)	GSE122211	Expression profiling of E. coli K-12 MG1655	GSM3461166	MG_glc	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	100	50	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	glycerol stocks of E. coli strains were inoculated into 0.2%(w/v) glucose M9 minimal media. M9 minimal media was also supplemented with 1 ml trace element solution (100X), excluding MG_no_te_1 and MG_no_te_2. The culture was incubated at 37 ℃ overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37 ℃ with agitation to the mid-log phase (OD600 ≈ 0.5). 10mM glutamate was added to the media MG_glu_1 and MG_glu_2. PGCGROWTHCONDITIONS	SRR8164486	MCO000002697	37 ℃	Temperature	True
characteristics	glucose 2 g/L		media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463565	wt_glc__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	SRR8173227	MCO000003239	2g/L glucose	Medium supplement	True
characteristics	glucose 2 g/L		media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463566	wt_glc__2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	SRR8173228	MCO000003239	2g/L glucose	Medium supplement	True
characteristics	glucose 2 g/L		media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463567	wt_glc__3	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	SRR8173229	MCO000003239	2g/L glucose	Medium supplement	True
characteristics	glucose 2 g/L		media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463568	wt_glc__4	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	SRR8173230	MCO000003239	2g/L glucose	Medium supplement	True
characteristics	glucose 2 g/L		media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463573	gth__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	SRR8173235	MCO000003239	2g/L glucose	Medium supplement	True
characteristics	glucose 2 g/L		media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463574	gth__2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	SRR8173236	MCO000003239	2g/L glucose	Medium supplement	True
characteristics	glucose 2 g/L		media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463577	met_glc__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	SRR8173239	MCO000003239	2g/L glucose	Medium supplement	True
characteristics	glucose 2 g/L		media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463578	met_glc__2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	SRR8173240	MCO000003239	2g/L glucose	Medium supplement	True
characteristics	glucose 2 g/L		media : <Air> anaerobic </Air> <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463579	no3_anaero__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: anaerobic M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	SRR8173241	MCO000003239	2g/L glucose	Medium supplement	True
characteristics	glucose 2 g/L		media : <Air> anaerobic </Air> <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463580	no3_anaero__2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: anaerobic M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	SRR8173242	MCO000003239	2g/L glucose	Medium supplement	True
characteristics	glucose 2 g/L		media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3854833	wt_glc_5__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	SRR9204648	MCO000003239	2g/L glucose	Medium supplement	True
characteristics	glucose 2 g/L		media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3854834	wt_glc_6__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	SRR9204649	MCO000003239	2g/L glucose	Medium supplement	True
characteristics	glucose 2 g/L		media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> and 100 mg/L adenine 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3854837	ade_glc__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 2g/L glucose and 100 mg/L adenine PGCGROWTHCONDITIONS	SRR9204652	MCO000003239	2g/L glucose	Medium supplement	True
characteristics	glucose 2 g/L		media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> and 100 mg/L adenine 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3854838	ade_glc__2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 2g/L glucose and 100 mg/L adenine PGCGROWTHCONDITIONS	SRR9204653	MCO000003239	2g/L glucose	Medium supplement	True
characteristics	glucose 2 g/L		media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE122296	Expression profiling of multiple Escherichia coli strains on glucose minimal media	GSM3463601	MG1655_1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122296/GSE122296.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	SRR8173221	MCO000003239	2g/L glucose	Medium supplement	True
characteristics	glucose 2 g/L		media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE122296	Expression profiling of multiple Escherichia coli strains on glucose minimal media	GSM3463602	MG1655_2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122296/GSE122296.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	SRR8173222	MCO000003239	2g/L glucose	Medium supplement	True
characteristics	mm		supplement : <Anti> Cytidine </Anti> <Supp> ( 1 mM ) </Supp> 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463571	cytd_rib__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	supplement: Cytidine (1 mM) PGCGROWTHCONDITIONS	SRR8173233	MCO000011586	( 1 mM )	Medium supplement	True
characteristics	mm		supplement : <Anti> Cytidine </Anti> <Supp> ( 1 mM ) </Supp> 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463572	cytd_rib__2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	supplement: Cytidine (1 mM) PGCGROWTHCONDITIONS	SRR8173234	MCO000011586	( 1 mM )	Medium supplement	True
characteristics	glucose 120 mM		media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose and 1 mM cytidine </Supp> 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3854835	bw_delpurR_cytd__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	83	59	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 2g/L glucose and 1 mM cytidine PGCGROWTHCONDITIONS	SRR9204650	MCO000002775	2g/L glucose and 1 mM cytidine	Medium supplement	True
characteristics	glucose 120 mM		media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose and 1 mM cytidine </Supp> 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3854836	bw_delpurR_cytd__2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	83	59	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 2g/L glucose and 1 mM cytidine PGCGROWTHCONDITIONS	SRR9204651	MCO000002775	2g/L glucose and 1 mM cytidine	Medium supplement	True
characteristics	Organism		<Gtype> material type </Gtype> : <Gtype> whole organism </Gtype> 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE123554	Reconstruction of transcriptional regulatory networks of Fis and H-NS in Escherichia coli from genome wide data analysis	GSM3507068	delta-fis rep1		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE123554/GSE123554.soft.gz	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	material type: whole organism PGCGROWTHCONDITIONS	SRR8309841	MCO000002467	whole organism	Genetic background	True
characteristics	Organism		<Gtype> material type </Gtype> : <Gtype> whole organism </Gtype> 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE123554	Reconstruction of transcriptional regulatory networks of Fis and H-NS in Escherichia coli from genome wide data analysis	GSM3507069	delta-fis rep2		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE123554/GSE123554.soft.gz	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	material type: whole organism PGCGROWTHCONDITIONS	SRR8309842	MCO000002467	whole organism	Genetic background	True
characteristics	Organism		<Gtype> material type </Gtype> : <Gtype> whole organism </Gtype> 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE123554	Reconstruction of transcriptional regulatory networks of Fis and H-NS in Escherichia coli from genome wide data analysis	GSM3507070	delta-hns rep1		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE123554/GSE123554.soft.gz	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	material type: whole organism PGCGROWTHCONDITIONS	SRR8309843	MCO000002467	whole organism	Genetic background	True
characteristics	Organism		<Gtype> material type </Gtype> : <Gtype> whole organism </Gtype> 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE123554	Reconstruction of transcriptional regulatory networks of Fis and H-NS in Escherichia coli from genome wide data analysis	GSM3507071	delta-hns rep2		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE123554/GSE123554.soft.gz	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	material type: whole organism PGCGROWTHCONDITIONS	SRR8309844	MCO000002467	whole organism	Genetic background	True
characteristics	wild type		genotype/variation : <Gtype> naive ( wild type ) </Gtype> 	GPL26204	GPL26204: NextSeq 550 (Escherichia coli K-12)	GSE126710	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GSM3611666	E. coli K-12 MG1655_R1 [MG_1]	31208335	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE126710/GSE126710.soft.gz	100	75	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: naive (wild type) PGCGROWTHCONDITIONS	SRR8587784	MCO000002470	naive ( wild type )	Genetic background	True
characteristics	wild type		genotype/variation : <Gtype> naive ( wild type ) </Gtype> 	GPL26204	GPL26204: NextSeq 550 (Escherichia coli K-12)	GSE126710	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GSM3611667	E. coli K-12 MG1655_R2 [MG_2]	31208335	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE126710/GSE126710.soft.gz	100	75	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: naive (wild type) PGCGROWTHCONDITIONS	SRR8587785	MCO000002470	naive ( wild type )	Genetic background	True
characteristics	wild type		genotype/variation : <Gtype> naive ( wild type ) </Gtype> 	GPL26204	GPL26204: NextSeq 550 (Escherichia coli K-12)	GSE126710	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GSM3611668	E. coli K-12 MG1655_R3 [MG_3]	31208335	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE126710/GSE126710.soft.gz	100	75	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: naive (wild type) PGCGROWTHCONDITIONS	SRR8587786	MCO000002470	naive ( wild type )	Genetic background	True
source_name	wt		<Gtype> WT </Gtype> _ <Phase> mid-log phase </Phase> bacteria culture 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013462	WT_1	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	WT_mid-log phase bacteria culture PGCGROWTHCONDITIONS	SRR9919224	MCO000002470	WT	Genetic background	True
source_name	wt		<Gtype> WT </Gtype> _ <Phase> mid-log phase </Phase> bacteria culture 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013463	WT_2	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	WT_mid-log phase bacteria culture PGCGROWTHCONDITIONS	SRR9919225	MCO000002470	WT	Genetic background	True
source_name	wt		<Gtype> WT </Gtype> _ H2O2 _ <Phase> mid-log phase </Phase> bacteria culture 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013464	WT_H2O2_1	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	WT_H2O2_mid-log phase bacteria culture PGCGROWTHCONDITIONS	SRR9919226	MCO000002470	WT	Genetic background	True
source_name	wt		<Gtype> WT </Gtype> _ H2O2 _ <Phase> mid-log phase </Phase> bacteria culture 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013465	WT_H2O2_2	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	WT_H2O2_mid-log phase bacteria culture PGCGROWTHCONDITIONS	SRR9919227	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype : <Gtype> WT </Gtype> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275442	WT_LB_R1	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: WT PGCGROWTHCONDITIONS	SRR10907640	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype : <Gtype> WT </Gtype> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275443	WT_LB_R2	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: WT PGCGROWTHCONDITIONS	SRR10907641	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype : <Gtype> WT </Gtype> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275444	WT_EtOH_R1	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: WT PGCGROWTHCONDITIONS	SRR10907642	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype : <Gtype> WT </Gtype> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275458	WT_01-KCl_R1	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: WT PGCGROWTHCONDITIONS	SRR10907656	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype : <Gtype> WT </Gtype> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275459	WT_01-KCl_R2	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: WT PGCGROWTHCONDITIONS	SRR10907657	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype : <Gtype> WT </Gtype> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275460	WT_115-KCl_R1	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: WT PGCGROWTHCONDITIONS	SRR10907658	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype : <Gtype> WT </Gtype> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275461	WT_115-KCl_R2	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: WT PGCGROWTHCONDITIONS	SRR10907659	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype : <Gtype> WT </Gtype> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275466	WT_M9-P_R1	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: WT PGCGROWTHCONDITIONS	SRR10907664	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype : <Gtype> WT </Gtype> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275467	WT_M9-P_R2	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: WT PGCGROWTHCONDITIONS	SRR10907665	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype : <Gtype> WT </Gtype> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275472	WT_ZnCl2_R1	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: WT PGCGROWTHCONDITIONS	SRR10907670	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype : <Gtype> WT </Gtype> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275473	WT_ZnCl2_R2	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: WT PGCGROWTHCONDITIONS	SRR10907671	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype : <Gtype> WT </Gtype> 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104402	WT_1	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: WT PGCGROWTHCONDITIONS	SRR794848	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype : <Gtype> WT </Gtype> 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104403	WT_2	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: WT PGCGROWTHCONDITIONS	SRR794849	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype : <Gtype> WT </Gtype> 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104404	WT_3	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: WT PGCGROWTHCONDITIONS	SRR794850	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype : <Gtype> WT </Gtype> 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104405	wt_T_1	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: WT PGCGROWTHCONDITIONS	SRR794851	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype : <Gtype> WT </Gtype> 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104406	wt_T_2	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: WT PGCGROWTHCONDITIONS	SRR794852	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype : <Gtype> WT </Gtype> 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104407	wt_T_3	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: WT PGCGROWTHCONDITIONS	SRR794853	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype : <Gtype> WT </Gtype> 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104408	wt_un_1	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: WT PGCGROWTHCONDITIONS	SRR794854	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype : <Gtype> WT </Gtype> 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104410	wt_un_3	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: WT PGCGROWTHCONDITIONS	SRR794856	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype : <Gtype> WT </Gtype> 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104423	WT_minus_2DG_1	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: WT PGCGROWTHCONDITIONS	SRR794869	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype : <Gtype> WT </Gtype> 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104424	WT_minus_2DG_2	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: WT PGCGROWTHCONDITIONS	SRR794870	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype : <Gtype> WT </Gtype> 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104425	WT_minus_2DG_3	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: WT PGCGROWTHCONDITIONS	SRR794871	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype : <Gtype> WT </Gtype> 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104426	WT_plus_2DG_1	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: WT PGCGROWTHCONDITIONS	SRR794872	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype : <Gtype> WT </Gtype> 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104427	WT_plus_2DG_2	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: WT PGCGROWTHCONDITIONS	SRR794873	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype : <Gtype> WT </Gtype> 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104428	WT_plus_2DG_3	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: WT PGCGROWTHCONDITIONS	SRR794874	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variation : <Gtype> WT </Gtype> 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE54900	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GSM1326347	WT with Fe 1 (RNA-seq)	25222563	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variation: WT PGCGROWTHCONDITIONS	SRR1168133	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variation : <Gtype> WT </Gtype> 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE54900	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GSM1326348	WT with Fe 2 (RNA-seq)	25222563	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variation: WT PGCGROWTHCONDITIONS	SRR1168134	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variation : <Gtype> WT </Gtype> 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE54900	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GSM1326349	WT with DPD 1 (RNA-seq)	25222563	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variation: WT PGCGROWTHCONDITIONS	SRR1168135	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variation : <Gtype> WT </Gtype> 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE54900	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GSM1326350	WT with DPD 2 (RNA-seq)	25222563	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variation: WT PGCGROWTHCONDITIONS	SRR1168136	MCO000002470	WT	Genetic background	True
source_name	wt		<Gtype> WT </Gtype> _ <Supp> glucose </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602347	WT glucose 1	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	WT_glucose PGCGROWTHCONDITIONS	SRR1787590	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variation : <Gtype> WT </Gtype> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602347	WT glucose 1	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variation: WT PGCGROWTHCONDITIONS	SRR1787590	MCO000002470	WT	Genetic background	True
source_name	wt		<Gtype> WT </Gtype> _ <Supp> glucose </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602348	WT glucose 2	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	WT_glucose PGCGROWTHCONDITIONS	SRR1787591	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variation : <Gtype> WT </Gtype> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602348	WT glucose 2	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variation: WT PGCGROWTHCONDITIONS	SRR1787591	MCO000002470	WT	Genetic background	True
source_name	wt		<Gtype> WT </Gtype> _ <Supp> fructose </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602349	WT fructose 1	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	WT_fructose PGCGROWTHCONDITIONS	SRR1787592	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variation : <Gtype> WT </Gtype> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602349	WT fructose 1	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variation: WT PGCGROWTHCONDITIONS	SRR1787592	MCO000002470	WT	Genetic background	True
source_name	wt		<Gtype> WT </Gtype> _ <Supp> fructose </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602350	WT fructose 2	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	WT_fructose PGCGROWTHCONDITIONS	SRR1787593	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variation : <Gtype> WT </Gtype> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602350	WT fructose 2	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variation: WT PGCGROWTHCONDITIONS	SRR1787593	MCO000002470	WT	Genetic background	True
source_name	wt		<Gtype> WT </Gtype> _ <Supp> acetate </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602351	WT acetate 1	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	WT_acetate PGCGROWTHCONDITIONS	SRR1787594	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variation : <Gtype> WT </Gtype> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602351	WT acetate 1	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variation: WT PGCGROWTHCONDITIONS	SRR1787594	MCO000002470	WT	Genetic background	True
source_name	wt		<Gtype> WT </Gtype> _ <Supp> acetate </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602352	WT acetate 2	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	WT_acetate PGCGROWTHCONDITIONS	SRR1787595	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variation : <Gtype> WT </Gtype> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602352	WT acetate 2	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variation: WT PGCGROWTHCONDITIONS	SRR1787595	MCO000002470	WT	Genetic background	True
source_name	wt		<Gtype> WT </Gtype> <Supp> PQ </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65711	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GSM1603386	WT PQ 1	26279566	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	WT PQ PGCGROWTHCONDITIONS	SRR1796598	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variation : <Gtype> WT </Gtype> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65711	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GSM1603386	WT PQ 1	26279566	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variation: WT PGCGROWTHCONDITIONS	SRR1796598	MCO000002470	WT	Genetic background	True
source_name	wt		<Gtype> WT </Gtype> <Supp> PQ </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65711	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GSM1603387	WT PQ 2	26279566	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	WT PQ PGCGROWTHCONDITIONS	SRR1796599	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variation : <Gtype> WT </Gtype> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65711	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GSM1603387	WT PQ 2	26279566	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variation: WT PGCGROWTHCONDITIONS	SRR1796599	MCO000002470	WT	Genetic background	True
source_name	wt		<Gtype> WT </Gtype> <pH> pH5 .5 </pH> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623160	WT pH5.5 1	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	WT pH5.5 PGCGROWTHCONDITIONS	SRR1824557	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variation : <Gtype> WT </Gtype> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623160	WT pH5.5 1	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variation: WT PGCGROWTHCONDITIONS	SRR1824557	MCO000002470	WT	Genetic background	True
source_name	wt		<Gtype> WT </Gtype> <pH> pH5 .5 </pH> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623161	WT pH5.5 2	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	WT pH5.5 PGCGROWTHCONDITIONS	SRR1824558	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variation : <Gtype> WT </Gtype> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623161	WT pH5.5 2	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variation: WT PGCGROWTHCONDITIONS	SRR1824558	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900470	Parent LB rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547467	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variation : <Gtype> WT </Gtype> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900470	Parent LB rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variation: WT PGCGROWTHCONDITIONS	SRR2547467	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900472	cysG KO LB rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547469	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900474	cysH KO LB rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547471	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900475	cysH KO LB rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547472	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900476	dcd KO LB rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547473	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900477	dcd KO LB rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547474	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900478	fadr KO LB rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547475	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900479	fadr KO LB rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547476	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900480	ppk KO LB rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547477	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900482	wzc KO LB rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547479	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900483	wzc KO LB rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547480	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900485	yghD KO LB rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547482	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900486	fepA KO LB rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547483	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900488	lacA KO LB rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547485	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900490	Parent M9 rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547487	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variation : <Gtype> WT </Gtype> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900490	Parent M9 rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variation: WT PGCGROWTHCONDITIONS	SRR2547487	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900491	Parent M9 rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547488	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variation : <Gtype> WT </Gtype> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900491	Parent M9 rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variation: WT PGCGROWTHCONDITIONS	SRR2547488	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900492	dcd KO M9 rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547489	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900493	dcd KO M9 rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547490	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900494	fadr KO M9 rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547491	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900495	fadr KO M9 rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547492	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900496	ppk KO M9 rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547493	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900497	ppk KO M9 rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547494	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900498	wzc KO M9 rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547495	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900499	wzc KO M9 rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547496	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900500	yghD KO M9 rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547497	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900501	yghD KO M9 rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547498	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900502	fepA KO M9 rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547499	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900507	WT rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547504	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variation : <Gtype> WT </Gtype> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900507	WT rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variation: WT PGCGROWTHCONDITIONS	SRR2547504	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900509	mgtA KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547506	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900510	mgtA KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547507	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900513	gabT KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547510	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900514	gabT KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547511	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900515	sdhC KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547512	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900516	sdhC KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547513	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900518	putP KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547515	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900520	putP KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547517	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900521	rfbA KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547518	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900522	rfbA KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547519	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900524	entF KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547521	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900525	entF KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547522	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900526	entF KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547523	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900527	kefB KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547524	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900529	kefB KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547526	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900530	cysA KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547527	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900531	cysA KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547528	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900532	cysA KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547529	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900534	galE KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547531	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900536	mhpD KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547533	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900537	mhpD KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547534	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900538	mhpD KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547535	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900539	fliY KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547536	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900540	fliY KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547537	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900541	fliY KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547538	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900542	lplA KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547539	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900543	lplA KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547540	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900544	lplA KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547541	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900545	khc KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547542	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900546	khc KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547543	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900547	khc KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547544	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900548	ugpC KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547545	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900549	ugpC KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547546	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900550	ugpC KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547547	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900551	trpD KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547548	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900552	trpD KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547549	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900553	trpD KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547550	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900554	aspC KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547551	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900555	aspC KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547552	MCO000002470	WT	Genetic background	True
growth_protocol	wt		For the first batch ( from <Gtype> WT </Gtype> _ <Med> LB </Med> _ 1 to lacA _ M9 _ 2 ) , fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at <Temp> 37 °C </Temp> . 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3 % glucose and grown for 12 h at <Temp> 37 °C </Temp> . At 12 h , cells were harvested for the RNA-seq . For the second batch ( from <Gtype> WT </Gtype> _ 1 to aspC _ 3 ) , a 1:100 dilution from an overnight culture in M9 0.4 % glucose was done . When the late stationary phase was reached , the samples were harvested . 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900556	aspC KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	For the first batch (from WT_LB_1 to lacA_M9_2), fresh colonies of E. coli cells were taken and inoculated in 1 ml LB and grown for 8 h at 37°C. 20 µL of grown culture was taken and transferred to 3 ml LB/M9 medium supplemented with 0.3% glucose and grown for 12 h at 37°C. At 12 h, cells were harvested for the RNA-seq. For the second batch (from WT_1 to aspC_3), a 1:100 dilution from an overnight culture in M9 0.4% glucose was done. When the late stationary phase was reached, the samples were harvested. PGCGROWTHCONDITIONS	SRR2547553	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variaion : <Gtype> WT </Gtype> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968346	WTRep1_0min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variaion: WT PGCGROWTHCONDITIONS	SRR2982421	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variaion : <Gtype> WT </Gtype> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968347	WTRep1_2min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variaion: WT PGCGROWTHCONDITIONS	SRR2982422	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variaion : <Gtype> WT </Gtype> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968348	WTRep1_4min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variaion: WT PGCGROWTHCONDITIONS	SRR2982423	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variaion : <Gtype> WT </Gtype> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968349	WTRep1_6min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variaion: WT PGCGROWTHCONDITIONS	SRR2982424	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variaion : <Gtype> WT </Gtype> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968350	WTRep1_8min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variaion: WT PGCGROWTHCONDITIONS	SRR2982425	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variaion : <Gtype> WT </Gtype> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968351	WTRep1_10min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variaion: WT PGCGROWTHCONDITIONS	SRR2982426	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variaion : <Gtype> WT </Gtype> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968352	WTRep1_15min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variaion: WT PGCGROWTHCONDITIONS	SRR2982427	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variaion : <Gtype> WT </Gtype> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968353	WTRep1_20min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variaion: WT PGCGROWTHCONDITIONS	SRR2982428	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variaion : <Gtype> WT </Gtype> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968354	WTRep2_0min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variaion: WT PGCGROWTHCONDITIONS	SRR2982429	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variaion : <Gtype> WT </Gtype> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968355	WTRep2_2min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variaion: WT PGCGROWTHCONDITIONS	SRR2982430	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variaion : <Gtype> WT </Gtype> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968356	WTRep2_4min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variaion: WT PGCGROWTHCONDITIONS	SRR2982431	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variaion : <Gtype> WT </Gtype> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968357	WTRep2_6min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variaion: WT PGCGROWTHCONDITIONS	SRR2982432	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variaion : <Gtype> WT </Gtype> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968358	WTRep2_8min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variaion: WT PGCGROWTHCONDITIONS	SRR2982433	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variaion : <Gtype> WT </Gtype> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968359	WTRep2_10min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variaion: WT PGCGROWTHCONDITIONS	SRR2982434	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variaion : <Gtype> WT </Gtype> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968360	WTRep2_15min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variaion: WT PGCGROWTHCONDITIONS	SRR2982435	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variaion : <Gtype> WT </Gtype> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968361	WTRep2_20min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variaion: WT PGCGROWTHCONDITIONS	SRR2982436	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype : <Gtype> WT </Gtype> 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE88980	Revealing the genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles and unexpected importance of narU under osmotic stress in Escherichia coli K-12 MG1655 [RNA-seq]	GSM2356687	WT NaCl 1	28526842	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88980/GSE88980.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: WT PGCGROWTHCONDITIONS	SRR4435464	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype : <Gtype> WT </Gtype> 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE88980	Revealing the genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles and unexpected importance of narU under osmotic stress in Escherichia coli K-12 MG1655 [RNA-seq]	GSM2356688	WT NaCl 2	28526842	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88980/GSE88980.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: WT PGCGROWTHCONDITIONS	SRR4435465	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variation : <Gtype> -LCB- delta -RCB- perC : : kanR </Gtype> , coisogenic to <Gtype> WT </Gtype> 	GPL14548-GPL20262	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	GSE91001	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GSM2418921	ATCACG-D1	28224117	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE91001/GSE91001.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variation: {delta}perC::kanR, coisogenic to WT PGCGROWTHCONDITIONS	SRR5085370	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variation : <Gtype> -LCB- delta -RCB- perC : : kanR </Gtype> , coisogenic to <Gtype> WT </Gtype> 	GPL14548-GPL20262	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	GSE91001	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GSM2418922	CGATGT-D2	28224117	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE91001/GSE91001.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variation: {delta}perC::kanR, coisogenic to WT PGCGROWTHCONDITIONS	SRR5085371	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variation : <Gtype> -LCB- delta -RCB- perC : : kanR </Gtype> , coisogenic to <Gtype> WT </Gtype> 	GPL14548-GPL20262	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	GSE91001	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GSM2418923	TTAGGC-D3	28224117	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE91001/GSE91001.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variation: {delta}perC::kanR, coisogenic to WT PGCGROWTHCONDITIONS	SRR5085373	MCO000002470	WT	Genetic background	True
characteristics	wt		replicates : <Gtype> WT </Gtype> replicate 1 / induced 	GPL18956	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	GSE92601	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GSM2433298	WT1_IPTG	29807996	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	replicates: WT replicate 1 / induced PGCGROWTHCONDITIONS	SRR5121117	MCO000002470	WT	Genetic background	True
characteristics	wt		replicates : <Gtype> WT </Gtype> replicate 2 / induced 	GPL18956	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	GSE92601	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GSM2433299	WT2_IPTG	29807996	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	replicates: WT replicate 2 / induced PGCGROWTHCONDITIONS	SRR5121118	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variation : <Gtype> WT </Gtype> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE97406	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GSM2564001	WT rep 1		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variation: WT PGCGROWTHCONDITIONS	SRR5416993	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variation : <Gtype> WT </Gtype> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE97406	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GSM2564002	WT rep 2		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variation: WT PGCGROWTHCONDITIONS	SRR5416994	MCO000002470	WT	Genetic background	True
characteristics	wt		genotype/variation : <Gtype> WT </Gtype> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE97406	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GSM2564003	WT rep 3		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype/variation: WT PGCGROWTHCONDITIONS	SRR5416995	MCO000002470	WT	Genetic background	True
characteristics	glucose 4 g/L		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013462	WT_1	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919224	MCO000002778	4g/L glucose	Medium supplement	True
characteristics	glucose 4 g/L		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013463	WT_2	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919225	MCO000002778	4g/L glucose	Medium supplement	True
characteristics	glucose 4 g/L		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013464	WT_H2O2_1	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919226	MCO000002778	4g/L glucose	Medium supplement	True
characteristics	glucose 4 g/L		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013465	WT_H2O2_2	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919227	MCO000002778	4g/L glucose	Medium supplement	True
characteristics	glucose 4 g/L		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013466	GMOS_1	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919228	MCO000002778	4g/L glucose	Medium supplement	True
characteristics	glucose 4 g/L		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013467	GMOS_2	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919229	MCO000002778	4g/L glucose	Medium supplement	True
characteristics	glucose 4 g/L		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013468	GMOS_H2O2_1	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919230	MCO000002778	4g/L glucose	Medium supplement	True
characteristics	glucose 4 g/L		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013470	EC ALE-1_1	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919232	MCO000002778	4g/L glucose	Medium supplement	True
characteristics	glucose 4 g/L		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013471	EC ALE-1_2	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919233	MCO000002778	4g/L glucose	Medium supplement	True
characteristics	glucose 4 g/L		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013472	EC ALE-1_H2O2_1	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919234	MCO000002778	4g/L glucose	Medium supplement	True
characteristics	glucose 4 g/L		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013473	EC ALE-1_H2O2_2	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919235	MCO000002778	4g/L glucose	Medium supplement	True
characteristics	glucose 4 g/L		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013474	EC ALE-2_1	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919236	MCO000002778	4g/L glucose	Medium supplement	True
characteristics	glucose 4 g/L		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013475	EC ALE-2_2	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919237	MCO000002778	4g/L glucose	Medium supplement	True
characteristics	glucose 4 g/L		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013476	EC ALE-2_H2O2_1	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919238	MCO000002778	4g/L glucose	Medium supplement	True
characteristics	glucose 4 g/L		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013477	EC ALE-2_H2O2_2	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919239	MCO000002778	4g/L glucose	Medium supplement	True
characteristics	glucose 4 g/L		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013478	EC ALE-3_1	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919240	MCO000002778	4g/L glucose	Medium supplement	True
characteristics	glucose 4 g/L		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013479	EC ALE-3_2	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919241	MCO000002778	4g/L glucose	Medium supplement	True
characteristics	glucose 4 g/L		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013480	EC ALE-3_H2O2_1	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919242	MCO000002778	4g/L glucose	Medium supplement	True
characteristics	glucose 4 g/L		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013481	EC ALE-3_H2O2_2	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919243	MCO000002778	4g/L glucose	Medium supplement	True
characteristics	glucose 4 g/L		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013482	EC ALE-4_1	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919244	MCO000002778	4g/L glucose	Medium supplement	True
characteristics	glucose 4 g/L		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013483	EC ALE-4_2	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919245	MCO000002778	4g/L glucose	Medium supplement	True
characteristics	glucose 4 g/L		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013484	EC ALE-4_H2O2_1	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919246	MCO000002778	4g/L glucose	Medium supplement	True
characteristics	glucose 4 g/L		media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013485	EC ALE-4_H2O2_2	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	SRR9919247	MCO000002778	4g/L glucose	Medium supplement	True
characteristics	hydrogen peroxide 1 mM		treatment : <Supp> 2 mM Hydrogen peroxide </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013464	WT_H2O2_1	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	95	95	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 2 mM Hydrogen peroxide PGCGROWTHCONDITIONS	SRR9919226	MCO000003162	2 mM Hydrogen peroxide	Medium supplement	True
characteristics	hydrogen peroxide 1 mM		treatment : <Supp> 2 mM Hydrogen peroxide </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013465	WT_H2O2_2	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	95	95	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 2 mM Hydrogen peroxide PGCGROWTHCONDITIONS	SRR9919227	MCO000003162	2 mM Hydrogen peroxide	Medium supplement	True
characteristics	hydrogen peroxide 1 mM		treatment : <Supp> 2 mM Hydrogen peroxide </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013468	GMOS_H2O2_1	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	95	95	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 2 mM Hydrogen peroxide PGCGROWTHCONDITIONS	SRR9919230	MCO000003162	2 mM Hydrogen peroxide	Medium supplement	True
characteristics	hydrogen peroxide 1 mM		treatment : <Supp> 2 mM Hydrogen peroxide </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013472	EC ALE-1_H2O2_1	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	95	95	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 2 mM Hydrogen peroxide PGCGROWTHCONDITIONS	SRR9919234	MCO000003162	2 mM Hydrogen peroxide	Medium supplement	True
characteristics	hydrogen peroxide 1 mM		treatment : <Supp> 2 mM Hydrogen peroxide </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013473	EC ALE-1_H2O2_2	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	95	95	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 2 mM Hydrogen peroxide PGCGROWTHCONDITIONS	SRR9919235	MCO000003162	2 mM Hydrogen peroxide	Medium supplement	True
characteristics	hydrogen peroxide 1 mM		treatment : <Supp> 2 mM Hydrogen peroxide </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013476	EC ALE-2_H2O2_1	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	95	95	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 2 mM Hydrogen peroxide PGCGROWTHCONDITIONS	SRR9919238	MCO000003162	2 mM Hydrogen peroxide	Medium supplement	True
characteristics	hydrogen peroxide 1 mM		treatment : <Supp> 2 mM Hydrogen peroxide </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013477	EC ALE-2_H2O2_2	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	95	95	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 2 mM Hydrogen peroxide PGCGROWTHCONDITIONS	SRR9919239	MCO000003162	2 mM Hydrogen peroxide	Medium supplement	True
characteristics	hydrogen peroxide 1 mM		treatment : <Supp> 2 mM Hydrogen peroxide </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013480	EC ALE-3_H2O2_1	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	95	95	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 2 mM Hydrogen peroxide PGCGROWTHCONDITIONS	SRR9919242	MCO000003162	2 mM Hydrogen peroxide	Medium supplement	True
characteristics	hydrogen peroxide 1 mM		treatment : <Supp> 2 mM Hydrogen peroxide </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013481	EC ALE-3_H2O2_2	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	95	95	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 2 mM Hydrogen peroxide PGCGROWTHCONDITIONS	SRR9919243	MCO000003162	2 mM Hydrogen peroxide	Medium supplement	True
characteristics	hydrogen peroxide 1 mM		treatment : <Supp> 2 mM Hydrogen peroxide </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013484	EC ALE-4_H2O2_1	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	95	95	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 2 mM Hydrogen peroxide PGCGROWTHCONDITIONS	SRR9919246	MCO000003162	2 mM Hydrogen peroxide	Medium supplement	True
characteristics	hydrogen peroxide 1 mM		treatment : <Supp> 2 mM Hydrogen peroxide </Supp> 	GPL24377	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	GSE135516	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GSM4013485	EC ALE-4_H2O2_2	31651953	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	95	95	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 2 mM Hydrogen peroxide PGCGROWTHCONDITIONS	SRR9919247	MCO000003162	2 mM Hydrogen peroxide	Medium supplement	True
data_processing	ion		<Supp> Supplementary </Supp> _ files _ format _ and _ content : <Gtype> * </Gtype> _ strand.wig : <Gtype> In </Gtype> the wig files , the scores represent the counts of uniquely aligned reads whose 5 ' ends mapped . 	GPL23030-GPL28314	GPL23030: Illumina MiSeq (Escherichia coli str. K-12 substr. W3110). GPL28314: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. W3110)	GSE147611	Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria	GSM4435425	sigma70WT_RNA-seq_rep1	33568644	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE147611/GSE147611.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Supplementary_files_format_and_content: *_strand.wig: In the wig files, the scores represent the counts of uniquely aligned reads whose 5’ ends mapped. PGCGROWTHCONDITIONS	SRR11431046	MCO000000580	In	Genetic background	True
data_processing	ion		<Supp> Supplementary </Supp> _ files _ format _ and _ content : <Gtype> * </Gtype> _ strand.wig : <Gtype> In </Gtype> the wig files , the scores represent the counts of uniquely aligned reads whose 5 ' ends mapped . 	GPL23030-GPL28314	GPL23030: Illumina MiSeq (Escherichia coli str. K-12 substr. W3110). GPL28314: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. W3110)	GSE147611	Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria	GSM4435426	sigma70WT_RNA-seq_rep2	33568644	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE147611/GSE147611.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Supplementary_files_format_and_content: *_strand.wig: In the wig files, the scores represent the counts of uniquely aligned reads whose 5’ ends mapped. PGCGROWTHCONDITIONS	SRR11431047	MCO000000580	In	Genetic background	True
data_processing	ion		<Supp> Supplementary </Supp> _ files _ format _ and _ content : <Gtype> * </Gtype> _ strand.wig : <Gtype> In </Gtype> the wig files , the scores represent the counts of uniquely aligned reads whose 5 ' ends mapped . 	GPL23030-GPL28314	GPL23030: Illumina MiSeq (Escherichia coli str. K-12 substr. W3110). GPL28314: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. W3110)	GSE147611	Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria	GSM4435427	sigma70WT_RNA-seq_rep3	33568644	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE147611/GSE147611.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Supplementary_files_format_and_content: *_strand.wig: In the wig files, the scores represent the counts of uniquely aligned reads whose 5’ ends mapped. PGCGROWTHCONDITIONS	SRR11431048	MCO000000580	In	Genetic background	True
data_processing	ion		<Supp> Supplementary </Supp> _ files _ format _ and _ content : <Gtype> * </Gtype> _ strand.wig : <Gtype> In </Gtype> the wig files , the scores represent the counts of uniquely aligned reads whose 5 ' ends mapped . 	GPL23030-GPL28314	GPL23030: Illumina MiSeq (Escherichia coli str. K-12 substr. W3110). GPL28314: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. W3110)	GSE147611	Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria	GSM4435428	sigma70greAB-_RNA-seq_rep1	33568644	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE147611/GSE147611.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Supplementary_files_format_and_content: *_strand.wig: In the wig files, the scores represent the counts of uniquely aligned reads whose 5’ ends mapped. PGCGROWTHCONDITIONS	SRR11431049	MCO000000580	In	Genetic background	True
data_processing	ion		<Supp> Supplementary </Supp> _ files _ format _ and _ content : <Gtype> * </Gtype> _ strand.wig : <Gtype> In </Gtype> the wig files , the scores represent the counts of uniquely aligned reads whose 5 ' ends mapped . 	GPL23030-GPL28314	GPL23030: Illumina MiSeq (Escherichia coli str. K-12 substr. W3110). GPL28314: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. W3110)	GSE147611	Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria	GSM4435429	sigma70greAB-_RNA-seq_rep2	33568644	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE147611/GSE147611.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Supplementary_files_format_and_content: *_strand.wig: In the wig files, the scores represent the counts of uniquely aligned reads whose 5’ ends mapped. PGCGROWTHCONDITIONS	SRR11431050	MCO000000580	In	Genetic background	True
data_processing	ion		<Supp> Supplementary </Supp> _ files _ format _ and _ content : <Gtype> * </Gtype> _ strand.wig : <Gtype> In </Gtype> the wig files , the scores represent the counts of uniquely aligned reads whose 5 ' ends mapped . 	GPL23030-GPL28314	GPL23030: Illumina MiSeq (Escherichia coli str. K-12 substr. W3110). GPL28314: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. W3110)	GSE147611	Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria	GSM4435430	sigma70greAB-_RNA-seq_rep3	33568644	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE147611/GSE147611.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Supplementary_files_format_and_content: *_strand.wig: In the wig files, the scores represent the counts of uniquely aligned reads whose 5’ ends mapped. PGCGROWTHCONDITIONS	SRR11431051	MCO000000580	In	Genetic background	True
data_processing	ion		<Supp> Supplementary </Supp> _ files _ format _ and _ content : <Gtype> In </Gtype> the . txt files the first column is the coordinate of the base corresponding to NC _ 000913.3 and the second column is the number of normalized reads at that position . All 0 values were given a pseudocount of 0.01 . Counts are normalized so that the averages of ssrA , ssrS , and rnpB are stable throughout the decay from 0 to 20 minutes 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE95318	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GSM2507165	WTA_time0	28351917	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Supplementary_files_format_and_content: In the .txt files the first column is the coordinate of the base corresponding to NC_000913.3 and the second column is the number of normalized reads at that position. All 0 values were given a pseudocount of 0.01. Counts are normalized so that the averages of ssrA, ssrS, and rnpB are stable throughout the decay from 0 to 20 minutes PGCGROWTHCONDITIONS	SRR5282299	MCO000000580	In	Genetic background	True
data_processing	ion		<Supp> Supplementary </Supp> _ files _ format _ and _ content : <Gtype> In </Gtype> the . txt files the first column is the coordinate of the base corresponding to NC _ 000913.3 and the second column is the number of normalized reads at that position . All 0 values were given a pseudocount of 0.01 . Counts are normalized so that the averages of ssrA , ssrS , and rnpB are stable throughout the decay from 0 to 20 minutes 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE95318	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GSM2507166	WTA_time2.5	28351917	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Supplementary_files_format_and_content: In the .txt files the first column is the coordinate of the base corresponding to NC_000913.3 and the second column is the number of normalized reads at that position. All 0 values were given a pseudocount of 0.01. Counts are normalized so that the averages of ssrA, ssrS, and rnpB are stable throughout the decay from 0 to 20 minutes PGCGROWTHCONDITIONS	SRR5282300	MCO000000580	In	Genetic background	True
data_processing	ion		<Supp> Supplementary </Supp> _ files _ format _ and _ content : <Gtype> In </Gtype> the . txt files the first column is the coordinate of the base corresponding to NC _ 000913.3 and the second column is the number of normalized reads at that position . All 0 values were given a pseudocount of 0.01 . Counts are normalized so that the averages of ssrA , ssrS , and rnpB are stable throughout the decay from 0 to 20 minutes 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE95318	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GSM2507167	WTA_time5	28351917	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Supplementary_files_format_and_content: In the .txt files the first column is the coordinate of the base corresponding to NC_000913.3 and the second column is the number of normalized reads at that position. All 0 values were given a pseudocount of 0.01. Counts are normalized so that the averages of ssrA, ssrS, and rnpB are stable throughout the decay from 0 to 20 minutes PGCGROWTHCONDITIONS	SRR5282301	MCO000000580	In	Genetic background	True
data_processing	ion		<Supp> Supplementary </Supp> _ files _ format _ and _ content : <Gtype> In </Gtype> the . txt files the first column is the coordinate of the base corresponding to NC _ 000913.3 and the second column is the number of normalized reads at that position . All 0 values were given a pseudocount of 0.01 . Counts are normalized so that the averages of ssrA , ssrS , and rnpB are stable throughout the decay from 0 to 20 minutes 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE95318	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GSM2507168	WTA_time7.5	28351917	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Supplementary_files_format_and_content: In the .txt files the first column is the coordinate of the base corresponding to NC_000913.3 and the second column is the number of normalized reads at that position. All 0 values were given a pseudocount of 0.01. Counts are normalized so that the averages of ssrA, ssrS, and rnpB are stable throughout the decay from 0 to 20 minutes PGCGROWTHCONDITIONS	SRR5282302	MCO000000580	In	Genetic background	True
data_processing	ion		<Supp> Supplementary </Supp> _ files _ format _ and _ content : <Gtype> In </Gtype> the . txt files the first column is the coordinate of the base corresponding to NC _ 000913.3 and the second column is the number of normalized reads at that position . All 0 values were given a pseudocount of 0.01 . Counts are normalized so that the averages of ssrA , ssrS , and rnpB are stable throughout the decay from 0 to 20 minutes 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE95318	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GSM2507169	WTA_time10	28351917	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Supplementary_files_format_and_content: In the .txt files the first column is the coordinate of the base corresponding to NC_000913.3 and the second column is the number of normalized reads at that position. All 0 values were given a pseudocount of 0.01. Counts are normalized so that the averages of ssrA, ssrS, and rnpB are stable throughout the decay from 0 to 20 minutes PGCGROWTHCONDITIONS	SRR5282303	MCO000000580	In	Genetic background	True
data_processing	ion		<Supp> Supplementary </Supp> _ files _ format _ and _ content : <Gtype> In </Gtype> the . txt files the first column is the coordinate of the base corresponding to NC _ 000913.3 and the second column is the number of normalized reads at that position . All 0 values were given a pseudocount of 0.01 . Counts are normalized so that the averages of ssrA , ssrS , and rnpB are stable throughout the decay from 0 to 20 minutes 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE95318	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GSM2507170	WTA_time20	28351917	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Supplementary_files_format_and_content: In the .txt files the first column is the coordinate of the base corresponding to NC_000913.3 and the second column is the number of normalized reads at that position. All 0 values were given a pseudocount of 0.01. Counts are normalized so that the averages of ssrA, ssrS, and rnpB are stable throughout the decay from 0 to 20 minutes PGCGROWTHCONDITIONS	SRR5282304	MCO000000580	In	Genetic background	True
data_processing	ion		<Supp> Supplementary </Supp> _ files _ format _ and _ content : <Gtype> In </Gtype> the . txt files the first column is the coordinate of the base corresponding to NC _ 000913.3 and the second column is the number of normalized reads at that position . All 0 values were given a pseudocount of 0.01 . Counts are normalized so that the averages of ssrA , ssrS , and rnpB are stable throughout the decay from 0 to 20 minutes 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE95318	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GSM2507171	WTB_time0	28351917	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Supplementary_files_format_and_content: In the .txt files the first column is the coordinate of the base corresponding to NC_000913.3 and the second column is the number of normalized reads at that position. All 0 values were given a pseudocount of 0.01. Counts are normalized so that the averages of ssrA, ssrS, and rnpB are stable throughout the decay from 0 to 20 minutes PGCGROWTHCONDITIONS	SRR5282305	MCO000000580	In	Genetic background	True
data_processing	ion		<Supp> Supplementary </Supp> _ files _ format _ and _ content : <Gtype> In </Gtype> the . txt files the first column is the coordinate of the base corresponding to NC _ 000913.3 and the second column is the number of normalized reads at that position . All 0 values were given a pseudocount of 0.01 . Counts are normalized so that the averages of ssrA , ssrS , and rnpB are stable throughout the decay from 0 to 20 minutes 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE95318	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GSM2507172	WTB_time2.5	28351917	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Supplementary_files_format_and_content: In the .txt files the first column is the coordinate of the base corresponding to NC_000913.3 and the second column is the number of normalized reads at that position. All 0 values were given a pseudocount of 0.01. Counts are normalized so that the averages of ssrA, ssrS, and rnpB are stable throughout the decay from 0 to 20 minutes PGCGROWTHCONDITIONS	SRR5282306	MCO000000580	In	Genetic background	True
data_processing	ion		<Supp> Supplementary </Supp> _ files _ format _ and _ content : <Gtype> In </Gtype> the . txt files the first column is the coordinate of the base corresponding to NC _ 000913.3 and the second column is the number of normalized reads at that position . All 0 values were given a pseudocount of 0.01 . Counts are normalized so that the averages of ssrA , ssrS , and rnpB are stable throughout the decay from 0 to 20 minutes 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE95318	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GSM2507173	WTB_time7.5	28351917	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Supplementary_files_format_and_content: In the .txt files the first column is the coordinate of the base corresponding to NC_000913.3 and the second column is the number of normalized reads at that position. All 0 values were given a pseudocount of 0.01. Counts are normalized so that the averages of ssrA, ssrS, and rnpB are stable throughout the decay from 0 to 20 minutes PGCGROWTHCONDITIONS	SRR5282307	MCO000000580	In	Genetic background	True
data_processing	ion		<Supp> Supplementary </Supp> _ files _ format _ and _ content : <Gtype> In </Gtype> the . txt files the first column is the coordinate of the base corresponding to NC _ 000913.3 and the second column is the number of normalized reads at that position . All 0 values were given a pseudocount of 0.01 . Counts are normalized so that the averages of ssrA , ssrS , and rnpB are stable throughout the decay from 0 to 20 minutes 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE95318	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GSM2507174	rnc-_time0	28351917	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Supplementary_files_format_and_content: In the .txt files the first column is the coordinate of the base corresponding to NC_000913.3 and the second column is the number of normalized reads at that position. All 0 values were given a pseudocount of 0.01. Counts are normalized so that the averages of ssrA, ssrS, and rnpB are stable throughout the decay from 0 to 20 minutes PGCGROWTHCONDITIONS	SRR5282308	MCO000000580	In	Genetic background	True
data_processing	ion		<Supp> Supplementary </Supp> _ files _ format _ and _ content : <Gtype> In </Gtype> the . txt files the first column is the coordinate of the base corresponding to NC _ 000913.3 and the second column is the number of normalized reads at that position . All 0 values were given a pseudocount of 0.01 . Counts are normalized so that the averages of ssrA , ssrS , and rnpB are stable throughout the decay from 0 to 20 minutes 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE95318	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GSM2507175	rnc-_time2.5	28351917	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Supplementary_files_format_and_content: In the .txt files the first column is the coordinate of the base corresponding to NC_000913.3 and the second column is the number of normalized reads at that position. All 0 values were given a pseudocount of 0.01. Counts are normalized so that the averages of ssrA, ssrS, and rnpB are stable throughout the decay from 0 to 20 minutes PGCGROWTHCONDITIONS	SRR5282309	MCO000000580	In	Genetic background	True
data_processing	ion		<Supp> Supplementary </Supp> _ files _ format _ and _ content : <Gtype> In </Gtype> the . txt files the first column is the coordinate of the base corresponding to NC _ 000913.3 and the second column is the number of normalized reads at that position . All 0 values were given a pseudocount of 0.01 . Counts are normalized so that the averages of ssrA , ssrS , and rnpB are stable throughout the decay from 0 to 20 minutes 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE95318	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GSM2507176	rnc-_time5	28351917	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Supplementary_files_format_and_content: In the .txt files the first column is the coordinate of the base corresponding to NC_000913.3 and the second column is the number of normalized reads at that position. All 0 values were given a pseudocount of 0.01. Counts are normalized so that the averages of ssrA, ssrS, and rnpB are stable throughout the decay from 0 to 20 minutes PGCGROWTHCONDITIONS	SRR5282310	MCO000000580	In	Genetic background	True
data_processing	ion		<Supp> Supplementary </Supp> _ files _ format _ and _ content : <Gtype> In </Gtype> the . txt files the first column is the coordinate of the base corresponding to NC _ 000913.3 and the second column is the number of normalized reads at that position . All 0 values were given a pseudocount of 0.01 . Counts are normalized so that the averages of ssrA , ssrS , and rnpB are stable throughout the decay from 0 to 20 minutes 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE95318	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GSM2507177	rnc-_time7.5	28351917	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Supplementary_files_format_and_content: In the .txt files the first column is the coordinate of the base corresponding to NC_000913.3 and the second column is the number of normalized reads at that position. All 0 values were given a pseudocount of 0.01. Counts are normalized so that the averages of ssrA, ssrS, and rnpB are stable throughout the decay from 0 to 20 minutes PGCGROWTHCONDITIONS	SRR5282311	MCO000000580	In	Genetic background	True
data_processing	ion		<Supp> Supplementary </Supp> _ files _ format _ and _ content : <Gtype> In </Gtype> the . txt files the first column is the coordinate of the base corresponding to NC _ 000913.3 and the second column is the number of normalized reads at that position . All 0 values were given a pseudocount of 0.01 . Counts are normalized so that the averages of ssrA , ssrS , and rnpB are stable throughout the decay from 0 to 20 minutes 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE95318	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GSM2507178	rnc-_time10	28351917	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Supplementary_files_format_and_content: In the .txt files the first column is the coordinate of the base corresponding to NC_000913.3 and the second column is the number of normalized reads at that position. All 0 values were given a pseudocount of 0.01. Counts are normalized so that the averages of ssrA, ssrS, and rnpB are stable throughout the decay from 0 to 20 minutes PGCGROWTHCONDITIONS	SRR5282312	MCO000000580	In	Genetic background	True
data_processing	ion		<Supp> Supplementary </Supp> _ files _ format _ and _ content : <Gtype> In </Gtype> the . txt files the first column is the coordinate of the base corresponding to NC _ 000913.3 and the second column is the number of normalized reads at that position . All 0 values were given a pseudocount of 0.01 . Counts are normalized so that the averages of ssrA , ssrS , and rnpB are stable throughout the decay from 0 to 20 minutes 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE95318	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GSM2507179	rnc-_time20	28351917	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Supplementary_files_format_and_content: In the .txt files the first column is the coordinate of the base corresponding to NC_000913.3 and the second column is the number of normalized reads at that position. All 0 values were given a pseudocount of 0.01. Counts are normalized so that the averages of ssrA, ssrS, and rnpB are stable throughout the decay from 0 to 20 minutes PGCGROWTHCONDITIONS	SRR5282313	MCO000000580	In	Genetic background	True
characteristics	rifampicin 50 µM		treatment group : <Supp> rifampicin time point 0 </Supp> 	GPL10328	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	GSE21341	genome-wide measurement of mRNA lifetime in Escherichia coli	GSM533304	time point 0	20671182	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE21341/GSE21341.soft.gz	80	68	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment group: rifampicin time point 0 PGCGROWTHCONDITIONS	SRR057747	MCO000011583	rifampicin time point 0	Medium supplement	True
characteristics	rifampicin		treatment group : <Supp> rifampicin time point </Supp> 2 	GPL10328	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	GSE21341	genome-wide measurement of mRNA lifetime in Escherichia coli	GSM533305	time point 2	20671182	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE21341/GSE21341.soft.gz	100	65	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment group: rifampicin time point 2 PGCGROWTHCONDITIONS	SRR057748	MCO000000828	rifampicin time point	Medium supplement	True
characteristics	rifampicin 50 µM		treatment group : <Supp> rifampicin time point 4 </Supp> 	GPL10328	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	GSE21341	genome-wide measurement of mRNA lifetime in Escherichia coli	GSM533306	time point 4	20671182	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE21341/GSE21341.soft.gz	80	63	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment group: rifampicin time point 4 PGCGROWTHCONDITIONS	SRR057749	MCO000011583	rifampicin time point 4	Medium supplement	True
characteristics	rifampicin 50 µM		treatment group : <Supp> rifampicin time point 6 </Supp> 	GPL10328	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	GSE21341	genome-wide measurement of mRNA lifetime in Escherichia coli	GSM533307	time point 6	20671182	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE21341/GSE21341.soft.gz	80	63	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment group: rifampicin time point 6 PGCGROWTHCONDITIONS	SRR057750	MCO000011583	rifampicin time point 6	Medium supplement	True
characteristics	rifampicin 50 µM		treatment group : <Supp> rifampicin time point 8 </Supp> 	GPL10328	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	GSE21341	genome-wide measurement of mRNA lifetime in Escherichia coli	GSM533308	time point 8	20671182	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE21341/GSE21341.soft.gz	80	63	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment group: rifampicin time point 8 PGCGROWTHCONDITIONS	SRR057751	MCO000011583	rifampicin time point 8	Medium supplement	True
characteristics	wild type		genotype : <Gtype> wild-type </Gtype> 	GPL16760	GPL16760: Illumina Genome Analyzer II (Escherichia coli BL21(DE3))	GSE44928	Physiology study of Escherichia coli harboring high intracellular ATP driven by artificial Pck expression	GSM1094082	BL21_2		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE44928/GSE44928.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype: wild-type PGCGROWTHCONDITIONS	SRR771533	MCO000002470	wild-type	Genetic background	True
characteristics	wild type		genotype : <Gtype> wild-type </Gtype> 	GPL15206-GPL17096	GPL15206: Illumina HiSeq 2000 (Escherichia coli BW25113). GPL17096: Illumina HiSeq 2000 (Streptomyces coelicolor A3(2))	GSE46507	Comparison of the nucleotide-resolution, genome-wide, 5'-end maps of the transcriptomes of Escherichia coli K12 strain BW25113 and Streptomyces coelicolor A3(2) strain M145	GSM1131348	E. coli - TAP		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE46507/GSE46507.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype: wild-type PGCGROWTHCONDITIONS	SRR836184	MCO000002470	wild-type	Genetic background	True
characteristics	wild type		genotype : <Gtype> wild-type </Gtype> 	GPL15206-GPL17096	GPL15206: Illumina HiSeq 2000 (Escherichia coli BW25113). GPL17096: Illumina HiSeq 2000 (Streptomyces coelicolor A3(2))	GSE46507	Comparison of the nucleotide-resolution, genome-wide, 5'-end maps of the transcriptomes of Escherichia coli K12 strain BW25113 and Streptomyces coelicolor A3(2) strain M145	GSM1131349	E. coli + TAP		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE46507/GSE46507.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype: wild-type PGCGROWTHCONDITIONS	SRR836185	MCO000002470	wild-type	Genetic background	True
characteristics	iptg		condition : <Gtype> LB </Gtype> +3 g/L Glc +0.1 <Supp> mM IPTG </Supp> 	GPL16760	GPL16760: Illumina Genome Analyzer II (Escherichia coli BL21(DE3))	GSE44928	Physiology study of Escherichia coli harboring high intracellular ATP driven by artificial Pck expression	GSM1094082	BL21_2		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE44928/GSE44928.soft.gz	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	condition: LB+3g/L Glc +0.1mM IPTG PGCGROWTHCONDITIONS	SRR771533	MCO000002105	mM IPTG	Medium supplement	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104381	pHDB3_1	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794827	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104386	pLCV1_3	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794832	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104387	MG1655-aMG_1	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794833	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104388	MG1655-aMG_2	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794834	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104389	MG1655-aMG_3	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794835	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104390	MG1655+aMG_1	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794836	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104391	MG1655+aMG_2	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794837	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104392	MG1655+aMG_3	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794838	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104393	SgrR_1	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794839	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104394	SgrR_2	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794840	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104395	SgrR_3	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794841	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104396	sgrS_T_1	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794842	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104397	sgrS_T_2	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794843	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104398	sgrS_T_3	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794844	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104399	sgrS_un_1	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794845	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104400	sgrS_un_2	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794846	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104401	sgrS_un_3	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794847	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104402	WT_1	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794848	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104403	WT_2	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794849	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104404	WT_3	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794850	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104405	wt_T_1	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794851	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104406	wt_T_2	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794852	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104407	wt_T_3	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794853	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104408	wt_un_1	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794854	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104410	wt_un_3	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794856	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104411	CV108_minus_aMG_1	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794857	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104412	CV108_minus_aMG_2	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794858	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104413	CV108_minus_aMG_3	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794859	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104414	CV108_plus_aMG_1	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794860	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104415	CV108_plus_aMG_2	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794861	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104416	CV108_plus_aMG_3	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794862	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104417	MG1655_minus_aMG_1	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794863	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104418	MG1655_minus_aMG_2	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794864	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104419	MG1655_minus_aMG_3	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794865	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104420	MG1655_plus_aMG_1	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794866	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104421	MG1655_plus_aMG_2	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794867	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104422	MG1655_plus_aMG_3	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794868	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104423	WT_minus_2DG_1	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794869	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104424	WT_minus_2DG_2	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794870	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104425	WT_minus_2DG_3	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794871	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104426	WT_plus_2DG_1	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794872	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104427	WT_plus_2DG_2	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794873	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE45443	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GSM1104428	WT_plus_2DG_3	23716638	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	SRR794874	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174823	Mid log_wildtype_glc minimal media_aerobic rep1	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922260	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174824	Mid log_wildtype_glc minimal media_aerobic rep2	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922261	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174825	Mid log_wildtype_glc minimal media_aerobic rep3	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922262	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174826	Mid log_wildtype_glc minimal media + adenine_aerobic	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922263	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174827	Mid log_wildtype_glc minimal media + L-tryptophan_aerobic	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922264	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174828	Mid log_wildtype_glc minimal media_anaerobic rep1	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922265	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174829	Mid log_wildtype_glc minimal media_anaerobic rep2	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922266	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174830	Mid log_wildtype_glc minimal media_anaerobic rep3	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922267	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174831	Mid log_nac KO_glc minimal media_aerobic	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922268	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174832	Mid log_nac KO_glc minimal media + adenine_aerobic	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922269	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174833	Mid log_cra KO_glc minimal media_aerobic	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922270	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174834	Mid log_cra KO_glc minimal media + L-tryptophan_aerobic	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922271	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174835	Mid log_mntR KO_glc minimal media_aerobic	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922272	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		E. coli cultures were grown at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> with glucose as the primary carbon source and harvested at mid exponetial phase . <Air> Aerobic </Air> E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles . Condition specific media supplementation was added as described else where . 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174836	Mid log_mntR KO_glc minimal media_anaerobic	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where. PGCGROWTHCONDITIONS	SRR922273	MCO000011679	Aerobic	Aeration	True
source_name	aerobic		<Air> Aerobic </Air> culture 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360031	Wild-type (MG1655) T0 RNA rep 2	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic culture PGCGROWTHCONDITIONS	SRR1211036	MCO000011679	Aerobic	Aeration	True
source_name	aerobic		<Air> Aerobic </Air> culture 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360032	Wild-type (MG1655) T1 RNA rep 1	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic culture PGCGROWTHCONDITIONS	SRR1211037	MCO000011679	Aerobic	Aeration	True
source_name	aerobic		<Air> Aerobic </Air> culture 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360033	Wild-type (MG1655) T1 RNA rep 2	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic culture PGCGROWTHCONDITIONS	SRR1211038	MCO000011679	Aerobic	Aeration	True
source_name	aerobic		<Air> Aerobic </Air> culture 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360034	Wild-type (MG1655) T2 RNA rep 1	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic culture PGCGROWTHCONDITIONS	SRR1211039	MCO000011679	Aerobic	Aeration	True
source_name	aerobic		<Air> Aerobic </Air> culture 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360035	Wild-type (MG1655) T2 RNA rep 2	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic culture PGCGROWTHCONDITIONS	SRR1211040	MCO000011679	Aerobic	Aeration	True
source_name	aerobic		<Air> Aerobic </Air> culture 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360036	Mutant (EP61) T0 RNA rep 1	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic culture PGCGROWTHCONDITIONS	SRR1211041	MCO000011679	Aerobic	Aeration	True
source_name	aerobic		<Air> Aerobic </Air> culture 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360037	Mutant (EP61) T0 RNA rep 2	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic culture PGCGROWTHCONDITIONS	SRR1211042	MCO000011679	Aerobic	Aeration	True
source_name	aerobic		<Air> Aerobic </Air> culture 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360038	Mutant (EP61) T1 RNA rep 1	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic culture PGCGROWTHCONDITIONS	SRR1211043	MCO000011679	Aerobic	Aeration	True
source_name	aerobic		<Air> Aerobic </Air> culture 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360039	Mutant (EP61) T1 RNA rep 2	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic culture PGCGROWTHCONDITIONS	SRR1211044	MCO000011679	Aerobic	Aeration	True
source_name	aerobic		<Air> Aerobic </Air> culture 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360040	Mutant (EP61) T2 RNA rep 1	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic culture PGCGROWTHCONDITIONS	SRR1211045	MCO000011679	Aerobic	Aeration	True
source_name	aerobic		<Air> Aerobic </Air> culture 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360041	Mutant (EP61) T2 RNA rep 2	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic culture PGCGROWTHCONDITIONS	SRR1211046	MCO000011679	Aerobic	Aeration	True
source_name	aerobic		<Air> Aerobic </Air> culture 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360042	Wild-type (MG1655) T0 RP rep 1	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic culture PGCGROWTHCONDITIONS	SRR1211047	MCO000011679	Aerobic	Aeration	True
source_name	aerobic		<Air> Aerobic </Air> culture 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360043	Wild-type (MG1655) T0 RP rep 2	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic culture PGCGROWTHCONDITIONS	SRR1211048	MCO000011679	Aerobic	Aeration	True
source_name	aerobic		<Air> Aerobic </Air> culture 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360044	Wild-type (MG1655) T1 RP rep 1	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic culture PGCGROWTHCONDITIONS	SRR1211049	MCO000011679	Aerobic	Aeration	True
source_name	aerobic		<Air> Aerobic </Air> culture 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360045	Wild-type (MG1655) T1 RP rep 2	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic culture PGCGROWTHCONDITIONS	SRR1211050	MCO000011679	Aerobic	Aeration	True
source_name	aerobic		<Air> Aerobic </Air> culture 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360046	Wild-type (MG1655) T2 RP rep 1	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic culture PGCGROWTHCONDITIONS	SRR1211051	MCO000011679	Aerobic	Aeration	True
source_name	aerobic		<Air> Aerobic </Air> culture 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360047	Wild-type (MG1655) T2 RP rep 2	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic culture PGCGROWTHCONDITIONS	SRR1211052	MCO000011679	Aerobic	Aeration	True
source_name	aerobic		<Air> Aerobic </Air> culture 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360048	Mutant (EP61) T0 RP rep 1	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic culture PGCGROWTHCONDITIONS	SRR1211053	MCO000011679	Aerobic	Aeration	True
source_name	aerobic		<Air> Aerobic </Air> culture 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360049	Mutant (EP61) T0 RP rep 2	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic culture PGCGROWTHCONDITIONS	SRR1211054	MCO000011679	Aerobic	Aeration	True
source_name	aerobic		<Air> Aerobic </Air> culture 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360050	Mutant (EP61) T1 RP rep 1	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic culture PGCGROWTHCONDITIONS	SRR1211055	MCO000011679	Aerobic	Aeration	True
source_name	aerobic		<Air> Aerobic </Air> culture 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360051	Mutant (EP61) T1 RP rep 2	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic culture PGCGROWTHCONDITIONS	SRR1211056	MCO000011679	Aerobic	Aeration	True
source_name	aerobic		<Air> Aerobic </Air> culture 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360052	Mutant (EP61) T2 RP rep 1	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic culture PGCGROWTHCONDITIONS	SRR1211057	MCO000011679	Aerobic	Aeration	True
source_name	aerobic		<Air> Aerobic </Air> culture 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE56372	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GSM1360053	Mutant (EP61) T2 RP rep 2	24927582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic culture PGCGROWTHCONDITIONS	SRR1211058	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> and anaerobic cultures were grown in 600 mL aliquots of DM25 and incubated at <Temp> 37 °C </Temp> with an orbital shaking of 150 RPM and inoculated with 1/100th volume of overnight culture . Aerobic cultures were grown for 9 h while anaerobic cultures were grown for 16 h. 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE80451	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GSM2127617	Aerobic 1	28103245	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80451/GSE80451.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic and anaerobic cultures were grown in 600 mL aliquots of DM25 and incubated at 37°C with an orbital shaking of 150 RPM and inoculated with 1/100th volume of overnight culture. Aerobic cultures were grown for 9 h while anaerobic cultures were grown for 16 h. PGCGROWTHCONDITIONS	SRR3403686	MCO000011679	Aerobic	Aeration	True
characteristics	aerobic		growth environment : <Air> Aerobic </Air> 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE80451	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GSM2127617	Aerobic 1	28103245	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80451/GSE80451.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth environment: Aerobic PGCGROWTHCONDITIONS	SRR3403686	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> and anaerobic cultures were grown in 600 mL aliquots of DM25 and incubated at <Temp> 37 °C </Temp> with an orbital shaking of 150 RPM and inoculated with 1/100th volume of overnight culture . Aerobic cultures were grown for 9 h while anaerobic cultures were grown for 16 h. 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE80451	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GSM2127618	Aerobic 2	28103245	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80451/GSE80451.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic and anaerobic cultures were grown in 600 mL aliquots of DM25 and incubated at 37°C with an orbital shaking of 150 RPM and inoculated with 1/100th volume of overnight culture. Aerobic cultures were grown for 9 h while anaerobic cultures were grown for 16 h. PGCGROWTHCONDITIONS	SRR3403687	MCO000011679	Aerobic	Aeration	True
characteristics	aerobic		growth environment : <Air> Aerobic </Air> 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE80451	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GSM2127618	Aerobic 2	28103245	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80451/GSE80451.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth environment: Aerobic PGCGROWTHCONDITIONS	SRR3403687	MCO000011679	Aerobic	Aeration	True
growth_protocol	aerobic		<Air> Aerobic </Air> and anaerobic cultures were grown in 600 mL aliquots of DM25 and incubated at <Temp> 37 °C </Temp> with an orbital shaking of 150 RPM and inoculated with 1/100th volume of overnight culture . Aerobic cultures were grown for 9 h while anaerobic cultures were grown for 16 h. 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE80451	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GSM2127619	Aerobic 3	28103245	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80451/GSE80451.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic and anaerobic cultures were grown in 600 mL aliquots of DM25 and incubated at 37°C with an orbital shaking of 150 RPM and inoculated with 1/100th volume of overnight culture. Aerobic cultures were grown for 9 h while anaerobic cultures were grown for 16 h. PGCGROWTHCONDITIONS	SRR3403688	MCO000011679	Aerobic	Aeration	True
characteristics	aerobic		growth environment : <Air> Aerobic </Air> 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE80451	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GSM2127619	Aerobic 3	28103245	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80451/GSE80451.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth environment: Aerobic PGCGROWTHCONDITIONS	SRR3403688	MCO000011679	Aerobic	Aeration	True
growth_protocol	W2 minimal medium		E. coli K12 MG1655 was grown to <Phase> mid-log phase </Phase> ( <OD> O.D. 600nm 0.5 </OD> ) or to stationary phase ( <OD> O.D. 600nm 1.5 </OD> ) <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> or <Med> W2 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> and 0.2 % glutamine . For heatshock conditions , cells were grown to mid-log phase and incubated at 42oC for 10 min . 	GPL17137	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	GSE46737	Genome-scale reconstruction of the sigma factor network in E. coli	GSM1137316	E. coli stationary 1	24461193	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE46737/GSE46737.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 MG1655 was grown to mid-log phase (O.D.600nm 0.5) or to stationary phase (O.D.600nm 1.5) aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose or W2 minimal media supplemented with 0.2% glucose and 0.2% glutamine. For heatshock conditions, cells were grown to mid-log phase and incubated at 42oC for 10 min. PGCGROWTHCONDITIONS	SRR847728	MCO000003317	W2 minimal media	Medium	True
growth_protocol	W2 minimal medium		E. coli K12 MG1655 was grown to <Phase> mid-log phase </Phase> ( <OD> O.D. 600nm 0.5 </OD> ) or to stationary phase ( <OD> O.D. 600nm 1.5 </OD> ) <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> or <Med> W2 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> and 0.2 % glutamine . For heatshock conditions , cells were grown to mid-log phase and incubated at 42oC for 10 min . 	GPL17137	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	GSE46737	Genome-scale reconstruction of the sigma factor network in E. coli	GSM1137318	E. coli glutamine 1	24461193	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE46737/GSE46737.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 MG1655 was grown to mid-log phase (O.D.600nm 0.5) or to stationary phase (O.D.600nm 1.5) aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose or W2 minimal media supplemented with 0.2% glucose and 0.2% glutamine. For heatshock conditions, cells were grown to mid-log phase and incubated at 42oC for 10 min. PGCGROWTHCONDITIONS	SRR847730	MCO000003317	W2 minimal media	Medium	True
growth_protocol	W2 minimal medium		E. coli K12 MG1655 was grown to <Phase> mid-log phase </Phase> ( <OD> O.D. 600nm 0.5 </OD> ) or to stationary phase ( <OD> O.D. 600nm 1.5 </OD> ) <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> or <Med> W2 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> and 0.2 % glutamine . For heatshock conditions , cells were grown to mid-log phase and incubated at 42oC for 10 min . 	GPL17137	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	GSE46737	Genome-scale reconstruction of the sigma factor network in E. coli	GSM1137319	E. coli glutamine 2	24461193	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE46737/GSE46737.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 MG1655 was grown to mid-log phase (O.D.600nm 0.5) or to stationary phase (O.D.600nm 1.5) aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose or W2 minimal media supplemented with 0.2% glucose and 0.2% glutamine. For heatshock conditions, cells were grown to mid-log phase and incubated at 42oC for 10 min. PGCGROWTHCONDITIONS	SRR847731	MCO000003317	W2 minimal media	Medium	True
growth_protocol	W2 minimal medium		E. coli K12 MG1655 was grown to <Phase> mid-log phase </Phase> ( <OD> O.D. 600nm 0.5 </OD> ) or to stationary phase ( <OD> O.D. 600nm 1.5 </OD> ) <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> or <Med> W2 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> and 0.2 % glutamine . For heatshock conditions , cells were grown to mid-log phase and incubated at 42oC for 10 min . 	GPL17137	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	GSE46737	Genome-scale reconstruction of the sigma factor network in E. coli	GSM1137320	E. coli heatshock 1	24461193	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE46737/GSE46737.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 MG1655 was grown to mid-log phase (O.D.600nm 0.5) or to stationary phase (O.D.600nm 1.5) aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose or W2 minimal media supplemented with 0.2% glucose and 0.2% glutamine. For heatshock conditions, cells were grown to mid-log phase and incubated at 42oC for 10 min. PGCGROWTHCONDITIONS	SRR847732	MCO000003317	W2 minimal media	Medium	True
growth_protocol	W2 minimal medium		E. coli K12 MG1655 was grown to <Phase> mid-log phase </Phase> ( <OD> O.D. 600nm 0.5 </OD> ) or to stationary phase ( <OD> O.D. 600nm 1.5 </OD> ) <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> or <Med> W2 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> and 0.2 % glutamine . For heatshock conditions , cells were grown to mid-log phase and incubated at 42oC for 10 min . 	GPL17137	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	GSE46737	Genome-scale reconstruction of the sigma factor network in E. coli	GSM1137321	E. coli heatshock 2	24461193	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE46737/GSE46737.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K12 MG1655 was grown to mid-log phase (O.D.600nm 0.5) or to stationary phase (O.D.600nm 1.5) aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose or W2 minimal media supplemented with 0.2% glucose and 0.2% glutamine. For heatshock conditions, cells were grown to mid-log phase and incubated at 42oC for 10 min. PGCGROWTHCONDITIONS	SRR847733	MCO000003317	W2 minimal media	Medium	True
source_name	L-glutamine 0.2%		Cells at mid-log phase ( OD600nm 0.5 ) in W2 media supplemented with <Supp> 0.2 % glucose </Supp> and <Supp> 0.2 % glutamine </Supp> 	GPL17137	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	GSE46737	Genome-scale reconstruction of the sigma factor network in E. coli	GSM1137318	E. coli glutamine 1	24461193	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE46737/GSE46737.soft.gz	100	93	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells at mid-log phase (OD600nm 0.5) in W2 media supplemented with 0.2% glucose and 0.2% glutamine PGCGROWTHCONDITIONS	SRR847730	MCO000002720	0.2 % glutamine	Medium supplement	True
source_name	L-glutamine 0.2%		Cells at mid-log phase ( OD600nm 0.5 ) in W2 media supplemented with <Supp> 0.2 % glucose </Supp> and <Supp> 0.2 % glutamine </Supp> 	GPL17137	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	GSE46737	Genome-scale reconstruction of the sigma factor network in E. coli	GSM1137319	E. coli glutamine 2	24461193	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE46737/GSE46737.soft.gz	100	93	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells at mid-log phase (OD600nm 0.5) in W2 media supplemented with 0.2% glucose and 0.2% glutamine PGCGROWTHCONDITIONS	SRR847731	MCO000002720	0.2 % glutamine	Medium supplement	True
characteristics	MOPS		culture/growth condition : <Supp> MOPS-P 2h </Supp> 	GPL10328-GPL14548	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE48151	Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coliK12 through accurate full-length transcripts assembling	GSM1170035	M-P2h_r1_HiSeq	23899370	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48151/GSE48151.soft.gz	100	62	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	culture/growth condition: MOPS-P 2h PGCGROWTHCONDITIONS	SRR915696	MCO000001665	MOPS-P 2h	Medium supplement	True
characteristics	MOPS		culture/growth condition : <Supp> MOPS-P 2h </Supp> 	GPL10328-GPL14548	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE48151	Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coliK12 through accurate full-length transcripts assembling	GSM1170036	M-P2h_r2_HiSeq	23899370	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48151/GSE48151.soft.gz	100	62	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	culture/growth condition: MOPS-P 2h PGCGROWTHCONDITIONS	SRR915697	MCO000001665	MOPS-P 2h	Medium supplement	True
source_name	wt		<Gtype> WT WT </Gtype> 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174823	Mid log_wildtype_glc minimal media_aerobic rep1	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	100	57	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	WT PGCGROWTHCONDITIONS	SRR922260	MCO000002470	WT WT	Genetic background	True
source_name	wt		<Gtype> WT WT </Gtype> 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174824	Mid log_wildtype_glc minimal media_aerobic rep2	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	100	57	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	WT PGCGROWTHCONDITIONS	SRR922261	MCO000002470	WT WT	Genetic background	True
source_name	wt		<Gtype> WT WT </Gtype> 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174825	Mid log_wildtype_glc minimal media_aerobic rep3	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	100	57	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	WT PGCGROWTHCONDITIONS	SRR922262	MCO000002470	WT WT	Genetic background	True
source_name	wt		<Gtype> WT WT </Gtype> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE97406	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GSM2564001	WT rep 1		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	100	57	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	WT PGCGROWTHCONDITIONS	SRR5416993	MCO000002470	WT WT	Genetic background	True
source_name	wt		<Gtype> WT WT </Gtype> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE97406	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GSM2564002	WT rep 2		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	100	57	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	WT PGCGROWTHCONDITIONS	SRR5416994	MCO000002470	WT WT	Genetic background	True
source_name	wt		<Gtype> WT WT </Gtype> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE97406	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GSM2564003	WT rep 3		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	100	57	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	WT PGCGROWTHCONDITIONS	SRR5416995	MCO000002470	WT WT	Genetic background	True
characteristics	wild type		genotype/variation : <Gtype> wild type ; MG1655 </Gtype> 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174823	Mid log_wildtype_glc minimal media_aerobic rep1	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	100	72	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type; MG1655 PGCGROWTHCONDITIONS	SRR922260	MCO000002470	wild type ; MG1655	Genetic background	True
characteristics	wild type		genotype/variation : <Gtype> wild type ; MG1655 </Gtype> 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174824	Mid log_wildtype_glc minimal media_aerobic rep2	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	100	72	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type; MG1655 PGCGROWTHCONDITIONS	SRR922261	MCO000002470	wild type ; MG1655	Genetic background	True
characteristics	wild type		genotype/variation : <Gtype> wild type ; MG1655 </Gtype> 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174825	Mid log_wildtype_glc minimal media_aerobic rep3	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	100	72	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type; MG1655 PGCGROWTHCONDITIONS	SRR922262	MCO000002470	wild type ; MG1655	Genetic background	True
characteristics	wild type		genotype/variation : <Gtype> wild type ; MG1655 </Gtype> 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174826	Mid log_wildtype_glc minimal media + adenine_aerobic	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	100	72	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type; MG1655 PGCGROWTHCONDITIONS	SRR922263	MCO000002470	wild type ; MG1655	Genetic background	True
characteristics	wild type		genotype/variation : <Gtype> wild type ; MG1655 </Gtype> 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174827	Mid log_wildtype_glc minimal media + L-tryptophan_aerobic	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	100	72	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type; MG1655 PGCGROWTHCONDITIONS	SRR922264	MCO000002470	wild type ; MG1655	Genetic background	True
characteristics	wild type		genotype/variation : <Gtype> wild type ; MG1655 </Gtype> 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174828	Mid log_wildtype_glc minimal media_anaerobic rep1	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	100	72	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type; MG1655 PGCGROWTHCONDITIONS	SRR922265	MCO000002470	wild type ; MG1655	Genetic background	True
characteristics	wild type		genotype/variation : <Gtype> wild type ; MG1655 </Gtype> 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174829	Mid log_wildtype_glc minimal media_anaerobic rep2	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	100	72	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type; MG1655 PGCGROWTHCONDITIONS	SRR922266	MCO000002470	wild type ; MG1655	Genetic background	True
characteristics	wild type		genotype/variation : <Gtype> wild type ; MG1655 </Gtype> 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174830	Mid log_wildtype_glc minimal media_anaerobic rep3	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	100	72	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type; MG1655 PGCGROWTHCONDITIONS	SRR922267	MCO000002470	wild type ; MG1655	Genetic background	True
characteristics	glucose 2 g/l		basal media : <Med> M9 + 4 g/L glc ( glucose minimal media ) </Med> 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174823	Mid log_wildtype_glc minimal media_aerobic rep1	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	92	51	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS	SRR922260	MCO000002776	M9 + 4 g/L glc ( glucose minimal media )	Medium	True
characteristics	glucose 2 g/l		basal media : <Med> M9 + 4 g/L glc ( glucose minimal media ) </Med> 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174824	Mid log_wildtype_glc minimal media_aerobic rep2	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	92	51	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS	SRR922261	MCO000002776	M9 + 4 g/L glc ( glucose minimal media )	Medium	True
characteristics	glucose 2 g/l		basal media : <Med> M9 + 4 g/L glc ( glucose minimal media ) </Med> 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174825	Mid log_wildtype_glc minimal media_aerobic rep3	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	92	51	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS	SRR922262	MCO000002776	M9 + 4 g/L glc ( glucose minimal media )	Medium	True
characteristics	glucose 2 g/l		basal media : <Med> M9 + 4 g/L glc ( glucose minimal media ) </Med> 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174826	Mid log_wildtype_glc minimal media + adenine_aerobic	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	92	51	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS	SRR922263	MCO000002776	M9 + 4 g/L glc ( glucose minimal media )	Medium	True
characteristics	glucose 2 g/l		basal media : <Med> M9 + 4 g/L glc ( glucose minimal media ) </Med> 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174827	Mid log_wildtype_glc minimal media + L-tryptophan_aerobic	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	92	51	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS	SRR922264	MCO000002776	M9 + 4 g/L glc ( glucose minimal media )	Medium	True
characteristics	glucose 2 g/l		basal media : <Med> M9 + 4 g/L glc ( glucose minimal media ) </Med> 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174828	Mid log_wildtype_glc minimal media_anaerobic rep1	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	92	51	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS	SRR922265	MCO000002776	M9 + 4 g/L glc ( glucose minimal media )	Medium	True
characteristics	glucose 2 g/l		basal media : <Med> M9 + 4 g/L glc ( glucose minimal media ) </Med> 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174829	Mid log_wildtype_glc minimal media_anaerobic rep2	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	92	51	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS	SRR922266	MCO000002776	M9 + 4 g/L glc ( glucose minimal media )	Medium	True
characteristics	glucose 2 g/l		basal media : <Med> M9 + 4 g/L glc ( glucose minimal media ) </Med> 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174830	Mid log_wildtype_glc minimal media_anaerobic rep3	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	92	51	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS	SRR922267	MCO000002776	M9 + 4 g/L glc ( glucose minimal media )	Medium	True
characteristics	glucose 2 g/l		basal media : <Med> M9 + 4 g/L glc ( glucose minimal media ) </Med> 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174831	Mid log_nac KO_glc minimal media_aerobic	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	92	51	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS	SRR922268	MCO000002776	M9 + 4 g/L glc ( glucose minimal media )	Medium	True
characteristics	glucose 2 g/l		basal media : <Med> M9 + 4 g/L glc ( glucose minimal media ) </Med> 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174832	Mid log_nac KO_glc minimal media + adenine_aerobic	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	92	51	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS	SRR922269	MCO000002776	M9 + 4 g/L glc ( glucose minimal media )	Medium	True
characteristics	glucose 2 g/l		basal media : <Med> M9 + 4 g/L glc ( glucose minimal media ) </Med> 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174833	Mid log_cra KO_glc minimal media_aerobic	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	92	51	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS	SRR922270	MCO000002776	M9 + 4 g/L glc ( glucose minimal media )	Medium	True
characteristics	glucose 2 g/l		basal media : <Med> M9 + 4 g/L glc ( glucose minimal media ) </Med> 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174834	Mid log_cra KO_glc minimal media + L-tryptophan_aerobic	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	92	51	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS	SRR922271	MCO000002776	M9 + 4 g/L glc ( glucose minimal media )	Medium	True
characteristics	glucose 2 g/l		basal media : <Med> M9 + 4 g/L glc ( glucose minimal media ) </Med> 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174835	Mid log_mntR KO_glc minimal media_aerobic	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	92	51	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS	SRR922272	MCO000002776	M9 + 4 g/L glc ( glucose minimal media )	Medium	True
characteristics	glucose 2 g/l		basal media : <Med> M9 + 4 g/L glc ( glucose minimal media ) </Med> 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174836	Mid log_mntR KO_glc minimal media_anaerobic	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	92	51	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS	SRR922273	MCO000002776	M9 + 4 g/L glc ( glucose minimal media )	Medium	True
source_name	wt		<Gtype> WT + </Gtype> <Supp> ade </Supp> 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174826	Mid log_wildtype_glc minimal media + adenine_aerobic	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	WT + ade PGCGROWTHCONDITIONS	SRR922263	MCO000002470	WT +	Genetic background	True
source_name	wt		<Gtype> WT + </Gtype> <Supp> L-trp </Supp> 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174827	Mid log_wildtype_glc minimal media + L-tryptophan_aerobic	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	WT + L-trp PGCGROWTHCONDITIONS	SRR922264	MCO000002470	WT +	Genetic background	True
characteristics	stationary phase		growth phase : <Phase> stationary </Phase> 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331415	LB 2.0 B1 TEX neg L1 GA	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	77	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth phase: stationary PGCGROWTHCONDITIONS	SRR1173971	MCO000002866	stationary	Growth phase	True
characteristics	stationary phase		growth phase : <Phase> stationary </Phase> 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331416	LB 2.0 B1 TEX neg L2 HS2	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	77	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth phase: stationary PGCGROWTHCONDITIONS	SRR1173972	MCO000002866	stationary	Growth phase	True
characteristics	stationary phase		growth phase : <Phase> stationary </Phase> 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331417	LB 2.0 B1 TEX pos L1 GA	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	77	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth phase: stationary PGCGROWTHCONDITIONS	SRR1173973	MCO000002866	stationary	Growth phase	True
characteristics	stationary phase		growth phase : <Phase> stationary </Phase> 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331418	LB 2.0 B1 TEX pos L2 HS2	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	77	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth phase: stationary PGCGROWTHCONDITIONS	SRR1173974	MCO000002866	stationary	Growth phase	True
characteristics	stationary phase		growth phase : <Phase> stationary </Phase> 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331419	LB 2.0 B2 TEX neg L1 HS1	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	77	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth phase: stationary PGCGROWTHCONDITIONS	SRR1173975	MCO000002866	stationary	Growth phase	True
characteristics	stationary phase		growth phase : <Phase> stationary </Phase> 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331420	LB 2.0 B2 TEX neg L1 HS2	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	77	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth phase: stationary PGCGROWTHCONDITIONS	SRR1173976	MCO000002866	stationary	Growth phase	True
characteristics	stationary phase		growth phase : <Phase> stationary </Phase> 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331421	LB 2.0 B2 TEX neg L2 HS2	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	77	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth phase: stationary PGCGROWTHCONDITIONS	SRR1173977	MCO000002866	stationary	Growth phase	True
characteristics	stationary phase		growth phase : <Phase> stationary </Phase> 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331422	LB 2.0 B2 TEX pos L1 HS1	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	77	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth phase: stationary PGCGROWTHCONDITIONS	SRR1173978	MCO000002866	stationary	Growth phase	True
characteristics	stationary phase		growth phase : <Phase> stationary </Phase> 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331423	LB 2.0 B2 TEX pos L1 HS2	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	77	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth phase: stationary PGCGROWTHCONDITIONS	SRR1173979	MCO000002866	stationary	Growth phase	True
characteristics	stationary phase		growth phase : <Phase> stationary </Phase> 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331424	LB 2.0 B2 TEX pos L2 HS2	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	77	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth phase: stationary PGCGROWTHCONDITIONS	SRR1173980	MCO000002866	stationary	Growth phase	True
characteristics	wild type		genotype : <Gtype> rne wild-type </Gtype> 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE58285	Direct entry by RNase E is a major pathway for the degradation and processing of RNA in Escherichia coli	GSM1405877	rne wild-type	25237058	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE58285/GSE58285.soft.gz	100	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype: rne wild-type PGCGROWTHCONDITIONS	SRR1363864	MCO000002470	rne wild-type	Genetic background	True
growth_protocol	MOPS minimal medium		<Gtype> Wild type </Gtype> E. coli K-12 ( strain BW38038 ) and BW39452 ( ΔrpoS ) cultures were grown on <Med> MOPS glucose minimal medium </Med> with <Supp> 0.2 % glucose </Supp> as sole carbon source at <Temp> 37 °C </Temp> , pH was initially 7.4 , and the agitation speed was 500 rpm . Culture samples were harvested during logarithmic growth and following entry into stationary phase for the WT and rpoS mutant . OD600 measurements were made on a Beckman Coulter DU 800 spectrophotometer . Samples were harvested directly into ice-cold RNAlater at a 1:1 dilution to protect RNA from degradation and cells then were pelleted by centrifugation at 8000rpm for 10 minutes . Cell pellets were stored at -80 °C in an equal volume of RNAlater prior to RNA extraction . 	GPL18814	GPL18814: Illumina HiSeq 2000 (Escherichia coli BW38028)	GSE58556	RNA sequencing based analysis of the bacterial transcriptome	GSM1413874	WT_glucose_log	25483350	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE58556/GSE58556.soft.gz	100	83	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Wild type E. coli K-12 (strain BW38038) and BW39452(ΔrpoS) cultures were grown on MOPS glucose minimal medium with 0.2% glucose as sole carbon source at 37°C, pH was initially 7.4,  and the agitation speed was 500 rpm. Culture samples were harvested during logarithmic growth and  following entry into stationary phase for the WT and rpoS mutant. OD600 measurements were made on a Beckman Coulter DU 800 spectrophotometer. Samples were harvested directly into ice-cold RNAlater at a 1:1 dilution to protect RNA from degradation and cells then were pelleted by centrifugation at 8000rpm for 10 minutes. Cell pellets were stored at -80°C in an equal volume of RNAlater prior to RNA extraction. PGCGROWTHCONDITIONS	SRR1411272	MCO000002528	MOPS glucose minimal medium	Medium	True
characteristics	log phase		treatment : <Phase> log phase sample </Phase> 	GPL18814	GPL18814: Illumina HiSeq 2000 (Escherichia coli BW38028)	GSE58556	RNA sequencing based analysis of the bacterial transcriptome	GSM1413874	WT_glucose_log	25483350	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE58556/GSE58556.soft.gz	100	72	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	treatment: log phase sample PGCGROWTHCONDITIONS	SRR1411272	MCO000002864	log phase sample	Growth phase	True
treatment_protocol	iptg		At OD ~ 0.3 , cultures were induced with <Supp> 1mM IPTG </Supp> for the appropriate length of time . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE58637	MicL, a new σE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein	GSM1415871	ribosome profiling MicL t0	25030700	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE58637/GSE58637.soft.gz	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	At OD ~0.3, cultures were induced with 1mM IPTG for the appropriate length of time. PGCGROWTHCONDITIONS	SRR1425203	MCO000002105	1mM IPTG	Medium supplement	True
treatment_protocol	iptg		At OD ~ 0.3 , cultures were induced with <Supp> 1mM IPTG </Supp> for the appropriate length of time . 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE58637	MicL, a new σE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein	GSM1415872	ribosome profiling MicL t20	25030700	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE58637/GSE58637.soft.gz	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	At OD ~0.3, cultures were induced with 1mM IPTG for the appropriate length of time. PGCGROWTHCONDITIONS	SRR1425204	MCO000002105	1mM IPTG	Medium supplement	True
characteristics	iptg		treatment : <Supp> 1mM IPTG </Supp> 	GPL14548-GPL21433	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE77617	Operon mRNAs are organized into ORF-centric structures that predict translation efficiency	GSM2462936	mRNA-seq 37°C in WT with control plasmid	28139975	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE77617/GSE77617.soft.gz	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	treatment: 1mM IPTG PGCGROWTHCONDITIONS	SRR5186139	MCO000002105	1mM IPTG	Medium supplement	True
characteristics	iptg		treatment : <Supp> 1mM IPTG </Supp> 	GPL14548-GPL21433	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE77617	Operon mRNAs are organized into ORF-centric structures that predict translation efficiency	GSM2462937	mRNA-seq 37°C in WT with plasmid expressing mini-ORF CUA	28139975	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE77617/GSE77617.soft.gz	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	treatment: 1mM IPTG PGCGROWTHCONDITIONS	SRR5186140	MCO000002105	1mM IPTG	Medium supplement	True
characteristics	iptg		treatment : <Supp> 1mM IPTG </Supp> 	GPL14548-GPL21433	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE77617	Operon mRNAs are organized into ORF-centric structures that predict translation efficiency	GSM2462938	mRNA-seq 37°C in WT with plasmid expressing mini-ORF CUG	28139975	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE77617/GSE77617.soft.gz	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	treatment: 1mM IPTG PGCGROWTHCONDITIONS	SRR5186141	MCO000002105	1mM IPTG	Medium supplement	True
characteristics	wild type		genotype : <Gtype> Wild-type </Gtype> 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE60107	Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli	GSM1465035	WT_RNA-Seq	2575788830486791	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE60107/GSE60107.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype: Wild-type PGCGROWTHCONDITIONS	SRR1536586	MCO000002470	Wild-type	Genetic background	True
characteristics	mutant		genotype : <Gtype> RNase II mutant </Gtype> 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE60107	Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli	GSM1465036	∆rnb_RNA-Seq	2575788830486791	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE60107/GSE60107.soft.gz	100	57	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: RNase II mutant PGCGROWTHCONDITIONS	SRR1536587	MCO000002469	RNase II mutant	Genetic background	True
characteristics	mutant		genotype : <Gtype> RNase R mutant </Gtype> 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE60107	Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli	GSM1465037	∆rnr_RNA-Seq	2575788830486791	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE60107/GSE60107.soft.gz	100	60	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: RNase R mutant PGCGROWTHCONDITIONS	SRR1536588	MCO000002469	RNase R mutant	Genetic background	True
characteristics	mutant		genotype : <Gtype> PNPase mutant </Gtype> 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE60107	Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli	GSM1465038	∆pnp_RNA-Seq	2575788830486791	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE60107/GSE60107.soft.gz	100	63	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: PNPase mutant PGCGROWTHCONDITIONS	SRR1536589	MCO000002469	PNPase mutant	Genetic background	True
growth_protocol	LB medium		<Med> LB medium , </Med> <Temp> 37 °C </Temp> , airated , constant pH 7.5 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE65244	Temporal gene expression in Escherichia coli	GSM1590712	Wt – 60 min		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65244/GSE65244.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS	SRR1771414	MCO000002533	LB medium ,	Medium	True
growth_protocol	LB medium		<Med> LB medium , </Med> <Temp> 37 °C </Temp> , airated , constant pH 7.5 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE65244	Temporal gene expression in Escherichia coli	GSM1590717	Fis – 60 min		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65244/GSE65244.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS	SRR1771419	MCO000002533	LB medium ,	Medium	True
growth_protocol	LB medium		<Med> LB medium , </Med> <Temp> 37 °C </Temp> , airated , constant pH 7.5 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE65244	Temporal gene expression in Escherichia coli	GSM1590718	Fis – 120 min		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65244/GSE65244.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS	SRR1771420	MCO000002533	LB medium ,	Medium	True
growth_protocol	LB medium		<Med> LB medium , </Med> <Temp> 37 °C </Temp> , airated , constant pH 7.5 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE65244	Temporal gene expression in Escherichia coli	GSM1590719	Fis – 180 min		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65244/GSE65244.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS	SRR1771421	MCO000002533	LB medium ,	Medium	True
growth_protocol	LB medium		<Med> LB medium , </Med> <Temp> 37 °C </Temp> , airated , constant pH 7.5 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE65244	Temporal gene expression in Escherichia coli	GSM1590720	Fis – 420 min		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65244/GSE65244.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS	SRR1771422	MCO000002533	LB medium ,	Medium	True
growth_protocol	LB medium		<Med> LB medium , </Med> <Temp> 37 °C </Temp> , airated , constant pH 7.5 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE65244	Temporal gene expression in Escherichia coli	GSM1590721	Hns – 60 min		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65244/GSE65244.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS	SRR1771423	MCO000002533	LB medium ,	Medium	True
growth_protocol	LB medium		<Med> LB medium , </Med> <Temp> 37 °C </Temp> , airated , constant pH 7.5 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE65244	Temporal gene expression in Escherichia coli	GSM1590722	Hns – 120 min		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65244/GSE65244.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS	SRR1771424	MCO000002533	LB medium ,	Medium	True
characteristics	paraquat 250 µM		treated with : <Supp> 250 uM of paraquat </Supp> at mid-log pahse for <Supp> 20 min </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65711	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GSM1603386	WT PQ 1	26279566	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	92	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treated with: 250 uM of paraquat at mid-log pahse for 20 min PGCGROWTHCONDITIONS	SRR1796598	MCO000011582	250 uM of paraquat	Medium supplement	True
characteristics	paraquat 250 µM		treated with : <Supp> 250 uM of paraquat </Supp> at mid-log pahse for <Supp> 20 min </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65711	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GSM1603387	WT PQ 2	26279566	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	92	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treated with: 250 uM of paraquat at mid-log pahse for 20 min PGCGROWTHCONDITIONS	SRR1796599	MCO000011582	250 uM of paraquat	Medium supplement	True
characteristics	paraquat 250 µM		treated with : <Supp> 250 uM of paraquat </Supp> at mid-log pahse for <Supp> 20 min </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65711	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GSM1603388	ΔoxyR PQ 1	26279566	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	92	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treated with: 250 uM of paraquat at mid-log pahse for 20 min PGCGROWTHCONDITIONS	SRR1796600	MCO000011582	250 uM of paraquat	Medium supplement	True
characteristics	paraquat 250 µM		treated with : <Supp> 250 uM of paraquat </Supp> at mid-log pahse for <Supp> 20 min </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65711	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GSM1603389	ΔoxyR PQ 2	26279566	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	92	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treated with: 250 uM of paraquat at mid-log pahse for 20 min PGCGROWTHCONDITIONS	SRR1796601	MCO000011582	250 uM of paraquat	Medium supplement	True
characteristics	paraquat 250 µM		treated with : <Supp> 250 uM of paraquat </Supp> at mid-log pahse for <Supp> 20 min </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65711	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GSM1603391	ΔsoxR PQ 2	26279566	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	92	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treated with: 250 uM of paraquat at mid-log pahse for 20 min PGCGROWTHCONDITIONS	SRR1796603	MCO000011582	250 uM of paraquat	Medium supplement	True
characteristics	paraquat 250 µM		treated with : <Supp> 250 uM of paraquat </Supp> at mid-log pahse for <Supp> 20 min </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65711	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GSM1603392	ΔsoxS PQ 1	26279566	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	92	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treated with: 250 uM of paraquat at mid-log pahse for 20 min PGCGROWTHCONDITIONS	SRR1796604	MCO000011582	250 uM of paraquat	Medium supplement	True
characteristics	paraquat 250 µM		treated with : <Supp> 250 uM of paraquat </Supp> at mid-log pahse for <Supp> 20 min </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65711	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GSM1603393	ΔsoxS PQ 2	26279566	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	92	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treated with: 250 uM of paraquat at mid-log pahse for 20 min PGCGROWTHCONDITIONS	SRR1796605	MCO000011582	250 uM of paraquat	Medium supplement	True
characteristics	OD600 of 0.3		growth phase : <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623160	WT pH5.5 1	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	100	86	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth phase: mid-log phase (OD600 = 0.3) PGCGROWTHCONDITIONS	SRR1824557	MCO000002564	OD600 = 0.3	Optical Density (OD)	True
characteristics	OD600 of 0.3		growth phase : <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623161	WT pH5.5 2	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	100	86	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth phase: mid-log phase (OD600 = 0.3) PGCGROWTHCONDITIONS	SRR1824558	MCO000002564	OD600 = 0.3	Optical Density (OD)	True
characteristics	OD600 of 0.3		growth phase : <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623162	ΔgadE pH5.5 1	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	100	86	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth phase: mid-log phase (OD600 = 0.3) PGCGROWTHCONDITIONS	SRR1824559	MCO000002564	OD600 = 0.3	Optical Density (OD)	True
characteristics	OD600 of 0.3		growth phase : <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623163	ΔgadE pH5.5 2	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	100	86	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth phase: mid-log phase (OD600 = 0.3) PGCGROWTHCONDITIONS	SRR1824560	MCO000002564	OD600 = 0.3	Optical Density (OD)	True
characteristics	OD600 of 0.3		growth phase : <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623164	ΔgadW pH5.5 1	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	100	86	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth phase: mid-log phase (OD600 = 0.3) PGCGROWTHCONDITIONS	SRR1824561	MCO000002564	OD600 = 0.3	Optical Density (OD)	True
characteristics	OD600 of 0.3		growth phase : <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623165	ΔgadW pH5.5 2	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	100	86	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth phase: mid-log phase (OD600 = 0.3) PGCGROWTHCONDITIONS	SRR1824562	MCO000002564	OD600 = 0.3	Optical Density (OD)	True
characteristics	OD600 of 0.3		growth phase : <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623166	ΔgadX pH5.5 1	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	100	86	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth phase: mid-log phase (OD600 = 0.3) PGCGROWTHCONDITIONS	SRR1824563	MCO000002564	OD600 = 0.3	Optical Density (OD)	True
characteristics	OD600 of 0.3		growth phase : <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623167	ΔgadX pH5.5 2	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	100	86	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth phase: mid-log phase (OD600 = 0.3) PGCGROWTHCONDITIONS	SRR1824564	MCO000002564	OD600 = 0.3	Optical Density (OD)	True
characteristics	T cell		<Gtype> cell type </Gtype> : Escherichia coli str . <Strain> K-12 </Strain> substr . <Substrain> MG1655 </Substrain> 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE67218	Transcriptional expression level of E. coli at 37 ℃ in LB media	GSM1642593	RNA-seq 37C LB rep1		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE67218/GSE67218.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	cell type: Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS	SRR1927169	MCO000011472	cell type	Genetic background	True
characteristics	T cell		<Gtype> cell type </Gtype> : Escherichia coli str . <Strain> K-12 </Strain> substr . <Substrain> MG1655 </Substrain> 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE67218	Transcriptional expression level of E. coli at 37 ℃ in LB media	GSM1642594	RNA-seq 37C LB rep2		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE67218/GSE67218.soft.gz	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	cell type: Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS	SRR1927170	MCO000011472	cell type	Genetic background	True
characteristics	glucose 0.5%		treatment : <Supp> 0.3 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900470	Parent LB rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.3% glucose PGCGROWTHCONDITIONS	SRR2547467	MCO000002772	0.3 % glucose	Medium supplement	True
characteristics	glucose 0.5%		treatment : <Supp> 0.3 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900472	cysG KO LB rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.3% glucose PGCGROWTHCONDITIONS	SRR2547469	MCO000002772	0.3 % glucose	Medium supplement	True
characteristics	glucose 0.5%		treatment : <Supp> 0.3 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900474	cysH KO LB rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.3% glucose PGCGROWTHCONDITIONS	SRR2547471	MCO000002772	0.3 % glucose	Medium supplement	True
characteristics	glucose 0.5%		treatment : <Supp> 0.3 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900475	cysH KO LB rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.3% glucose PGCGROWTHCONDITIONS	SRR2547472	MCO000002772	0.3 % glucose	Medium supplement	True
characteristics	glucose 0.5%		treatment : <Supp> 0.3 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900476	dcd KO LB rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.3% glucose PGCGROWTHCONDITIONS	SRR2547473	MCO000002772	0.3 % glucose	Medium supplement	True
characteristics	glucose 0.5%		treatment : <Supp> 0.3 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900477	dcd KO LB rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.3% glucose PGCGROWTHCONDITIONS	SRR2547474	MCO000002772	0.3 % glucose	Medium supplement	True
characteristics	glucose 0.5%		treatment : <Supp> 0.3 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900478	fadr KO LB rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.3% glucose PGCGROWTHCONDITIONS	SRR2547475	MCO000002772	0.3 % glucose	Medium supplement	True
characteristics	glucose 0.5%		treatment : <Supp> 0.3 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900479	fadr KO LB rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.3% glucose PGCGROWTHCONDITIONS	SRR2547476	MCO000002772	0.3 % glucose	Medium supplement	True
characteristics	glucose 0.5%		treatment : <Supp> 0.3 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900480	ppk KO LB rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.3% glucose PGCGROWTHCONDITIONS	SRR2547477	MCO000002772	0.3 % glucose	Medium supplement	True
characteristics	glucose 0.5%		treatment : <Supp> 0.3 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900482	wzc KO LB rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.3% glucose PGCGROWTHCONDITIONS	SRR2547479	MCO000002772	0.3 % glucose	Medium supplement	True
characteristics	glucose 0.5%		treatment : <Supp> 0.3 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900483	wzc KO LB rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.3% glucose PGCGROWTHCONDITIONS	SRR2547480	MCO000002772	0.3 % glucose	Medium supplement	True
characteristics	glucose 0.5%		treatment : <Supp> 0.3 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900485	yghD KO LB rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.3% glucose PGCGROWTHCONDITIONS	SRR2547482	MCO000002772	0.3 % glucose	Medium supplement	True
characteristics	glucose 0.5%		treatment : <Supp> 0.3 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900486	fepA KO LB rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.3% glucose PGCGROWTHCONDITIONS	SRR2547483	MCO000002772	0.3 % glucose	Medium supplement	True
characteristics	glucose 0.5%		treatment : <Supp> 0.3 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900488	lacA KO LB rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.3% glucose PGCGROWTHCONDITIONS	SRR2547485	MCO000002772	0.3 % glucose	Medium supplement	True
characteristics	glucose 0.5%		treatment : <Supp> 0.3 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900490	Parent M9 rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.3% glucose PGCGROWTHCONDITIONS	SRR2547487	MCO000002772	0.3 % glucose	Medium supplement	True
characteristics	glucose 0.5%		treatment : <Supp> 0.3 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900491	Parent M9 rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.3% glucose PGCGROWTHCONDITIONS	SRR2547488	MCO000002772	0.3 % glucose	Medium supplement	True
characteristics	glucose 0.5%		treatment : <Supp> 0.3 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900492	dcd KO M9 rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.3% glucose PGCGROWTHCONDITIONS	SRR2547489	MCO000002772	0.3 % glucose	Medium supplement	True
characteristics	glucose 0.5%		treatment : <Supp> 0.3 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900493	dcd KO M9 rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.3% glucose PGCGROWTHCONDITIONS	SRR2547490	MCO000002772	0.3 % glucose	Medium supplement	True
characteristics	glucose 0.5%		treatment : <Supp> 0.3 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900494	fadr KO M9 rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.3% glucose PGCGROWTHCONDITIONS	SRR2547491	MCO000002772	0.3 % glucose	Medium supplement	True
characteristics	glucose 0.5%		treatment : <Supp> 0.3 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900495	fadr KO M9 rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.3% glucose PGCGROWTHCONDITIONS	SRR2547492	MCO000002772	0.3 % glucose	Medium supplement	True
characteristics	glucose 0.5%		treatment : <Supp> 0.3 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900496	ppk KO M9 rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.3% glucose PGCGROWTHCONDITIONS	SRR2547493	MCO000002772	0.3 % glucose	Medium supplement	True
characteristics	glucose 0.5%		treatment : <Supp> 0.3 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900497	ppk KO M9 rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.3% glucose PGCGROWTHCONDITIONS	SRR2547494	MCO000002772	0.3 % glucose	Medium supplement	True
characteristics	glucose 0.5%		treatment : <Supp> 0.3 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900498	wzc KO M9 rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.3% glucose PGCGROWTHCONDITIONS	SRR2547495	MCO000002772	0.3 % glucose	Medium supplement	True
characteristics	glucose 0.5%		treatment : <Supp> 0.3 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900499	wzc KO M9 rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.3% glucose PGCGROWTHCONDITIONS	SRR2547496	MCO000002772	0.3 % glucose	Medium supplement	True
characteristics	glucose 0.5%		treatment : <Supp> 0.3 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900500	yghD KO M9 rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.3% glucose PGCGROWTHCONDITIONS	SRR2547497	MCO000002772	0.3 % glucose	Medium supplement	True
characteristics	glucose 0.5%		treatment : <Supp> 0.3 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900501	yghD KO M9 rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.3% glucose PGCGROWTHCONDITIONS	SRR2547498	MCO000002772	0.3 % glucose	Medium supplement	True
characteristics	glucose 0.5%		treatment : <Supp> 0.3 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900502	fepA KO M9 rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.3% glucose PGCGROWTHCONDITIONS	SRR2547499	MCO000002772	0.3 % glucose	Medium supplement	True
source_name	glucose		Whole cell , WT , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900507	WT rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, WT, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547504	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , mgtA KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900509	mgtA KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, mgtA KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547506	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , mgtA KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900510	mgtA KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, mgtA KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547507	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , gabT KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900513	gabT KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, gabT KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547510	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , gabT KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900514	gabT KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, gabT KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547511	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , sdhC KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900515	sdhC KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, sdhC KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547512	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , sdhC KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900516	sdhC KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, sdhC KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547513	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , putP KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900518	putP KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, putP KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547515	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , putP KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900520	putP KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, putP KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547517	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , rfbA KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900521	rfbA KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, rfbA KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547518	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , rfbA KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900522	rfbA KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, rfbA KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547519	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , entF KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900524	entF KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, entF KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547521	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , entF KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900525	entF KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, entF KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547522	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , entF KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900526	entF KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, entF KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547523	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , kefB KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900527	kefB KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, kefB KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547524	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , kefB KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900529	kefB KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, kefB KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547526	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , cysA KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900530	cysA KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, cysA KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547527	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , cysA KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900531	cysA KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, cysA KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547528	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , cysA KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900532	cysA KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, cysA KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547529	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , galE KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900534	galE KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, galE KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547531	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , mhpD KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900536	mhpD KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, mhpD KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547533	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , mhpD KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900537	mhpD KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, mhpD KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547534	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , mhpD KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900538	mhpD KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, mhpD KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547535	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , fliY KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900539	fliY KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, fliY KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547536	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , fliY KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900540	fliY KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, fliY KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547537	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , fliY KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900541	fliY KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, fliY KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547538	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , lplA KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900542	lplA KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, lplA KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547539	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , lplA KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900543	lplA KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, lplA KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547540	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , lplA KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900544	lplA KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, lplA KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547541	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , khc KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900545	khc KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, khc KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547542	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , khc KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900546	khc KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, khc KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547543	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , khc KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900547	khc KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, khc KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547544	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , ugpC KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900548	ugpC KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, ugpC KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547545	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , ugpC KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900549	ugpC KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, ugpC KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547546	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , ugpC KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900550	ugpC KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, ugpC KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547547	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , trpD KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900551	trpD KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, trpD KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547548	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , trpD KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900552	trpD KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, trpD KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547549	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , trpD KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900553	trpD KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, trpD KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547550	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , aspC KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900554	aspC KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, aspC KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547551	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , aspC KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900555	aspC KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, aspC KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547552	MCO000000245	% glucose	Medium supplement	True
source_name	glucose		Whole cell , aspC KO , M9 and 0.4 <Supp> % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900556	aspC KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Whole cell, aspC KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	SRR2547553	MCO000000245	% glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900507	WT rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547504	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900509	mgtA KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547506	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900510	mgtA KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547507	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900513	gabT KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547510	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900514	gabT KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547511	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900515	sdhC KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547512	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900516	sdhC KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547513	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900518	putP KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547515	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900520	putP KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547517	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900521	rfbA KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547518	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900522	rfbA KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547519	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900524	entF KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547521	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900525	entF KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547522	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900526	entF KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547523	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900527	kefB KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547524	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900529	kefB KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547526	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900530	cysA KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547527	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900531	cysA KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547528	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900532	cysA KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547529	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900534	galE KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547531	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900536	mhpD KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547533	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900537	mhpD KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547534	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900538	mhpD KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547535	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900539	fliY KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547536	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900540	fliY KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547537	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900541	fliY KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547538	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900542	lplA KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547539	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900543	lplA KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547540	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900544	lplA KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547541	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900545	khc KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547542	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900546	khc KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547543	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900547	khc KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547544	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900548	ugpC KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547545	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900549	ugpC KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547546	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900550	ugpC KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547547	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900551	trpD KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547548	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900552	trpD KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547549	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900553	trpD KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547550	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900554	aspC KO rep1	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547551	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900555	aspC KO rep2	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547552	MCO000002771	0.4 % glucose	Medium supplement	True
characteristics	glucose 0.4%		treatment : <Supp> 0.4 % glucose </Supp> 	GPL20227	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	GSE73672	Targeted experimentation to increase functional coverage in omics dataset	GSM1900556	aspC KO rep3	27713404	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: 0.4% glucose PGCGROWTHCONDITIONS	SRR2547553	MCO000002771	0.4 % glucose	Medium supplement	True
growth_protocol	OD600 of 0.8		Overnight cultures of bacteria were diluted 1:100 in fresh LB broth and grown to logarithmic phase at an <OD> OD600 of about 0.8 </OD> . 	GPL21021	GPL21021: Illumina HiSeq 2500 (Escherichia coli O157:H7 str. EDL933)	GSE73969	RNA-seq to profile the H-NS transcriptome in EHEC O157:H7 strain EDL933	GSM1906887	wt_1	2717363528288207	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73969/GSE73969.soft.gz	100	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Overnight cultures of bacteria were diluted 1:100 in fresh LB broth and grown to logarithmic phase at an OD600 of about 0.8. PGCGROWTHCONDITIONS	SRR2637695	MCO000003177	OD600 of about 0.8	Optical Density (OD)	True
growth_protocol	OD600 of 0.8		Overnight cultures of bacteria were diluted 1:100 in fresh LB broth and grown to logarithmic phase at an <OD> OD600 of about 0.8 </OD> . 	GPL21021	GPL21021: Illumina HiSeq 2500 (Escherichia coli O157:H7 str. EDL933)	GSE73969	RNA-seq to profile the H-NS transcriptome in EHEC O157:H7 strain EDL933	GSM1906888	wt_2	2717363528288207	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73969/GSE73969.soft.gz	100	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Overnight cultures of bacteria were diluted 1:100 in fresh LB broth and grown to logarithmic phase at an OD600 of about 0.8. PGCGROWTHCONDITIONS	SRR2637696	MCO000003177	OD600 of about 0.8	Optical Density (OD)	True
growth_protocol	OD600 of 0.8		Overnight cultures of bacteria were diluted 1:100 in fresh LB broth and grown to logarithmic phase at an <OD> OD600 of about 0.8 </OD> . 	GPL21021	GPL21021: Illumina HiSeq 2500 (Escherichia coli O157:H7 str. EDL933)	GSE73969	RNA-seq to profile the H-NS transcriptome in EHEC O157:H7 strain EDL933	GSM1906889	hns_1	2717363528288207	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73969/GSE73969.soft.gz	100	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Overnight cultures of bacteria were diluted 1:100 in fresh LB broth and grown to logarithmic phase at an OD600 of about 0.8. PGCGROWTHCONDITIONS	SRR2637697	MCO000003177	OD600 of about 0.8	Optical Density (OD)	True
growth_protocol	OD600 of 0.8		Overnight cultures of bacteria were diluted 1:100 in fresh LB broth and grown to logarithmic phase at an <OD> OD600 of about 0.8 </OD> . 	GPL21021	GPL21021: Illumina HiSeq 2500 (Escherichia coli O157:H7 str. EDL933)	GSE73969	RNA-seq to profile the H-NS transcriptome in EHEC O157:H7 strain EDL933	GSM1906890	hns_2	2717363528288207	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73969/GSE73969.soft.gz	100	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Overnight cultures of bacteria were diluted 1:100 in fresh LB broth and grown to logarithmic phase at an OD600 of about 0.8. PGCGROWTHCONDITIONS	SRR2637698	MCO000003177	OD600 of about 0.8	Optical Density (OD)	True
growth_protocol	glucose 0.5%		M9 defined medium ( 0.6 % Na2HPO4 , 0.3 % KH2PO4 , 0.05 % NaCl , 0.01 % NH4Cl , 0.1 mM CaCl2 , 1 mM MgSO4 , 5 x 10 − 4 % Thiamin ) supplemented with <Supp> 0.5 % glucose </Supp> and 0.1 % amino acids was used for RNA-seq experiments . 	GPL15982	GPL15982: Illumina HiSeq 1000 (Escherichia coli str. K-12 substr. MG1655)	GSE74809	Growth-phase dependent regulation of transcription by Rsd and 6S RNA	GSM1933982	rpoS_TS_1	29686109	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE74809/GSE74809.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS	SRR2932665	MCO000002772	0.5 % glucose	Medium supplement	True
growth_protocol	glucose 0.5%		M9 defined medium ( 0.6 % Na2HPO4 , 0.3 % KH2PO4 , 0.05 % NaCl , 0.01 % NH4Cl , 0.1 mM CaCl2 , 1 mM MgSO4 , 5 x 10 − 4 % Thiamin ) supplemented with <Supp> 0.5 % glucose </Supp> and 0.1 % amino acids was used for RNA-seq experiments . 	GPL15982	GPL15982: Illumina HiSeq 1000 (Escherichia coli str. K-12 substr. MG1655)	GSE74809	Growth-phase dependent regulation of transcription by Rsd and 6S RNA	GSM1933999	ssrS_LS_2	29686109	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE74809/GSE74809.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	M9 defined medium (0.6% Na2HPO4, 0.3% KH2PO4, 0.05% NaCl, 0.01% NH4Cl, 0.1 mM CaCl2, 1 mM MgSO4, 5 x 10−4% Thiamin) supplemented with 0.5% glucose and 0.1% amino acids was used for RNA-seq experiments. PGCGROWTHCONDITIONS	SRR2932682	MCO000002772	0.5 % glucose	Medium supplement	True
characteristics	stationary phase		growth phase : <Gtype> Late Stationary </Gtype> 	GPL15982	GPL15982: Illumina HiSeq 1000 (Escherichia coli str. K-12 substr. MG1655)	GSE74809	Growth-phase dependent regulation of transcription by Rsd and 6S RNA	GSM1933999	ssrS_LS_2	29686109	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE74809/GSE74809.soft.gz	84	84	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth phase: Late Stationary PGCGROWTHCONDITIONS	SRR2932682	MCO000002866	Late Stationary	Genetic background	True
growth_protocol	nicl2 5 µm		Transcriptomic analyses were carried out after growing bacteria in minimal media supplemented with <Supp> glucose </Supp> . Several Ni concentrations and exposure times were assayed . rcnA gene expression was taken as an internal control to arbitrate between the different conditions . rcnA is induced by Ni when cells are overloaded with this ion and must detoxify the cytoplasm by extruding excess metal via the RcnAB efflux system . rcnA induction was maximised after culture incubation for 10 min , and longer periods of incubation lead to a decline in rcnA expression ( Fig . S1 ) . For the RNA-Seq experiments , bacteria were grown until O.D600nm = 0.3 , were treated with <Supp> 50 µM NiCl2 </Supp> for 10 min and were frozen prior to RNA extraction . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE76167	Mechanisms of nickel toxicity in bacteria	GSM1975603	Rodrigue_1-WT-phiNi-1	2737513027668277	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE76167/GSE76167.soft.gz	95	95	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Transcriptomic analyses were carried out after growing bacteria in minimal media supplemented with glucose. Several Ni concentrations and exposure times were assayed. rcnA gene expression was taken as an internal control to arbitrate between the different conditions. rcnA is induced by Ni when cells are overloaded with this ion and must detoxify the cytoplasm by extruding excess metal via the RcnAB efflux system. rcnA induction was maximised after culture incubation for 10 min, and longer periods of incubation lead to a decline in rcnA expression (Fig. S1). For the RNA-Seq experiments, bacteria were grown until O.D600nm = 0.3, were treated with 50 µM NiCl2 for 10 min and were frozen prior to RNA extraction. PGCGROWTHCONDITIONS	SRR3033275SRR3033276SRR3033277SRR3033278SRR3033279	MCO000002790	50 µM NiCl2	Medium supplement	True
growth_protocol	nicl2 5 µm		Transcriptomic analyses were carried out after growing bacteria in minimal media supplemented with <Supp> glucose </Supp> . Several Ni concentrations and exposure times were assayed . rcnA gene expression was taken as an internal control to arbitrate between the different conditions . rcnA is induced by Ni when cells are overloaded with this ion and must detoxify the cytoplasm by extruding excess metal via the RcnAB efflux system . rcnA induction was maximised after culture incubation for 10 min , and longer periods of incubation lead to a decline in rcnA expression ( Fig . S1 ) . For the RNA-Seq experiments , bacteria were grown until O.D600nm = 0.3 , were treated with <Supp> 50 µM NiCl2 </Supp> for 10 min and were frozen prior to RNA extraction . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE76167	Mechanisms of nickel toxicity in bacteria	GSM1975604	Rodrigue_6-WT-phiNi-2	2737513027668277	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE76167/GSE76167.soft.gz	95	95	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Transcriptomic analyses were carried out after growing bacteria in minimal media supplemented with glucose. Several Ni concentrations and exposure times were assayed. rcnA gene expression was taken as an internal control to arbitrate between the different conditions. rcnA is induced by Ni when cells are overloaded with this ion and must detoxify the cytoplasm by extruding excess metal via the RcnAB efflux system. rcnA induction was maximised after culture incubation for 10 min, and longer periods of incubation lead to a decline in rcnA expression (Fig. S1). For the RNA-Seq experiments, bacteria were grown until O.D600nm = 0.3, were treated with 50 µM NiCl2 for 10 min and were frozen prior to RNA extraction. PGCGROWTHCONDITIONS	SRR3033280SRR3033281SRR3033282SRR3033283	MCO000002790	50 µM NiCl2	Medium supplement	True
growth_protocol	nicl2 5 µm		Transcriptomic analyses were carried out after growing bacteria in minimal media supplemented with <Supp> glucose </Supp> . Several Ni concentrations and exposure times were assayed . rcnA gene expression was taken as an internal control to arbitrate between the different conditions . rcnA is induced by Ni when cells are overloaded with this ion and must detoxify the cytoplasm by extruding excess metal via the RcnAB efflux system . rcnA induction was maximised after culture incubation for 10 min , and longer periods of incubation lead to a decline in rcnA expression ( Fig . S1 ) . For the RNA-Seq experiments , bacteria were grown until O.D600nm = 0.3 , were treated with <Supp> 50 µM NiCl2 </Supp> for 10 min and were frozen prior to RNA extraction . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE76167	Mechanisms of nickel toxicity in bacteria	GSM1975605	Rodrigue_9-WT-phiNi-3	2737513027668277	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE76167/GSE76167.soft.gz	95	95	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Transcriptomic analyses were carried out after growing bacteria in minimal media supplemented with glucose. Several Ni concentrations and exposure times were assayed. rcnA gene expression was taken as an internal control to arbitrate between the different conditions. rcnA is induced by Ni when cells are overloaded with this ion and must detoxify the cytoplasm by extruding excess metal via the RcnAB efflux system. rcnA induction was maximised after culture incubation for 10 min, and longer periods of incubation lead to a decline in rcnA expression (Fig. S1). For the RNA-Seq experiments, bacteria were grown until O.D600nm = 0.3, were treated with 50 µM NiCl2 for 10 min and were frozen prior to RNA extraction. PGCGROWTHCONDITIONS	SRR3033284SRR3033285SRR3033286SRR3033287	MCO000002790	50 µM NiCl2	Medium supplement	True
growth_protocol	nicl2 5 µm		Transcriptomic analyses were carried out after growing bacteria in minimal media supplemented with <Supp> glucose </Supp> . Several Ni concentrations and exposure times were assayed . rcnA gene expression was taken as an internal control to arbitrate between the different conditions . rcnA is induced by Ni when cells are overloaded with this ion and must detoxify the cytoplasm by extruding excess metal via the RcnAB efflux system . rcnA induction was maximised after culture incubation for 10 min , and longer periods of incubation lead to a decline in rcnA expression ( Fig . S1 ) . For the RNA-Seq experiments , bacteria were grown until O.D600nm = 0.3 , were treated with <Supp> 50 µM NiCl2 </Supp> for 10 min and were frozen prior to RNA extraction . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE76167	Mechanisms of nickel toxicity in bacteria	GSM1975606	Rodrigue_2-WT-Ni-1	2737513027668277	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE76167/GSE76167.soft.gz	95	95	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Transcriptomic analyses were carried out after growing bacteria in minimal media supplemented with glucose. Several Ni concentrations and exposure times were assayed. rcnA gene expression was taken as an internal control to arbitrate between the different conditions. rcnA is induced by Ni when cells are overloaded with this ion and must detoxify the cytoplasm by extruding excess metal via the RcnAB efflux system. rcnA induction was maximised after culture incubation for 10 min, and longer periods of incubation lead to a decline in rcnA expression (Fig. S1). For the RNA-Seq experiments, bacteria were grown until O.D600nm = 0.3, were treated with 50 µM NiCl2 for 10 min and were frozen prior to RNA extraction. PGCGROWTHCONDITIONS	SRR3033288SRR3033289SRR3033290SRR3033291SRR3033292	MCO000002790	50 µM NiCl2	Medium supplement	True
growth_protocol	nicl2 5 µm		Transcriptomic analyses were carried out after growing bacteria in minimal media supplemented with <Supp> glucose </Supp> . Several Ni concentrations and exposure times were assayed . rcnA gene expression was taken as an internal control to arbitrate between the different conditions . rcnA is induced by Ni when cells are overloaded with this ion and must detoxify the cytoplasm by extruding excess metal via the RcnAB efflux system . rcnA induction was maximised after culture incubation for 10 min , and longer periods of incubation lead to a decline in rcnA expression ( Fig . S1 ) . For the RNA-Seq experiments , bacteria were grown until O.D600nm = 0.3 , were treated with <Supp> 50 µM NiCl2 </Supp> for 10 min and were frozen prior to RNA extraction . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE76167	Mechanisms of nickel toxicity in bacteria	GSM1975607	Rodrigue_5-WT-Ni-2	2737513027668277	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE76167/GSE76167.soft.gz	95	95	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Transcriptomic analyses were carried out after growing bacteria in minimal media supplemented with glucose. Several Ni concentrations and exposure times were assayed. rcnA gene expression was taken as an internal control to arbitrate between the different conditions. rcnA is induced by Ni when cells are overloaded with this ion and must detoxify the cytoplasm by extruding excess metal via the RcnAB efflux system. rcnA induction was maximised after culture incubation for 10 min, and longer periods of incubation lead to a decline in rcnA expression (Fig. S1). For the RNA-Seq experiments, bacteria were grown until O.D600nm = 0.3, were treated with 50 µM NiCl2 for 10 min and were frozen prior to RNA extraction. PGCGROWTHCONDITIONS	SRR3033293SRR3033294SRR3033295SRR3033296	MCO000002790	50 µM NiCl2	Medium supplement	True
growth_protocol	nicl2 5 µm		Transcriptomic analyses were carried out after growing bacteria in minimal media supplemented with <Supp> glucose </Supp> . Several Ni concentrations and exposure times were assayed . rcnA gene expression was taken as an internal control to arbitrate between the different conditions . rcnA is induced by Ni when cells are overloaded with this ion and must detoxify the cytoplasm by extruding excess metal via the RcnAB efflux system . rcnA induction was maximised after culture incubation for 10 min , and longer periods of incubation lead to a decline in rcnA expression ( Fig . S1 ) . For the RNA-Seq experiments , bacteria were grown until O.D600nm = 0.3 , were treated with <Supp> 50 µM NiCl2 </Supp> for 10 min and were frozen prior to RNA extraction . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE76167	Mechanisms of nickel toxicity in bacteria	GSM1975608	Rodrigue_10-WT-Ni-3	2737513027668277	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE76167/GSE76167.soft.gz	95	95	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Transcriptomic analyses were carried out after growing bacteria in minimal media supplemented with glucose. Several Ni concentrations and exposure times were assayed. rcnA gene expression was taken as an internal control to arbitrate between the different conditions. rcnA is induced by Ni when cells are overloaded with this ion and must detoxify the cytoplasm by extruding excess metal via the RcnAB efflux system. rcnA induction was maximised after culture incubation for 10 min, and longer periods of incubation lead to a decline in rcnA expression (Fig. S1). For the RNA-Seq experiments, bacteria were grown until O.D600nm = 0.3, were treated with 50 µM NiCl2 for 10 min and were frozen prior to RNA extraction. PGCGROWTHCONDITIONS	SRR3033297SRR3033298SRR3033299SRR3033300SRR3033301	MCO000002790	50 µM NiCl2	Medium supplement	True
growth_protocol	OD600 of 0.3		E. coli strain NM580 ( genotype MG1655 ermBL-ermB ' : <Gtype> : LacZ </Gtype> ) cells were grown in LB broth ( <Temp> 37 °C </Temp> ) until <OD> OD600 of ~ 0.3 </OD> . 	GPL21726	GPL21726: Ion Torrent Proton (Escherichia coli)	GSE80251	Genome-wide transcriptome analyses of E. coli treated with ribosome-targeting antibiotics	GSM2122743	Untreated_replicate_1	27645242	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80251/GSE80251.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli strain NM580 (genotype MG1655 ermBL-ermB’::LacZ) cells were grown in LB broth (37°C) until OD600 of ~0.3. PGCGROWTHCONDITIONS	SRR3379590	MCO000002564	OD600 of ~ 0.3	Optical Density (OD)	True
growth_protocol	OD600 of 0.3		E. coli strain NM580 ( genotype MG1655 ermBL-ermB ' : <Gtype> : LacZ </Gtype> ) cells were grown in LB broth ( <Temp> 37 °C </Temp> ) until <OD> OD600 of ~ 0.3 </OD> . 	GPL21726	GPL21726: Ion Torrent Proton (Escherichia coli)	GSE80251	Genome-wide transcriptome analyses of E. coli treated with ribosome-targeting antibiotics	GSM2122744	Untreated_replicate_2	27645242	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80251/GSE80251.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli strain NM580 (genotype MG1655 ermBL-ermB’::LacZ) cells were grown in LB broth (37°C) until OD600 of ~0.3. PGCGROWTHCONDITIONS	SRR3379591	MCO000002564	OD600 of ~ 0.3	Optical Density (OD)	True
growth_protocol	OD600 of 0.3		E. coli strain NM580 ( genotype MG1655 ermBL-ermB ' : <Gtype> : LacZ </Gtype> ) cells were grown in LB broth ( <Temp> 37 °C </Temp> ) until <OD> OD600 of ~ 0.3 </OD> . 	GPL21726	GPL21726: Ion Torrent Proton (Escherichia coli)	GSE80251	Genome-wide transcriptome analyses of E. coli treated with ribosome-targeting antibiotics	GSM2122745	Untreated_replicate_3	27645242	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80251/GSE80251.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli strain NM580 (genotype MG1655 ermBL-ermB’::LacZ) cells were grown in LB broth (37°C) until OD600 of ~0.3. PGCGROWTHCONDITIONS	SRR3379592	MCO000002564	OD600 of ~ 0.3	Optical Density (OD)	True
growth_protocol	OD600 of 0.3		E. coli strain NM580 ( genotype MG1655 ermBL-ermB ' : <Gtype> : LacZ </Gtype> ) cells were grown in LB broth ( <Temp> 37 °C </Temp> ) until <OD> OD600 of ~ 0.3 </OD> . 	GPL21726	GPL21726: Ion Torrent Proton (Escherichia coli)	GSE80251	Genome-wide transcriptome analyses of E. coli treated with ribosome-targeting antibiotics	GSM2122746	Erythromycin_replicate_1	27645242	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80251/GSE80251.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli strain NM580 (genotype MG1655 ermBL-ermB’::LacZ) cells were grown in LB broth (37°C) until OD600 of ~0.3. PGCGROWTHCONDITIONS	SRR3379593	MCO000002564	OD600 of ~ 0.3	Optical Density (OD)	True
growth_protocol	OD600 of 0.3		E. coli strain NM580 ( genotype MG1655 ermBL-ermB ' : <Gtype> : LacZ </Gtype> ) cells were grown in LB broth ( <Temp> 37 °C </Temp> ) until <OD> OD600 of ~ 0.3 </OD> . 	GPL21726	GPL21726: Ion Torrent Proton (Escherichia coli)	GSE80251	Genome-wide transcriptome analyses of E. coli treated with ribosome-targeting antibiotics	GSM2122747	Erythromycin_replicate_2	27645242	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80251/GSE80251.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli strain NM580 (genotype MG1655 ermBL-ermB’::LacZ) cells were grown in LB broth (37°C) until OD600 of ~0.3. PGCGROWTHCONDITIONS	SRR3379594	MCO000002564	OD600 of ~ 0.3	Optical Density (OD)	True
growth_protocol	OD600 of 0.3		E. coli strain NM580 ( genotype MG1655 ermBL-ermB ' : <Gtype> : LacZ </Gtype> ) cells were grown in LB broth ( <Temp> 37 °C </Temp> ) until <OD> OD600 of ~ 0.3 </OD> . 	GPL21726	GPL21726: Ion Torrent Proton (Escherichia coli)	GSE80251	Genome-wide transcriptome analyses of E. coli treated with ribosome-targeting antibiotics	GSM2122748	Erythromycin_replicate_3	27645242	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80251/GSE80251.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli strain NM580 (genotype MG1655 ermBL-ermB’::LacZ) cells were grown in LB broth (37°C) until OD600 of ~0.3. PGCGROWTHCONDITIONS	SRR3379595	MCO000002564	OD600 of ~ 0.3	Optical Density (OD)	True
growth_protocol	OD600 of 0.3		E. coli strain NM580 ( genotype MG1655 ermBL-ermB ' : <Gtype> : LacZ </Gtype> ) cells were grown in LB broth ( <Temp> 37 °C </Temp> ) until <OD> OD600 of ~ 0.3 </OD> . 	GPL21726	GPL21726: Ion Torrent Proton (Escherichia coli)	GSE80251	Genome-wide transcriptome analyses of E. coli treated with ribosome-targeting antibiotics	GSM2122749	Clindamycin_replicate_1	27645242	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80251/GSE80251.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli strain NM580 (genotype MG1655 ermBL-ermB’::LacZ) cells were grown in LB broth (37°C) until OD600 of ~0.3. PGCGROWTHCONDITIONS	SRR3379596	MCO000002564	OD600 of ~ 0.3	Optical Density (OD)	True
growth_protocol	OD600 of 0.3		E. coli strain NM580 ( genotype MG1655 ermBL-ermB ' : <Gtype> : LacZ </Gtype> ) cells were grown in LB broth ( <Temp> 37 °C </Temp> ) until <OD> OD600 of ~ 0.3 </OD> . 	GPL21726	GPL21726: Ion Torrent Proton (Escherichia coli)	GSE80251	Genome-wide transcriptome analyses of E. coli treated with ribosome-targeting antibiotics	GSM2122750	Clindamycin_replicate_2	27645242	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80251/GSE80251.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli strain NM580 (genotype MG1655 ermBL-ermB’::LacZ) cells were grown in LB broth (37°C) until OD600 of ~0.3. PGCGROWTHCONDITIONS	SRR3379597	MCO000002564	OD600 of ~ 0.3	Optical Density (OD)	True
growth_protocol	OD600 of 0.3		E. coli strain NM580 ( genotype MG1655 ermBL-ermB ' : <Gtype> : LacZ </Gtype> ) cells were grown in LB broth ( <Temp> 37 °C </Temp> ) until <OD> OD600 of ~ 0.3 </OD> . 	GPL21726	GPL21726: Ion Torrent Proton (Escherichia coli)	GSE80251	Genome-wide transcriptome analyses of E. coli treated with ribosome-targeting antibiotics	GSM2122751	Clindamycin_replicate_3	27645242	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80251/GSE80251.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli strain NM580 (genotype MG1655 ermBL-ermB’::LacZ) cells were grown in LB broth (37°C) until OD600 of ~0.3. PGCGROWTHCONDITIONS	SRR3379598	MCO000002564	OD600 of ~ 0.3	Optical Density (OD)	True
growth_protocol	anaerobic		<Air> Aerobic and anaerobic </Air> cultures were grown in 600 mL aliquots of DM25 and incubated at <Temp> 37 °C </Temp> with an orbital shaking of 150 RPM and inoculated with 1/100th volume of overnight culture . Aerobic cultures were grown for 9 h while anaerobic cultures were grown for 16 h. 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE80451	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GSM2127617	Aerobic 1	28103245	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80451/GSE80451.soft.gz	100	60	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic and anaerobic cultures were grown in 600 mL aliquots of DM25 and incubated at 37°C with an orbital shaking of 150 RPM and inoculated with 1/100th volume of overnight culture. Aerobic cultures were grown for 9 h while anaerobic cultures were grown for 16 h. PGCGROWTHCONDITIONS	SRR3403686	MCO000011680	Aerobic and anaerobic	Aeration	True
growth_protocol	anaerobic		<Air> Aerobic and anaerobic </Air> cultures were grown in 600 mL aliquots of DM25 and incubated at <Temp> 37 °C </Temp> with an orbital shaking of 150 RPM and inoculated with 1/100th volume of overnight culture . Aerobic cultures were grown for 9 h while anaerobic cultures were grown for 16 h. 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE80451	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GSM2127618	Aerobic 2	28103245	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80451/GSE80451.soft.gz	100	60	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic and anaerobic cultures were grown in 600 mL aliquots of DM25 and incubated at 37°C with an orbital shaking of 150 RPM and inoculated with 1/100th volume of overnight culture. Aerobic cultures were grown for 9 h while anaerobic cultures were grown for 16 h. PGCGROWTHCONDITIONS	SRR3403687	MCO000011680	Aerobic and anaerobic	Aeration	True
growth_protocol	anaerobic		<Air> Aerobic and anaerobic </Air> cultures were grown in 600 mL aliquots of DM25 and incubated at <Temp> 37 °C </Temp> with an orbital shaking of 150 RPM and inoculated with 1/100th volume of overnight culture . Aerobic cultures were grown for 9 h while anaerobic cultures were grown for 16 h. 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE80451	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GSM2127619	Aerobic 3	28103245	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80451/GSE80451.soft.gz	100	60	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Aerobic and anaerobic cultures were grown in 600 mL aliquots of DM25 and incubated at 37°C with an orbital shaking of 150 RPM and inoculated with 1/100th volume of overnight culture. Aerobic cultures were grown for 9 h while anaerobic cultures were grown for 16 h. PGCGROWTHCONDITIONS	SRR3403688	MCO000011680	Aerobic and anaerobic	Aeration	True
characteristics	wildtype		genotype : <Gtype> Wildtype </Gtype> 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE81584	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GSM2157648	MG1655_1		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE81584/GSE81584.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: Wildtype PGCGROWTHCONDITIONS	SRR3584193SRR3584194SRR3584195	MCO000002470	Wildtype	Genetic background	True
characteristics	wildtype		genotype : <Gtype> Wildtype </Gtype> 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE81584	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GSM2157649	MG1655_2		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE81584/GSE81584.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: Wildtype PGCGROWTHCONDITIONS	SRR3584196SRR3584197SRR3584198	MCO000002470	Wildtype	Genetic background	True
characteristics	wildtype		genotype : <Gtype> Wildtype </Gtype> 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE81584	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GSM2157650	MG1655_3		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE81584/GSE81584.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: Wildtype PGCGROWTHCONDITIONS	SRR3584199SRR3584200	MCO000002470	Wildtype	Genetic background	True
characteristics	wildtype		genotype : <Gtype> Wildtype </Gtype> with <Supp> vector </Supp> 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE81584	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GSM2157654	MG1655_vector_1		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE81584/GSE81584.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: Wildtype with vector PGCGROWTHCONDITIONS	SRR3584208SRR3584209	MCO000002470	Wildtype	Genetic background	True
characteristics	wildtype		genotype : <Gtype> Wildtype </Gtype> with <Supp> vector </Supp> 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE81584	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GSM2157655	MG1655_vector_2		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE81584/GSE81584.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: Wildtype with vector PGCGROWTHCONDITIONS	SRR3584210SRR3584211	MCO000002470	Wildtype	Genetic background	True
characteristics	100.003		rpos level : <Supp> 100 % </Supp> 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE87856	The genome-wide transcriptional response to varying RpoS levels in Escherichia coli.	GSM2341961	100% rep1	28115545	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE87856/GSE87856.soft.gz	100	60	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	rpos level: 100% PGCGROWTHCONDITIONS	SRR4416202	MCO000002063	100 %	Medium supplement	True
characteristics	100.003		rpos level : <Supp> 100 % </Supp> 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE87856	The genome-wide transcriptional response to varying RpoS levels in Escherichia coli.	GSM2341964	100% rep2	28115545	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE87856/GSE87856.soft.gz	100	60	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	rpos level: 100% PGCGROWTHCONDITIONS	SRR4416205	MCO000002063	100 %	Medium supplement	True
characteristics	0		rpos level : <Supp> 0 % </Supp> 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE87856	The genome-wide transcriptional response to varying RpoS levels in Escherichia coli.	GSM2341962	0% rep1	28115545	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE87856/GSE87856.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	rpos level: 0% PGCGROWTHCONDITIONS	SRR4416203	MCO000000748	0 %	Medium supplement	True
characteristics	0		rpos level : <Supp> 0 % </Supp> 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE87856	The genome-wide transcriptional response to varying RpoS levels in Escherichia coli.	GSM2341965	0% rep2	28115545	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE87856/GSE87856.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	rpos level: 0% PGCGROWTHCONDITIONS	SRR4416206	MCO000000748	0 %	Medium supplement	True
characteristics	26.0 C		rpos level : <Supp> 26 % </Supp> 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE87856	The genome-wide transcriptional response to varying RpoS levels in Escherichia coli.	GSM2341963	26% rep1	28115545	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE87856/GSE87856.soft.gz	100	50	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	rpos level: 26% PGCGROWTHCONDITIONS	SRR4416204	MCO000003196	26 %	Medium supplement	True
characteristics	26.0 C		rpos level : <Supp> 26 % </Supp> 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE87856	The genome-wide transcriptional response to varying RpoS levels in Escherichia coli.	GSM2341966	26% rep2	28115545	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE87856/GSE87856.soft.gz	100	50	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	rpos level: 26% PGCGROWTHCONDITIONS	SRR4416207	MCO000003196	26 %	Medium supplement	True
growth_protocol	nacl 0.35 m		E. coli K-12 MG1655 WT and ΔompR were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . Then cells were treated with <Supp> 0.3 M of NaCl </Supp> at mid-log pahse for <Supp> 30 min </Supp> with agitation . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE88980	Revealing the genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles and unexpected importance of narU under osmotic stress in Escherichia coli K-12 MG1655 [RNA-seq]	GSM2356687	WT NaCl 1	28526842	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88980/GSE88980.soft.gz	84	83	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	E. coli K-12 MG1655 WT and ΔompR were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 0.3 M of NaCl at mid-log pahse for 30 min with agitation. PGCGROWTHCONDITIONS	SRR4435464	MCO000002726	0.3 M of NaCl	Medium supplement	True
growth_protocol	nacl 0.35 m		E. coli K-12 MG1655 WT and ΔompR were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . Then cells were treated with <Supp> 0.3 M of NaCl </Supp> at mid-log pahse for <Supp> 30 min </Supp> with agitation . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE88980	Revealing the genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles and unexpected importance of narU under osmotic stress in Escherichia coli K-12 MG1655 [RNA-seq]	GSM2356688	WT NaCl 2	28526842	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88980/GSE88980.soft.gz	84	83	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	E. coli K-12 MG1655 WT and ΔompR were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 0.3 M of NaCl at mid-log pahse for 30 min with agitation. PGCGROWTHCONDITIONS	SRR4435465	MCO000002726	0.3 M of NaCl	Medium supplement	True
growth_protocol	nacl 0.35 m		E. coli K-12 MG1655 WT and ΔompR were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . Then cells were treated with <Supp> 0.3 M of NaCl </Supp> at mid-log pahse for <Supp> 30 min </Supp> with agitation . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE88980	Revealing the genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles and unexpected importance of narU under osmotic stress in Escherichia coli K-12 MG1655 [RNA-seq]	GSM2356689	ΔompR NaCl 1	28526842	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88980/GSE88980.soft.gz	84	83	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	E. coli K-12 MG1655 WT and ΔompR were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 0.3 M of NaCl at mid-log pahse for 30 min with agitation. PGCGROWTHCONDITIONS	SRR4435466	MCO000002726	0.3 M of NaCl	Medium supplement	True
growth_protocol	nacl 0.35 m		E. coli K-12 MG1655 WT and ΔompR were grown to <Phase> mid-log phase </Phase> <Air> aerobically </Air> at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> . Then cells were treated with <Supp> 0.3 M of NaCl </Supp> at mid-log pahse for <Supp> 30 min </Supp> with agitation . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE88980	Revealing the genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles and unexpected importance of narU under osmotic stress in Escherichia coli K-12 MG1655 [RNA-seq]	GSM2356690	ΔompR NaCl 2	28526842	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88980/GSE88980.soft.gz	84	83	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	E. coli K-12 MG1655 WT and ΔompR were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. Then cells were treated with 0.3 M of NaCl at mid-log pahse for 30 min with agitation. PGCGROWTHCONDITIONS	SRR4435467	MCO000002726	0.3 M of NaCl	Medium supplement	True
characteristics	arabinose		induction : <Supp> 0.2 % arabinose </Supp> 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE90056	Translation efficiency is maintained during heat shock in Escherichia coli	GSM2396709	ecoli_k12_pBAD_30C_m_1	29183994	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90056/GSE90056.soft.gz	100	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	induction: 0.2% arabinose PGCGROWTHCONDITIONS	SRR5036057	MCO000000402	0.2 % arabinose	Medium supplement	True
characteristics	arabinose		induction : <Supp> 0.2 % arabinose </Supp> 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE90056	Translation efficiency is maintained during heat shock in Escherichia coli	GSM2396711	ecoli_k12_pBADsigma32wt_30C_m_1	29183994	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90056/GSE90056.soft.gz	100	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	induction: 0.2% arabinose PGCGROWTHCONDITIONS	SRR5036059	MCO000000402	0.2 % arabinose	Medium supplement	True
characteristics	arabinose		induction : <Supp> 0.2 % arabinose </Supp> 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE90056	Translation efficiency is maintained during heat shock in Escherichia coli	GSM2396713	ecoli_k12_pBAD_30C_m_2	29183994	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90056/GSE90056.soft.gz	100	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	induction: 0.2% arabinose PGCGROWTHCONDITIONS	SRR5036061	MCO000000402	0.2 % arabinose	Medium supplement	True
characteristics	arabinose		induction : <Supp> 0.2 % arabinose </Supp> 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE90056	Translation efficiency is maintained during heat shock in Escherichia coli	GSM2396715	ecoli_k12_pBADsigma32wt_30C_m_2	29183994	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90056/GSE90056.soft.gz	100	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	induction: 0.2% arabinose PGCGROWTHCONDITIONS	SRR5036063	MCO000000402	0.2 % arabinose	Medium supplement	True
characteristics	arabinose		induction : <Supp> 0.2 % arabinose </Supp> 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE90056	Translation efficiency is maintained during heat shock in Escherichia coli	GSM2396717	ecoli_k12_pBAD_30C_m_3	29183994	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90056/GSE90056.soft.gz	100	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	induction: 0.2% arabinose PGCGROWTHCONDITIONS	SRR5036065	MCO000000402	0.2 % arabinose	Medium supplement	True
characteristics	arabinose		induction : <Supp> 0.2 % arabinose </Supp> 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE90056	Translation efficiency is maintained during heat shock in Escherichia coli	GSM2396719	ecoli_k12_pBADsigma32wt_30C_m_3	29183994	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90056/GSE90056.soft.gz	100	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	induction: 0.2% arabinose PGCGROWTHCONDITIONS	SRR5036067	MCO000000402	0.2 % arabinose	Medium supplement	True
characteristics	arabinose		induction : <Supp> 0.2 % arabinose </Supp> 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE90056	Translation efficiency is maintained during heat shock in Escherichia coli	GSM2396739	ecoli_k12_pBAD_30C_m_4	29183994	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90056/GSE90056.soft.gz	100	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	induction: 0.2% arabinose PGCGROWTHCONDITIONS	SRR5036087	MCO000000402	0.2 % arabinose	Medium supplement	True
characteristics	arabinose		induction : <Supp> 0.2 % arabinose </Supp> 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE90056	Translation efficiency is maintained during heat shock in Escherichia coli	GSM2396741	ecoli_k12_pBADsigma32I54N_30C_m_1	29183994	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90056/GSE90056.soft.gz	100	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	induction: 0.2% arabinose PGCGROWTHCONDITIONS	SRR5036089	MCO000000402	0.2 % arabinose	Medium supplement	True
characteristics	arabinose		induction : <Supp> 0.2 % arabinose </Supp> 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE90056	Translation efficiency is maintained during heat shock in Escherichia coli	GSM2396743	ecoli_k12_pBADsigma32I54N_30C_m_2	29183994	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90056/GSE90056.soft.gz	100	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	induction: 0.2% arabinose PGCGROWTHCONDITIONS	SRR5036091	MCO000000402	0.2 % arabinose	Medium supplement	True
growth_protocol	LB agar		<Med> LB </Med> ( 5 ml ) was inoculated by a frozen stock of WT or perC-mutant strain and incubated at <Temp> 37 °C </Temp> with 225 rpm shaking . Flasks containing low-glucose DMEM were inoculated 1:100 with the overnight culture and incubated at <Temp> 37 °C </Temp> with 225 rpm shaking to mid-exponential phase ( OD600 0.3-0.5 ) . 	GPL14548-GPL20262	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	GSE91001	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GSM2418921	ATCACG-D1	28224117	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE91001/GSE91001.soft.gz	100	44	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	LB (5 ml) was inoculated by a frozen stock of WT or perC-mutant strain and incubated at 37°C with 225 rpm shaking. Flasks containing low-glucose DMEM were inoculated 1:100 with the overnight culture and incubated at 37°C with 225 rpm shaking to mid-exponential phase (OD600 0.3-0.5). PGCGROWTHCONDITIONS	SRR5085370	MCO000011703	LB	Medium	True
growth_protocol	LB agar		<Med> LB </Med> ( 5 ml ) was inoculated by a frozen stock of WT or perC-mutant strain and incubated at <Temp> 37 °C </Temp> with 225 rpm shaking . Flasks containing low-glucose DMEM were inoculated 1:100 with the overnight culture and incubated at <Temp> 37 °C </Temp> with 225 rpm shaking to mid-exponential phase ( OD600 0.3-0.5 ) . 	GPL14548-GPL20262	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	GSE91001	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GSM2418922	CGATGT-D2	28224117	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE91001/GSE91001.soft.gz	100	44	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	LB (5 ml) was inoculated by a frozen stock of WT or perC-mutant strain and incubated at 37°C with 225 rpm shaking. Flasks containing low-glucose DMEM were inoculated 1:100 with the overnight culture and incubated at 37°C with 225 rpm shaking to mid-exponential phase (OD600 0.3-0.5). PGCGROWTHCONDITIONS	SRR5085371	MCO000011703	LB	Medium	True
growth_protocol	LB agar		<Med> LB </Med> ( 5 ml ) was inoculated by a frozen stock of WT or perC-mutant strain and incubated at <Temp> 37 °C </Temp> with 225 rpm shaking . Flasks containing low-glucose DMEM were inoculated 1:100 with the overnight culture and incubated at <Temp> 37 °C </Temp> with 225 rpm shaking to mid-exponential phase ( OD600 0.3-0.5 ) . 	GPL14548-GPL20262	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	GSE91001	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GSM2418923	TTAGGC-D3	28224117	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE91001/GSE91001.soft.gz	100	44	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	LB (5 ml) was inoculated by a frozen stock of WT or perC-mutant strain and incubated at 37°C with 225 rpm shaking. Flasks containing low-glucose DMEM were inoculated 1:100 with the overnight culture and incubated at 37°C with 225 rpm shaking to mid-exponential phase (OD600 0.3-0.5). PGCGROWTHCONDITIONS	SRR5085373	MCO000011703	LB	Medium	True
data_processing	iptg		<Supp> Supplementary </Supp> _ files _ format _ and _ <Gtype> content : The </Gtype> columns in the processed files are the following in order : <Gtype> GeneID , Length , ORF1 </Gtype> _ 1 _ mapped _ reads ( 7655775 ) , ORF1 _ 1 _ <Supp> IPTG </Supp> _ mapped _ reads ( 7178582 ) , ORF1 _ 2 _ mapped _ reads ( 7706927 ) , ORF1 _ 2 _ <Supp> IPTG </Supp> _ mapped _ reads ( 7070827 ) , Svi3 _ 3 _ 1 _ mapped _ reads ( 8018710 ) , Svi3 _ 3 _ 1 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8299205 ) , Svi3 _ 3 _ 2 _ mapped _ reads ( 7313736 ) , Svi3 _ 3 _ 2 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8344539 ) , WT1 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8074159 ) , WT2 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8103887 ) , ORF1 _ 1 _ coverage , ORF1 _ 1 _ <Supp> IPTG </Supp> _ coverage , ORF1 _ 2 _ coverage , ORF1 _ 2 _ <Supp> IPTG </Supp> _ coverage , Svi3 _ 3 _ 1 _ coverage , Svi3 _ 3 _ 1 _ <Supp> IPTG </Supp> _ coverage , Svi3 _ 3 _ 2 _ coverage , Svi3 _ 3 _ 2 _ <Supp> IPTG </Supp> _ coverage , WT1 _ <Supp> IPTG </Supp> _ coverage , WT2 _ <Supp> IPTG </Supp> _ coverage , ORF1 _ 1 _ rpkm , ORF1 _ 1 _ <Supp> IPTG </Supp> _ rpkm , ORF1 _ 2 _ rpkm , ORF1 _ 2 _ <Supp> IPTG </Supp> _ rpkm , Svi3 _ 3 _ 1 _ rpkm , Svi3 _ 3 _ 1 _ <Supp> IPTG </Supp> _ rpkm , Svi3 _ 3 _ 2 _ rpkm , Svi3 _ 3 _ 2 _ <Supp> IPTG </Supp> _ rpkm , WT1 _ <Supp> IPTG </Supp> _ rpkm , WT2 _ <Supp> IPTG </Supp> _ rpkm , Symbol ( gene name ) , Description , KEGG Orthology , GO Component , GO Function , and GO Process 	GPL18956	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	GSE92601	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GSM2433290	ORF1_1_IPTG	29807996	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Supplementary_files_format_and_content: The columns in the processed files are the following in order:  GeneID, Length, ORF1_1_mapped_reads(7655775), ORF1_1_IPTG_mapped_reads(7178582), ORF1_2_mapped_reads(7706927), ORF1_2_IPTG_mapped_reads(7070827), Svi3_3_1_mapped_reads(8018710), Svi3_3_1_IPTG_mapped_reads(8299205), Svi3_3_2_mapped_reads(7313736), Svi3_3_2_IPTG_mapped_reads(8344539), WT1_IPTG_mapped_reads(8074159), WT2_IPTG_mapped_reads(8103887), ORF1_1_coverage, ORF1_1_IPTG_coverage, ORF1_2_coverage, ORF1_2_IPTG_coverage, Svi3_3_1_coverage, Svi3_3_1_IPTG_coverage, Svi3_3_2_coverage, Svi3_3_2_IPTG_coverage, WT1_IPTG_coverage, WT2_IPTG_coverage, ORF1_1_rpkm, ORF1_1_IPTG_rpkm, ORF1_2_rpkm, ORF1_2_IPTG_rpkm, Svi3_3_1_rpkm, Svi3_3_1_IPTG_rpkm, Svi3_3_2_rpkm, Svi3_3_2_IPTG_rpkm, WT1_IPTG_rpkm, WT2_IPTG_rpkm, Symbol (gene name), Description, KEGG Orthology, GO Component, GO Function, and GO Process PGCGROWTHCONDITIONS	SRR5121109	MCO000002105	IPTG	Medium supplement	True
data_processing	iptg		<Supp> Supplementary </Supp> _ files _ format _ and _ <Gtype> content : The </Gtype> columns in the processed files are the following in order : <Gtype> GeneID , Length , ORF1 </Gtype> _ 1 _ mapped _ reads ( 7655775 ) , ORF1 _ 1 _ <Supp> IPTG </Supp> _ mapped _ reads ( 7178582 ) , ORF1 _ 2 _ mapped _ reads ( 7706927 ) , ORF1 _ 2 _ <Supp> IPTG </Supp> _ mapped _ reads ( 7070827 ) , Svi3 _ 3 _ 1 _ mapped _ reads ( 8018710 ) , Svi3 _ 3 _ 1 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8299205 ) , Svi3 _ 3 _ 2 _ mapped _ reads ( 7313736 ) , Svi3 _ 3 _ 2 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8344539 ) , WT1 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8074159 ) , WT2 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8103887 ) , ORF1 _ 1 _ coverage , ORF1 _ 1 _ <Supp> IPTG </Supp> _ coverage , ORF1 _ 2 _ coverage , ORF1 _ 2 _ <Supp> IPTG </Supp> _ coverage , Svi3 _ 3 _ 1 _ coverage , Svi3 _ 3 _ 1 _ <Supp> IPTG </Supp> _ coverage , Svi3 _ 3 _ 2 _ coverage , Svi3 _ 3 _ 2 _ <Supp> IPTG </Supp> _ coverage , WT1 _ <Supp> IPTG </Supp> _ coverage , WT2 _ <Supp> IPTG </Supp> _ coverage , ORF1 _ 1 _ rpkm , ORF1 _ 1 _ <Supp> IPTG </Supp> _ rpkm , ORF1 _ 2 _ rpkm , ORF1 _ 2 _ <Supp> IPTG </Supp> _ rpkm , Svi3 _ 3 _ 1 _ rpkm , Svi3 _ 3 _ 1 _ <Supp> IPTG </Supp> _ rpkm , Svi3 _ 3 _ 2 _ rpkm , Svi3 _ 3 _ 2 _ <Supp> IPTG </Supp> _ rpkm , WT1 _ <Supp> IPTG </Supp> _ rpkm , WT2 _ <Supp> IPTG </Supp> _ rpkm , Symbol ( gene name ) , Description , KEGG Orthology , GO Component , GO Function , and GO Process 	GPL18956	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	GSE92601	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GSM2433291	ORF1_1	29807996	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Supplementary_files_format_and_content: The columns in the processed files are the following in order:  GeneID, Length, ORF1_1_mapped_reads(7655775), ORF1_1_IPTG_mapped_reads(7178582), ORF1_2_mapped_reads(7706927), ORF1_2_IPTG_mapped_reads(7070827), Svi3_3_1_mapped_reads(8018710), Svi3_3_1_IPTG_mapped_reads(8299205), Svi3_3_2_mapped_reads(7313736), Svi3_3_2_IPTG_mapped_reads(8344539), WT1_IPTG_mapped_reads(8074159), WT2_IPTG_mapped_reads(8103887), ORF1_1_coverage, ORF1_1_IPTG_coverage, ORF1_2_coverage, ORF1_2_IPTG_coverage, Svi3_3_1_coverage, Svi3_3_1_IPTG_coverage, Svi3_3_2_coverage, Svi3_3_2_IPTG_coverage, WT1_IPTG_coverage, WT2_IPTG_coverage, ORF1_1_rpkm, ORF1_1_IPTG_rpkm, ORF1_2_rpkm, ORF1_2_IPTG_rpkm, Svi3_3_1_rpkm, Svi3_3_1_IPTG_rpkm, Svi3_3_2_rpkm, Svi3_3_2_IPTG_rpkm, WT1_IPTG_rpkm, WT2_IPTG_rpkm, Symbol (gene name), Description, KEGG Orthology, GO Component, GO Function, and GO Process PGCGROWTHCONDITIONS	SRR5121110	MCO000002105	IPTG	Medium supplement	True
data_processing	iptg		<Supp> Supplementary </Supp> _ files _ format _ and _ <Gtype> content : The </Gtype> columns in the processed files are the following in order : <Gtype> GeneID , Length , ORF1 </Gtype> _ 1 _ mapped _ reads ( 7655775 ) , ORF1 _ 1 _ <Supp> IPTG </Supp> _ mapped _ reads ( 7178582 ) , ORF1 _ 2 _ mapped _ reads ( 7706927 ) , ORF1 _ 2 _ <Supp> IPTG </Supp> _ mapped _ reads ( 7070827 ) , Svi3 _ 3 _ 1 _ mapped _ reads ( 8018710 ) , Svi3 _ 3 _ 1 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8299205 ) , Svi3 _ 3 _ 2 _ mapped _ reads ( 7313736 ) , Svi3 _ 3 _ 2 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8344539 ) , WT1 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8074159 ) , WT2 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8103887 ) , ORF1 _ 1 _ coverage , ORF1 _ 1 _ <Supp> IPTG </Supp> _ coverage , ORF1 _ 2 _ coverage , ORF1 _ 2 _ <Supp> IPTG </Supp> _ coverage , Svi3 _ 3 _ 1 _ coverage , Svi3 _ 3 _ 1 _ <Supp> IPTG </Supp> _ coverage , Svi3 _ 3 _ 2 _ coverage , Svi3 _ 3 _ 2 _ <Supp> IPTG </Supp> _ coverage , WT1 _ <Supp> IPTG </Supp> _ coverage , WT2 _ <Supp> IPTG </Supp> _ coverage , ORF1 _ 1 _ rpkm , ORF1 _ 1 _ <Supp> IPTG </Supp> _ rpkm , ORF1 _ 2 _ rpkm , ORF1 _ 2 _ <Supp> IPTG </Supp> _ rpkm , Svi3 _ 3 _ 1 _ rpkm , Svi3 _ 3 _ 1 _ <Supp> IPTG </Supp> _ rpkm , Svi3 _ 3 _ 2 _ rpkm , Svi3 _ 3 _ 2 _ <Supp> IPTG </Supp> _ rpkm , WT1 _ <Supp> IPTG </Supp> _ rpkm , WT2 _ <Supp> IPTG </Supp> _ rpkm , Symbol ( gene name ) , Description , KEGG Orthology , GO Component , GO Function , and GO Process 	GPL18956	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	GSE92601	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GSM2433292	ORF1_2_IPTG	29807996	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Supplementary_files_format_and_content: The columns in the processed files are the following in order:  GeneID, Length, ORF1_1_mapped_reads(7655775), ORF1_1_IPTG_mapped_reads(7178582), ORF1_2_mapped_reads(7706927), ORF1_2_IPTG_mapped_reads(7070827), Svi3_3_1_mapped_reads(8018710), Svi3_3_1_IPTG_mapped_reads(8299205), Svi3_3_2_mapped_reads(7313736), Svi3_3_2_IPTG_mapped_reads(8344539), WT1_IPTG_mapped_reads(8074159), WT2_IPTG_mapped_reads(8103887), ORF1_1_coverage, ORF1_1_IPTG_coverage, ORF1_2_coverage, ORF1_2_IPTG_coverage, Svi3_3_1_coverage, Svi3_3_1_IPTG_coverage, Svi3_3_2_coverage, Svi3_3_2_IPTG_coverage, WT1_IPTG_coverage, WT2_IPTG_coverage, ORF1_1_rpkm, ORF1_1_IPTG_rpkm, ORF1_2_rpkm, ORF1_2_IPTG_rpkm, Svi3_3_1_rpkm, Svi3_3_1_IPTG_rpkm, Svi3_3_2_rpkm, Svi3_3_2_IPTG_rpkm, WT1_IPTG_rpkm, WT2_IPTG_rpkm, Symbol (gene name), Description, KEGG Orthology, GO Component, GO Function, and GO Process PGCGROWTHCONDITIONS	SRR5121111	MCO000002105	IPTG	Medium supplement	True
data_processing	iptg		<Supp> Supplementary </Supp> _ files _ format _ and _ <Gtype> content : The </Gtype> columns in the processed files are the following in order : <Gtype> GeneID , Length , ORF1 </Gtype> _ 1 _ mapped _ reads ( 7655775 ) , ORF1 _ 1 _ <Supp> IPTG </Supp> _ mapped _ reads ( 7178582 ) , ORF1 _ 2 _ mapped _ reads ( 7706927 ) , ORF1 _ 2 _ <Supp> IPTG </Supp> _ mapped _ reads ( 7070827 ) , Svi3 _ 3 _ 1 _ mapped _ reads ( 8018710 ) , Svi3 _ 3 _ 1 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8299205 ) , Svi3 _ 3 _ 2 _ mapped _ reads ( 7313736 ) , Svi3 _ 3 _ 2 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8344539 ) , WT1 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8074159 ) , WT2 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8103887 ) , ORF1 _ 1 _ coverage , ORF1 _ 1 _ <Supp> IPTG </Supp> _ coverage , ORF1 _ 2 _ coverage , ORF1 _ 2 _ <Supp> IPTG </Supp> _ coverage , Svi3 _ 3 _ 1 _ coverage , Svi3 _ 3 _ 1 _ <Supp> IPTG </Supp> _ coverage , Svi3 _ 3 _ 2 _ coverage , Svi3 _ 3 _ 2 _ <Supp> IPTG </Supp> _ coverage , WT1 _ <Supp> IPTG </Supp> _ coverage , WT2 _ <Supp> IPTG </Supp> _ coverage , ORF1 _ 1 _ rpkm , ORF1 _ 1 _ <Supp> IPTG </Supp> _ rpkm , ORF1 _ 2 _ rpkm , ORF1 _ 2 _ <Supp> IPTG </Supp> _ rpkm , Svi3 _ 3 _ 1 _ rpkm , Svi3 _ 3 _ 1 _ <Supp> IPTG </Supp> _ rpkm , Svi3 _ 3 _ 2 _ rpkm , Svi3 _ 3 _ 2 _ <Supp> IPTG </Supp> _ rpkm , WT1 _ <Supp> IPTG </Supp> _ rpkm , WT2 _ <Supp> IPTG </Supp> _ rpkm , Symbol ( gene name ) , Description , KEGG Orthology , GO Component , GO Function , and GO Process 	GPL18956	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	GSE92601	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GSM2433293	ORF1_2	29807996	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Supplementary_files_format_and_content: The columns in the processed files are the following in order:  GeneID, Length, ORF1_1_mapped_reads(7655775), ORF1_1_IPTG_mapped_reads(7178582), ORF1_2_mapped_reads(7706927), ORF1_2_IPTG_mapped_reads(7070827), Svi3_3_1_mapped_reads(8018710), Svi3_3_1_IPTG_mapped_reads(8299205), Svi3_3_2_mapped_reads(7313736), Svi3_3_2_IPTG_mapped_reads(8344539), WT1_IPTG_mapped_reads(8074159), WT2_IPTG_mapped_reads(8103887), ORF1_1_coverage, ORF1_1_IPTG_coverage, ORF1_2_coverage, ORF1_2_IPTG_coverage, Svi3_3_1_coverage, Svi3_3_1_IPTG_coverage, Svi3_3_2_coverage, Svi3_3_2_IPTG_coverage, WT1_IPTG_coverage, WT2_IPTG_coverage, ORF1_1_rpkm, ORF1_1_IPTG_rpkm, ORF1_2_rpkm, ORF1_2_IPTG_rpkm, Svi3_3_1_rpkm, Svi3_3_1_IPTG_rpkm, Svi3_3_2_rpkm, Svi3_3_2_IPTG_rpkm, WT1_IPTG_rpkm, WT2_IPTG_rpkm, Symbol (gene name), Description, KEGG Orthology, GO Component, GO Function, and GO Process PGCGROWTHCONDITIONS	SRR5121112	MCO000002105	IPTG	Medium supplement	True
data_processing	iptg		<Supp> Supplementary </Supp> _ files _ format _ and _ <Gtype> content : The </Gtype> columns in the processed files are the following in order : <Gtype> GeneID , Length , ORF1 </Gtype> _ 1 _ mapped _ reads ( 7655775 ) , ORF1 _ 1 _ <Supp> IPTG </Supp> _ mapped _ reads ( 7178582 ) , ORF1 _ 2 _ mapped _ reads ( 7706927 ) , ORF1 _ 2 _ <Supp> IPTG </Supp> _ mapped _ reads ( 7070827 ) , Svi3 _ 3 _ 1 _ mapped _ reads ( 8018710 ) , Svi3 _ 3 _ 1 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8299205 ) , Svi3 _ 3 _ 2 _ mapped _ reads ( 7313736 ) , Svi3 _ 3 _ 2 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8344539 ) , WT1 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8074159 ) , WT2 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8103887 ) , ORF1 _ 1 _ coverage , ORF1 _ 1 _ <Supp> IPTG </Supp> _ coverage , ORF1 _ 2 _ coverage , ORF1 _ 2 _ <Supp> IPTG </Supp> _ coverage , Svi3 _ 3 _ 1 _ coverage , Svi3 _ 3 _ 1 _ <Supp> IPTG </Supp> _ coverage , Svi3 _ 3 _ 2 _ coverage , Svi3 _ 3 _ 2 _ <Supp> IPTG </Supp> _ coverage , WT1 _ <Supp> IPTG </Supp> _ coverage , WT2 _ <Supp> IPTG </Supp> _ coverage , ORF1 _ 1 _ rpkm , ORF1 _ 1 _ <Supp> IPTG </Supp> _ rpkm , ORF1 _ 2 _ rpkm , ORF1 _ 2 _ <Supp> IPTG </Supp> _ rpkm , Svi3 _ 3 _ 1 _ rpkm , Svi3 _ 3 _ 1 _ <Supp> IPTG </Supp> _ rpkm , Svi3 _ 3 _ 2 _ rpkm , Svi3 _ 3 _ 2 _ <Supp> IPTG </Supp> _ rpkm , WT1 _ <Supp> IPTG </Supp> _ rpkm , WT2 _ <Supp> IPTG </Supp> _ rpkm , Symbol ( gene name ) , Description , KEGG Orthology , GO Component , GO Function , and GO Process 	GPL18956	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	GSE92601	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GSM2433294	Svi3_3_1_IPTG	29807996	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Supplementary_files_format_and_content: The columns in the processed files are the following in order:  GeneID, Length, ORF1_1_mapped_reads(7655775), ORF1_1_IPTG_mapped_reads(7178582), ORF1_2_mapped_reads(7706927), ORF1_2_IPTG_mapped_reads(7070827), Svi3_3_1_mapped_reads(8018710), Svi3_3_1_IPTG_mapped_reads(8299205), Svi3_3_2_mapped_reads(7313736), Svi3_3_2_IPTG_mapped_reads(8344539), WT1_IPTG_mapped_reads(8074159), WT2_IPTG_mapped_reads(8103887), ORF1_1_coverage, ORF1_1_IPTG_coverage, ORF1_2_coverage, ORF1_2_IPTG_coverage, Svi3_3_1_coverage, Svi3_3_1_IPTG_coverage, Svi3_3_2_coverage, Svi3_3_2_IPTG_coverage, WT1_IPTG_coverage, WT2_IPTG_coverage, ORF1_1_rpkm, ORF1_1_IPTG_rpkm, ORF1_2_rpkm, ORF1_2_IPTG_rpkm, Svi3_3_1_rpkm, Svi3_3_1_IPTG_rpkm, Svi3_3_2_rpkm, Svi3_3_2_IPTG_rpkm, WT1_IPTG_rpkm, WT2_IPTG_rpkm, Symbol (gene name), Description, KEGG Orthology, GO Component, GO Function, and GO Process PGCGROWTHCONDITIONS	SRR5121113	MCO000002105	IPTG	Medium supplement	True
data_processing	iptg		<Supp> Supplementary </Supp> _ files _ format _ and _ <Gtype> content : The </Gtype> columns in the processed files are the following in order : <Gtype> GeneID , Length , ORF1 </Gtype> _ 1 _ mapped _ reads ( 7655775 ) , ORF1 _ 1 _ <Supp> IPTG </Supp> _ mapped _ reads ( 7178582 ) , ORF1 _ 2 _ mapped _ reads ( 7706927 ) , ORF1 _ 2 _ <Supp> IPTG </Supp> _ mapped _ reads ( 7070827 ) , Svi3 _ 3 _ 1 _ mapped _ reads ( 8018710 ) , Svi3 _ 3 _ 1 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8299205 ) , Svi3 _ 3 _ 2 _ mapped _ reads ( 7313736 ) , Svi3 _ 3 _ 2 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8344539 ) , WT1 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8074159 ) , WT2 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8103887 ) , ORF1 _ 1 _ coverage , ORF1 _ 1 _ <Supp> IPTG </Supp> _ coverage , ORF1 _ 2 _ coverage , ORF1 _ 2 _ <Supp> IPTG </Supp> _ coverage , Svi3 _ 3 _ 1 _ coverage , Svi3 _ 3 _ 1 _ <Supp> IPTG </Supp> _ coverage , Svi3 _ 3 _ 2 _ coverage , Svi3 _ 3 _ 2 _ <Supp> IPTG </Supp> _ coverage , WT1 _ <Supp> IPTG </Supp> _ coverage , WT2 _ <Supp> IPTG </Supp> _ coverage , ORF1 _ 1 _ rpkm , ORF1 _ 1 _ <Supp> IPTG </Supp> _ rpkm , ORF1 _ 2 _ rpkm , ORF1 _ 2 _ <Supp> IPTG </Supp> _ rpkm , Svi3 _ 3 _ 1 _ rpkm , Svi3 _ 3 _ 1 _ <Supp> IPTG </Supp> _ rpkm , Svi3 _ 3 _ 2 _ rpkm , Svi3 _ 3 _ 2 _ <Supp> IPTG </Supp> _ rpkm , WT1 _ <Supp> IPTG </Supp> _ rpkm , WT2 _ <Supp> IPTG </Supp> _ rpkm , Symbol ( gene name ) , Description , KEGG Orthology , GO Component , GO Function , and GO Process 	GPL18956	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	GSE92601	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GSM2433295	Svi3_3_1	29807996	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Supplementary_files_format_and_content: The columns in the processed files are the following in order:  GeneID, Length, ORF1_1_mapped_reads(7655775), ORF1_1_IPTG_mapped_reads(7178582), ORF1_2_mapped_reads(7706927), ORF1_2_IPTG_mapped_reads(7070827), Svi3_3_1_mapped_reads(8018710), Svi3_3_1_IPTG_mapped_reads(8299205), Svi3_3_2_mapped_reads(7313736), Svi3_3_2_IPTG_mapped_reads(8344539), WT1_IPTG_mapped_reads(8074159), WT2_IPTG_mapped_reads(8103887), ORF1_1_coverage, ORF1_1_IPTG_coverage, ORF1_2_coverage, ORF1_2_IPTG_coverage, Svi3_3_1_coverage, Svi3_3_1_IPTG_coverage, Svi3_3_2_coverage, Svi3_3_2_IPTG_coverage, WT1_IPTG_coverage, WT2_IPTG_coverage, ORF1_1_rpkm, ORF1_1_IPTG_rpkm, ORF1_2_rpkm, ORF1_2_IPTG_rpkm, Svi3_3_1_rpkm, Svi3_3_1_IPTG_rpkm, Svi3_3_2_rpkm, Svi3_3_2_IPTG_rpkm, WT1_IPTG_rpkm, WT2_IPTG_rpkm, Symbol (gene name), Description, KEGG Orthology, GO Component, GO Function, and GO Process PGCGROWTHCONDITIONS	SRR5121114	MCO000002105	IPTG	Medium supplement	True
data_processing	iptg		<Supp> Supplementary </Supp> _ files _ format _ and _ <Gtype> content : The </Gtype> columns in the processed files are the following in order : <Gtype> GeneID , Length , ORF1 </Gtype> _ 1 _ mapped _ reads ( 7655775 ) , ORF1 _ 1 _ <Supp> IPTG </Supp> _ mapped _ reads ( 7178582 ) , ORF1 _ 2 _ mapped _ reads ( 7706927 ) , ORF1 _ 2 _ <Supp> IPTG </Supp> _ mapped _ reads ( 7070827 ) , Svi3 _ 3 _ 1 _ mapped _ reads ( 8018710 ) , Svi3 _ 3 _ 1 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8299205 ) , Svi3 _ 3 _ 2 _ mapped _ reads ( 7313736 ) , Svi3 _ 3 _ 2 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8344539 ) , WT1 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8074159 ) , WT2 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8103887 ) , ORF1 _ 1 _ coverage , ORF1 _ 1 _ <Supp> IPTG </Supp> _ coverage , ORF1 _ 2 _ coverage , ORF1 _ 2 _ <Supp> IPTG </Supp> _ coverage , Svi3 _ 3 _ 1 _ coverage , Svi3 _ 3 _ 1 _ <Supp> IPTG </Supp> _ coverage , Svi3 _ 3 _ 2 _ coverage , Svi3 _ 3 _ 2 _ <Supp> IPTG </Supp> _ coverage , WT1 _ <Supp> IPTG </Supp> _ coverage , WT2 _ <Supp> IPTG </Supp> _ coverage , ORF1 _ 1 _ rpkm , ORF1 _ 1 _ <Supp> IPTG </Supp> _ rpkm , ORF1 _ 2 _ rpkm , ORF1 _ 2 _ <Supp> IPTG </Supp> _ rpkm , Svi3 _ 3 _ 1 _ rpkm , Svi3 _ 3 _ 1 _ <Supp> IPTG </Supp> _ rpkm , Svi3 _ 3 _ 2 _ rpkm , Svi3 _ 3 _ 2 _ <Supp> IPTG </Supp> _ rpkm , WT1 _ <Supp> IPTG </Supp> _ rpkm , WT2 _ <Supp> IPTG </Supp> _ rpkm , Symbol ( gene name ) , Description , KEGG Orthology , GO Component , GO Function , and GO Process 	GPL18956	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	GSE92601	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GSM2433296	Svi3_3_2_IPTG	29807996	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Supplementary_files_format_and_content: The columns in the processed files are the following in order:  GeneID, Length, ORF1_1_mapped_reads(7655775), ORF1_1_IPTG_mapped_reads(7178582), ORF1_2_mapped_reads(7706927), ORF1_2_IPTG_mapped_reads(7070827), Svi3_3_1_mapped_reads(8018710), Svi3_3_1_IPTG_mapped_reads(8299205), Svi3_3_2_mapped_reads(7313736), Svi3_3_2_IPTG_mapped_reads(8344539), WT1_IPTG_mapped_reads(8074159), WT2_IPTG_mapped_reads(8103887), ORF1_1_coverage, ORF1_1_IPTG_coverage, ORF1_2_coverage, ORF1_2_IPTG_coverage, Svi3_3_1_coverage, Svi3_3_1_IPTG_coverage, Svi3_3_2_coverage, Svi3_3_2_IPTG_coverage, WT1_IPTG_coverage, WT2_IPTG_coverage, ORF1_1_rpkm, ORF1_1_IPTG_rpkm, ORF1_2_rpkm, ORF1_2_IPTG_rpkm, Svi3_3_1_rpkm, Svi3_3_1_IPTG_rpkm, Svi3_3_2_rpkm, Svi3_3_2_IPTG_rpkm, WT1_IPTG_rpkm, WT2_IPTG_rpkm, Symbol (gene name), Description, KEGG Orthology, GO Component, GO Function, and GO Process PGCGROWTHCONDITIONS	SRR5121115	MCO000002105	IPTG	Medium supplement	True
data_processing	iptg		<Supp> Supplementary </Supp> _ files _ format _ and _ <Gtype> content : The </Gtype> columns in the processed files are the following in order : <Gtype> GeneID , Length , ORF1 </Gtype> _ 1 _ mapped _ reads ( 7655775 ) , ORF1 _ 1 _ <Supp> IPTG </Supp> _ mapped _ reads ( 7178582 ) , ORF1 _ 2 _ mapped _ reads ( 7706927 ) , ORF1 _ 2 _ <Supp> IPTG </Supp> _ mapped _ reads ( 7070827 ) , Svi3 _ 3 _ 1 _ mapped _ reads ( 8018710 ) , Svi3 _ 3 _ 1 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8299205 ) , Svi3 _ 3 _ 2 _ mapped _ reads ( 7313736 ) , Svi3 _ 3 _ 2 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8344539 ) , WT1 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8074159 ) , WT2 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8103887 ) , ORF1 _ 1 _ coverage , ORF1 _ 1 _ <Supp> IPTG </Supp> _ coverage , ORF1 _ 2 _ coverage , ORF1 _ 2 _ <Supp> IPTG </Supp> _ coverage , Svi3 _ 3 _ 1 _ coverage , Svi3 _ 3 _ 1 _ <Supp> IPTG </Supp> _ coverage , Svi3 _ 3 _ 2 _ coverage , Svi3 _ 3 _ 2 _ <Supp> IPTG </Supp> _ coverage , WT1 _ <Supp> IPTG </Supp> _ coverage , WT2 _ <Supp> IPTG </Supp> _ coverage , ORF1 _ 1 _ rpkm , ORF1 _ 1 _ <Supp> IPTG </Supp> _ rpkm , ORF1 _ 2 _ rpkm , ORF1 _ 2 _ <Supp> IPTG </Supp> _ rpkm , Svi3 _ 3 _ 1 _ rpkm , Svi3 _ 3 _ 1 _ <Supp> IPTG </Supp> _ rpkm , Svi3 _ 3 _ 2 _ rpkm , Svi3 _ 3 _ 2 _ <Supp> IPTG </Supp> _ rpkm , WT1 _ <Supp> IPTG </Supp> _ rpkm , WT2 _ <Supp> IPTG </Supp> _ rpkm , Symbol ( gene name ) , Description , KEGG Orthology , GO Component , GO Function , and GO Process 	GPL18956	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	GSE92601	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GSM2433297	Svi3_3_2	29807996	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Supplementary_files_format_and_content: The columns in the processed files are the following in order:  GeneID, Length, ORF1_1_mapped_reads(7655775), ORF1_1_IPTG_mapped_reads(7178582), ORF1_2_mapped_reads(7706927), ORF1_2_IPTG_mapped_reads(7070827), Svi3_3_1_mapped_reads(8018710), Svi3_3_1_IPTG_mapped_reads(8299205), Svi3_3_2_mapped_reads(7313736), Svi3_3_2_IPTG_mapped_reads(8344539), WT1_IPTG_mapped_reads(8074159), WT2_IPTG_mapped_reads(8103887), ORF1_1_coverage, ORF1_1_IPTG_coverage, ORF1_2_coverage, ORF1_2_IPTG_coverage, Svi3_3_1_coverage, Svi3_3_1_IPTG_coverage, Svi3_3_2_coverage, Svi3_3_2_IPTG_coverage, WT1_IPTG_coverage, WT2_IPTG_coverage, ORF1_1_rpkm, ORF1_1_IPTG_rpkm, ORF1_2_rpkm, ORF1_2_IPTG_rpkm, Svi3_3_1_rpkm, Svi3_3_1_IPTG_rpkm, Svi3_3_2_rpkm, Svi3_3_2_IPTG_rpkm, WT1_IPTG_rpkm, WT2_IPTG_rpkm, Symbol (gene name), Description, KEGG Orthology, GO Component, GO Function, and GO Process PGCGROWTHCONDITIONS	SRR5121116	MCO000002105	IPTG	Medium supplement	True
data_processing	iptg		<Supp> Supplementary </Supp> _ files _ format _ and _ <Gtype> content : The </Gtype> columns in the processed files are the following in order : <Gtype> GeneID , Length , ORF1 </Gtype> _ 1 _ mapped _ reads ( 7655775 ) , ORF1 _ 1 _ <Supp> IPTG </Supp> _ mapped _ reads ( 7178582 ) , ORF1 _ 2 _ mapped _ reads ( 7706927 ) , ORF1 _ 2 _ <Supp> IPTG </Supp> _ mapped _ reads ( 7070827 ) , Svi3 _ 3 _ 1 _ mapped _ reads ( 8018710 ) , Svi3 _ 3 _ 1 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8299205 ) , Svi3 _ 3 _ 2 _ mapped _ reads ( 7313736 ) , Svi3 _ 3 _ 2 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8344539 ) , WT1 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8074159 ) , WT2 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8103887 ) , ORF1 _ 1 _ coverage , ORF1 _ 1 _ <Supp> IPTG </Supp> _ coverage , ORF1 _ 2 _ coverage , ORF1 _ 2 _ <Supp> IPTG </Supp> _ coverage , Svi3 _ 3 _ 1 _ coverage , Svi3 _ 3 _ 1 _ <Supp> IPTG </Supp> _ coverage , Svi3 _ 3 _ 2 _ coverage , Svi3 _ 3 _ 2 _ <Supp> IPTG </Supp> _ coverage , WT1 _ <Supp> IPTG </Supp> _ coverage , WT2 _ <Supp> IPTG </Supp> _ coverage , ORF1 _ 1 _ rpkm , ORF1 _ 1 _ <Supp> IPTG </Supp> _ rpkm , ORF1 _ 2 _ rpkm , ORF1 _ 2 _ <Supp> IPTG </Supp> _ rpkm , Svi3 _ 3 _ 1 _ rpkm , Svi3 _ 3 _ 1 _ <Supp> IPTG </Supp> _ rpkm , Svi3 _ 3 _ 2 _ rpkm , Svi3 _ 3 _ 2 _ <Supp> IPTG </Supp> _ rpkm , WT1 _ <Supp> IPTG </Supp> _ rpkm , WT2 _ <Supp> IPTG </Supp> _ rpkm , Symbol ( gene name ) , Description , KEGG Orthology , GO Component , GO Function , and GO Process 	GPL18956	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	GSE92601	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GSM2433298	WT1_IPTG	29807996	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Supplementary_files_format_and_content: The columns in the processed files are the following in order:  GeneID, Length, ORF1_1_mapped_reads(7655775), ORF1_1_IPTG_mapped_reads(7178582), ORF1_2_mapped_reads(7706927), ORF1_2_IPTG_mapped_reads(7070827), Svi3_3_1_mapped_reads(8018710), Svi3_3_1_IPTG_mapped_reads(8299205), Svi3_3_2_mapped_reads(7313736), Svi3_3_2_IPTG_mapped_reads(8344539), WT1_IPTG_mapped_reads(8074159), WT2_IPTG_mapped_reads(8103887), ORF1_1_coverage, ORF1_1_IPTG_coverage, ORF1_2_coverage, ORF1_2_IPTG_coverage, Svi3_3_1_coverage, Svi3_3_1_IPTG_coverage, Svi3_3_2_coverage, Svi3_3_2_IPTG_coverage, WT1_IPTG_coverage, WT2_IPTG_coverage, ORF1_1_rpkm, ORF1_1_IPTG_rpkm, ORF1_2_rpkm, ORF1_2_IPTG_rpkm, Svi3_3_1_rpkm, Svi3_3_1_IPTG_rpkm, Svi3_3_2_rpkm, Svi3_3_2_IPTG_rpkm, WT1_IPTG_rpkm, WT2_IPTG_rpkm, Symbol (gene name), Description, KEGG Orthology, GO Component, GO Function, and GO Process PGCGROWTHCONDITIONS	SRR5121117	MCO000002105	IPTG	Medium supplement	True
data_processing	iptg		<Supp> Supplementary </Supp> _ files _ format _ and _ <Gtype> content : The </Gtype> columns in the processed files are the following in order : <Gtype> GeneID , Length , ORF1 </Gtype> _ 1 _ mapped _ reads ( 7655775 ) , ORF1 _ 1 _ <Supp> IPTG </Supp> _ mapped _ reads ( 7178582 ) , ORF1 _ 2 _ mapped _ reads ( 7706927 ) , ORF1 _ 2 _ <Supp> IPTG </Supp> _ mapped _ reads ( 7070827 ) , Svi3 _ 3 _ 1 _ mapped _ reads ( 8018710 ) , Svi3 _ 3 _ 1 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8299205 ) , Svi3 _ 3 _ 2 _ mapped _ reads ( 7313736 ) , Svi3 _ 3 _ 2 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8344539 ) , WT1 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8074159 ) , WT2 _ <Supp> IPTG </Supp> _ mapped _ reads ( 8103887 ) , ORF1 _ 1 _ coverage , ORF1 _ 1 _ <Supp> IPTG </Supp> _ coverage , ORF1 _ 2 _ coverage , ORF1 _ 2 _ <Supp> IPTG </Supp> _ coverage , Svi3 _ 3 _ 1 _ coverage , Svi3 _ 3 _ 1 _ <Supp> IPTG </Supp> _ coverage , Svi3 _ 3 _ 2 _ coverage , Svi3 _ 3 _ 2 _ <Supp> IPTG </Supp> _ coverage , WT1 _ <Supp> IPTG </Supp> _ coverage , WT2 _ <Supp> IPTG </Supp> _ coverage , ORF1 _ 1 _ rpkm , ORF1 _ 1 _ <Supp> IPTG </Supp> _ rpkm , ORF1 _ 2 _ rpkm , ORF1 _ 2 _ <Supp> IPTG </Supp> _ rpkm , Svi3 _ 3 _ 1 _ rpkm , Svi3 _ 3 _ 1 _ <Supp> IPTG </Supp> _ rpkm , Svi3 _ 3 _ 2 _ rpkm , Svi3 _ 3 _ 2 _ <Supp> IPTG </Supp> _ rpkm , WT1 _ <Supp> IPTG </Supp> _ rpkm , WT2 _ <Supp> IPTG </Supp> _ rpkm , Symbol ( gene name ) , Description , KEGG Orthology , GO Component , GO Function , and GO Process 	GPL18956	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	GSE92601	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GSM2433299	WT2_IPTG	29807996	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Supplementary_files_format_and_content: The columns in the processed files are the following in order:  GeneID, Length, ORF1_1_mapped_reads(7655775), ORF1_1_IPTG_mapped_reads(7178582), ORF1_2_mapped_reads(7706927), ORF1_2_IPTG_mapped_reads(7070827), Svi3_3_1_mapped_reads(8018710), Svi3_3_1_IPTG_mapped_reads(8299205), Svi3_3_2_mapped_reads(7313736), Svi3_3_2_IPTG_mapped_reads(8344539), WT1_IPTG_mapped_reads(8074159), WT2_IPTG_mapped_reads(8103887), ORF1_1_coverage, ORF1_1_IPTG_coverage, ORF1_2_coverage, ORF1_2_IPTG_coverage, Svi3_3_1_coverage, Svi3_3_1_IPTG_coverage, Svi3_3_2_coverage, Svi3_3_2_IPTG_coverage, WT1_IPTG_coverage, WT2_IPTG_coverage, ORF1_1_rpkm, ORF1_1_IPTG_rpkm, ORF1_2_rpkm, ORF1_2_IPTG_rpkm, Svi3_3_1_rpkm, Svi3_3_1_IPTG_rpkm, Svi3_3_2_rpkm, Svi3_3_2_IPTG_rpkm, WT1_IPTG_rpkm, WT2_IPTG_rpkm, Symbol (gene name), Description, KEGG Orthology, GO Component, GO Function, and GO Process PGCGROWTHCONDITIONS	SRR5121118	MCO000002105	IPTG	Medium supplement	True
characteristics	plasmid PK8263 (4 µM IPTG-induced fnr)		induction : <Supp> induced 50 µM IPTG </Supp> 	GPL18956	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	GSE92601	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GSM2433290	ORF1_1_IPTG	29807996	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	90	58	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	induction: induced 50 µM IPTG PGCGROWTHCONDITIONS	SRR5121109	MCO000003316	induced 50 µM IPTG	Medium supplement	True
characteristics	plasmid PK8263 (4 µM IPTG-induced fnr)		induction : <Supp> induced 50 µM IPTG </Supp> 	GPL18956	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	GSE92601	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GSM2433292	ORF1_2_IPTG	29807996	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	90	58	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	induction: induced 50 µM IPTG PGCGROWTHCONDITIONS	SRR5121111	MCO000003316	induced 50 µM IPTG	Medium supplement	True
characteristics	plasmid PK8263 (4 µM IPTG-induced fnr)		induction : <Supp> induced 50 µM IPTG </Supp> 	GPL18956	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	GSE92601	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GSM2433294	Svi3_3_1_IPTG	29807996	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	90	58	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	induction: induced 50 µM IPTG PGCGROWTHCONDITIONS	SRR5121113	MCO000003316	induced 50 µM IPTG	Medium supplement	True
characteristics	plasmid PK8263 (4 µM IPTG-induced fnr)		induction : <Supp> induced 50 µM IPTG </Supp> 	GPL18956	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	GSE92601	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GSM2433296	Svi3_3_2_IPTG	29807996	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	90	58	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	induction: induced 50 µM IPTG PGCGROWTHCONDITIONS	SRR5121115	MCO000003316	induced 50 µM IPTG	Medium supplement	True
characteristics	plasmid PK8263 (4 µM IPTG-induced fnr)		induction : <Supp> induced 50 µM IPTG </Supp> 	GPL18956	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	GSE92601	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GSM2433298	WT1_IPTG	29807996	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	90	58	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	induction: induced 50 µM IPTG PGCGROWTHCONDITIONS	SRR5121117	MCO000003316	induced 50 µM IPTG	Medium supplement	True
characteristics	plasmid PK8263 (4 µM IPTG-induced fnr)		induction : <Supp> induced 50 µM IPTG </Supp> 	GPL18956	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	GSE92601	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GSM2433299	WT2_IPTG	29807996	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	90	58	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	induction: induced 50 µM IPTG PGCGROWTHCONDITIONS	SRR5121118	MCO000003316	induced 50 µM IPTG	Medium supplement	True
characteristics	30.0 C		time point ( minutes ) : <Supp> 30 </Supp> 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE93125	Transcriptomal changes of Escherichia coli TolC grown with the biofilm inhibitor Carolacton	GSM2445155	Eco_TolC_30min_control_A	28959742	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE93125/GSE93125.soft.gz	100	50	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	time point (minutes): 30 PGCGROWTHCONDITIONS	SRR5143868	MCO000002695	30	Medium supplement	True
characteristics	30.0 C		time point ( minutes ) : <Supp> 30 </Supp> 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE93125	Transcriptomal changes of Escherichia coli TolC grown with the biofilm inhibitor Carolacton	GSM2445157	Eco_TolC_30min_control_B	28959742	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE93125/GSE93125.soft.gz	100	50	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	time point (minutes): 30 PGCGROWTHCONDITIONS	SRR5143869	MCO000002695	30	Medium supplement	True
characteristics	30.0 C		time point ( minutes ) : <Supp> 30 </Supp> 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE93125	Transcriptomal changes of Escherichia coli TolC grown with the biofilm inhibitor Carolacton	GSM2445159	Eco_TolC_30min_Carolacton_A	28959742	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE93125/GSE93125.soft.gz	100	50	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	time point (minutes): 30 PGCGROWTHCONDITIONS	SRR5143870	MCO000002695	30	Medium supplement	True
characteristics	30.0 C		time point ( minutes ) : <Supp> 30 </Supp> 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE93125	Transcriptomal changes of Escherichia coli TolC grown with the biofilm inhibitor Carolacton	GSM2445161	Eco_TolC_30min_Carolacton_B	28959742	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE93125/GSE93125.soft.gz	100	50	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	time point (minutes): 30 PGCGROWTHCONDITIONS	SRR5143871	MCO000002695	30	Medium supplement	True
extract_protocol	rifampicin		Single colonies of P. putida strain DOT-T1E and E. coli MG1655 were grown overnight in Luria -- <Med> Bertani ( LB ) medium </Med> at <Temp> 30 °C </Temp> . Overnight cultures were diluted to a starting OD600 of 0.01 in the same medium and 50 ml aliquots were disposed in separate 250 ml Erlenmeyer flasks and incubated with shaking at 200 rpm . When cultures reached exponential phase ( 0.5 at OD600 ) , antibiotics were added at sub-lethal concentrations to the culture medium to reach a final concentration of 1 µg/ml kanamycin , 300 µg/ml ampicillin , 150 µg/ml chloramphenicol , 4 µg/ml tetracycline , 0.5 µg/ml ciprofloxacin , 300 µg/ml spectinomycin , 500 µg/ml <Supp> rifampicin and </Supp> 2 µg/ml gentamicin . Then cultures were incubated under the same conditions for one hour more . Cells were harvested by centrifugation at 8000 g for 10 min and suspended immediately in stop solution ( 95 % ( v/v ) ethanol , 5 % ( v/v ) phenol ) and pelleted by centrifugation . After that , total RNA was extracted with Trizol ( Invitrogen ) . Removal of DNA was carried out by treatment with DNase I ( Fermentas ) in combination with the RNase inhibitor RiboLock ( Fermentas ) . The integrity and quality of total RNA was assessed with an Agilent 2100 Bioanalyzer ( Agilent Technologies ) . 	GPL14548-GPL19659-GPL23101	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL19659: Illumina HiSeq 2000 (Pseudomonas putida). GPL23101: Illumina HiSeq 2000 (Escherichia coli; Pseudomonas putida)	GSE95310	Cross-talk between species that do not share often the same environment	GSM2501621	MG1655_LB1		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95310/GSE95310.soft.gz	100	83	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Single colonies of P. putida strain DOT-T1E and E. coli MG1655 were grown overnight in Luria–Bertani (LB) medium at 30°C. Overnight cultures were diluted to a starting OD600 of 0.01 in the same medium and 50 ml aliquots were disposed in separate 250 ml Erlenmeyer flasks and incubated with shaking at 200 rpm. When cultures reached exponential phase (0.5 at OD600), antibiotics were added at sub-lethal concentrations to the culture medium to reach a final concentration of 1 µg/ml kanamycin, 300 µg/ml ampicillin, 150 µg/ml chloramphenicol, 4 µg/ml tetracycline, 0.5 µg/ml ciprofloxacin, 300 µg/ml spectinomycin, 500 µg/ml rifampicin and 2 µg/ml gentamicin. Then cultures were incubated under the same conditions for one hour more. Cells were harvested by centrifugation at 8000 g for 10 min and suspended immediately in stop solution (95% (v/v) ethanol, 5% (v/v) phenol) and pelleted by centrifugation. After that, total RNA was extracted with Trizol (Invitrogen). Removal of DNA was carried out by treatment with DNase I (Fermentas) in combination with the RNase inhibitor RiboLock (Fermentas). The integrity and quality of total RNA was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies). PGCGROWTHCONDITIONS	SRR5282168	MCO000000828	rifampicin and	Medium supplement	True
extract_protocol	rifampicin		Single colonies of P. putida strain DOT-T1E and E. coli MG1655 were grown overnight in Luria -- <Med> Bertani ( LB ) medium </Med> at <Temp> 30 °C </Temp> . Overnight cultures were diluted to a starting OD600 of 0.01 in the same medium and 50 ml aliquots were disposed in separate 250 ml Erlenmeyer flasks and incubated with shaking at 200 rpm . When cultures reached exponential phase ( 0.5 at OD600 ) , antibiotics were added at sub-lethal concentrations to the culture medium to reach a final concentration of 1 µg/ml kanamycin , 300 µg/ml ampicillin , 150 µg/ml chloramphenicol , 4 µg/ml tetracycline , 0.5 µg/ml ciprofloxacin , 300 µg/ml spectinomycin , 500 µg/ml <Supp> rifampicin and </Supp> 2 µg/ml gentamicin . Then cultures were incubated under the same conditions for one hour more . Cells were harvested by centrifugation at 8000 g for 10 min and suspended immediately in stop solution ( 95 % ( v/v ) ethanol , 5 % ( v/v ) phenol ) and pelleted by centrifugation . After that , total RNA was extracted with Trizol ( Invitrogen ) . Removal of DNA was carried out by treatment with DNase I ( Fermentas ) in combination with the RNase inhibitor RiboLock ( Fermentas ) . The integrity and quality of total RNA was assessed with an Agilent 2100 Bioanalyzer ( Agilent Technologies ) . 	GPL14548-GPL19659-GPL23101	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL19659: Illumina HiSeq 2000 (Pseudomonas putida). GPL23101: Illumina HiSeq 2000 (Escherichia coli; Pseudomonas putida)	GSE95310	Cross-talk between species that do not share often the same environment	GSM2501622	MG1655_LB2		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95310/GSE95310.soft.gz	100	83	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Single colonies of P. putida strain DOT-T1E and E. coli MG1655 were grown overnight in Luria–Bertani (LB) medium at 30°C. Overnight cultures were diluted to a starting OD600 of 0.01 in the same medium and 50 ml aliquots were disposed in separate 250 ml Erlenmeyer flasks and incubated with shaking at 200 rpm. When cultures reached exponential phase (0.5 at OD600), antibiotics were added at sub-lethal concentrations to the culture medium to reach a final concentration of 1 µg/ml kanamycin, 300 µg/ml ampicillin, 150 µg/ml chloramphenicol, 4 µg/ml tetracycline, 0.5 µg/ml ciprofloxacin, 300 µg/ml spectinomycin, 500 µg/ml rifampicin and 2 µg/ml gentamicin. Then cultures were incubated under the same conditions for one hour more. Cells were harvested by centrifugation at 8000 g for 10 min and suspended immediately in stop solution (95% (v/v) ethanol, 5% (v/v) phenol) and pelleted by centrifugation. After that, total RNA was extracted with Trizol (Invitrogen). Removal of DNA was carried out by treatment with DNase I (Fermentas) in combination with the RNase inhibitor RiboLock (Fermentas). The integrity and quality of total RNA was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies). PGCGROWTHCONDITIONS	SRR5282169	MCO000000828	rifampicin and	Medium supplement	True
growth_protocol	MOPS minimal medium		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516609	1A_MG_t0	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304286	MCO000002528	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	True
growth_protocol	MOPS minimal medium		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516610	2A_MG_t10	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304287	MCO000002528	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	True
growth_protocol	MOPS minimal medium		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516611	3A_MG_t30	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304288	MCO000002528	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	True
growth_protocol	MOPS minimal medium		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516612	4A_MG_t60	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304289	MCO000002528	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	True
growth_protocol	MOPS minimal medium		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516613	5A_MG+Hg_t10	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304290	MCO000002528	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	True
growth_protocol	MOPS minimal medium		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516614	6A_MG+Hg_t30	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304291	MCO000002528	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	True
growth_protocol	MOPS minimal medium		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516615	7A_MG+Hg_t60	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304292	MCO000002528	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	True
growth_protocol	MOPS minimal medium		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516616	8A_MG+PMA_t10	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304293	MCO000002528	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	True
growth_protocol	MOPS minimal medium		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516617	9A_MG+PMA_t30	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304294	MCO000002528	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	True
growth_protocol	MOPS minimal medium		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516618	10A_MG+PMA_t60	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304295	MCO000002528	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	True
growth_protocol	MOPS minimal medium		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516619	1B_MG_t0	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304296	MCO000002528	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	True
growth_protocol	MOPS minimal medium		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516620	2B_MG_t10	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304297	MCO000002528	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	True
growth_protocol	MOPS minimal medium		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516621	3B_MG_t30	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304298	MCO000002528	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	True
growth_protocol	MOPS minimal medium		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516622	4B_MG_t60	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304299	MCO000002528	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	True
growth_protocol	MOPS minimal medium		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516623	5B_MG+Hg_t10	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304300	MCO000002528	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	True
growth_protocol	MOPS minimal medium		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516624	6B_MG+Hg_t30	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304301	MCO000002528	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	True
growth_protocol	MOPS minimal medium		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516625	7B_MG+Hg_t60	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304302	MCO000002528	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	True
growth_protocol	MOPS minimal medium		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516626	8B_MG+PMA_t10	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304303	MCO000002528	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	True
growth_protocol	MOPS minimal medium		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516627	9B_MG+PMA_t30	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304304	MCO000002528	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	True
growth_protocol	MOPS minimal medium		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516628	10B_MG+PMA_t60	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304305	MCO000002528	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	True
growth_protocol	MOPS minimal medium		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516629	1C_MG_t0	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304306	MCO000002528	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	True
growth_protocol	MOPS minimal medium		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516630	2C_MG_t10	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304307	MCO000002528	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	True
growth_protocol	MOPS minimal medium		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516631	3C_MG_t30	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304308	MCO000002528	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	True
growth_protocol	MOPS minimal medium		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516632	4C_MG_t60	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304309	MCO000002528	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	True
growth_protocol	MOPS minimal medium		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516633	5C_MG+Hg_t10	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304310	MCO000002528	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	True
growth_protocol	MOPS minimal medium		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516634	6C_MG+Hg_t30	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304311	MCO000002528	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	True
growth_protocol	MOPS minimal medium		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516635	7C_MG+Hg_t60	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304312	MCO000002528	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	True
growth_protocol	MOPS minimal medium		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516636	8C_MG+PMA_t10	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304313	MCO000002528	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	True
growth_protocol	MOPS minimal medium		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516637	9C_MG+PMA_t30	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304314	MCO000002528	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	True
growth_protocol	MOPS minimal medium		For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani ( LB ) agar overnight at <Temp> 37 °C </Temp> . A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in <Med> Neidhardt MOPS Minimal Medium ( NM3 ) </Med> ( Neidhardt et al. , 1974 , J Bacteriol ) ( 0.2 % final glucose concentration ) supplemented with <Supp> 20 mg/L uracil </Supp> and 500 µg/L thiamine , which was incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> overnight ( ~ 18 hr ) . The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each , which were incubated at <Temp> 37 °C </Temp> with shaking at <Agit> 250 rpm </Agit> . 	GPL15010	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	GSE95575	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GSM2516638	10C_MG+PMA_t60	29338696	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For each biological RNA-Seq replicate E coli K-12 MG1655 was subcultured from cyrostorage on Luria-Bertani (LB) agar overnight at 37°C. A half-dozen well-isolated colonies were used to inoculate a 20 ml starter culture in Neidhardt MOPS Minimal Medium (NM3) (Neidhardt et al., 1974, J Bacteriol) (0.2% final glucose concentration) supplemented with 20 mg/L uracil and 500 µg/L thiamine, which was incubated at 37°C with shaking at 250 rpm overnight (~18 hr). The overnight starter culture was diluted 1:30 to initiate the experimental culture and divided into three 500 ml flasks with 100 ml NM3 in each, which were incubated at 37°C with shaking at 250 rpm. PGCGROWTHCONDITIONS	SRR5304315	MCO000002528	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	True
growth_protocol	glucose 120 mM		Cells were grown in TB7 supplemented with <Supp> 22 mM glucose </Supp> until OD600 ~ 1.8 . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE97406	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GSM2563999	AR1-/AR2- rep 2		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8. PGCGROWTHCONDITIONS	SRR5416991	MCO000002775	22 mM glucose	Medium supplement	True
characteristics	glucose 120 mM		media : <Gtype> Tryptone </Gtype> broth buffered to pH 7 supplemented with <Supp> 22 mM glucose </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE97406	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GSM2563999	AR1-/AR2- rep 2		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose PGCGROWTHCONDITIONS	SRR5416991	MCO000002775	22 mM glucose	Medium supplement	True
growth_protocol	glucose 120 mM		Cells were grown in TB7 supplemented with <Supp> 22 mM glucose </Supp> until OD600 ~ 1.8 . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE97406	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GSM2564000	AR1-/AR2- rep 3		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8. PGCGROWTHCONDITIONS	SRR5416992	MCO000002775	22 mM glucose	Medium supplement	True
characteristics	glucose 120 mM		media : <Gtype> Tryptone </Gtype> broth buffered to pH 7 supplemented with <Supp> 22 mM glucose </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE97406	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GSM2564000	AR1-/AR2- rep 3		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose PGCGROWTHCONDITIONS	SRR5416992	MCO000002775	22 mM glucose	Medium supplement	True
growth_protocol	glucose 120 mM		Cells were grown in TB7 supplemented with <Supp> 22 mM glucose </Supp> until OD600 ~ 1.8 . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE97406	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GSM2564001	WT rep 1		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8. PGCGROWTHCONDITIONS	SRR5416993	MCO000002775	22 mM glucose	Medium supplement	True
characteristics	glucose 120 mM		media : <Gtype> Tryptone </Gtype> broth buffered to pH 7 supplemented with <Supp> 22 mM glucose </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE97406	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GSM2564001	WT rep 1		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose PGCGROWTHCONDITIONS	SRR5416993	MCO000002775	22 mM glucose	Medium supplement	True
growth_protocol	glucose 120 mM		Cells were grown in TB7 supplemented with <Supp> 22 mM glucose </Supp> until OD600 ~ 1.8 . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE97406	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GSM2564002	WT rep 2		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8. PGCGROWTHCONDITIONS	SRR5416994	MCO000002775	22 mM glucose	Medium supplement	True
characteristics	glucose 120 mM		media : <Gtype> Tryptone </Gtype> broth buffered to pH 7 supplemented with <Supp> 22 mM glucose </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE97406	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GSM2564002	WT rep 2		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose PGCGROWTHCONDITIONS	SRR5416994	MCO000002775	22 mM glucose	Medium supplement	True
growth_protocol	glucose 120 mM		Cells were grown in TB7 supplemented with <Supp> 22 mM glucose </Supp> until OD600 ~ 1.8 . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE97406	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GSM2564003	WT rep 3		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8. PGCGROWTHCONDITIONS	SRR5416995	MCO000002775	22 mM glucose	Medium supplement	True
characteristics	glucose 120 mM		media : <Gtype> Tryptone </Gtype> broth buffered to pH 7 supplemented with <Supp> 22 mM glucose </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE97406	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GSM2564003	WT rep 3		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose PGCGROWTHCONDITIONS	SRR5416995	MCO000002775	22 mM glucose	Medium supplement	True
growth_protocol	glucose 120 mM		Cells were grown in TB7 supplemented with <Supp> 22 mM glucose </Supp> until OD600 ~ 1.8 . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE97406	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GSM2564004	K100Q rep 1		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8. PGCGROWTHCONDITIONS	SRR5416996	MCO000002775	22 mM glucose	Medium supplement	True
characteristics	glucose 120 mM		media : <Gtype> Tryptone </Gtype> broth buffered to pH 7 supplemented with <Supp> 22 mM glucose </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE97406	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GSM2564004	K100Q rep 1		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose PGCGROWTHCONDITIONS	SRR5416996	MCO000002775	22 mM glucose	Medium supplement	True
growth_protocol	glucose 120 mM		Cells were grown in TB7 supplemented with <Supp> 22 mM glucose </Supp> until OD600 ~ 1.8 . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE97406	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GSM2564005	K100Q rep 2		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8. PGCGROWTHCONDITIONS	SRR5416997	MCO000002775	22 mM glucose	Medium supplement	True
characteristics	glucose 120 mM		media : <Gtype> Tryptone </Gtype> broth buffered to pH 7 supplemented with <Supp> 22 mM glucose </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE97406	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GSM2564005	K100Q rep 2		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose PGCGROWTHCONDITIONS	SRR5416997	MCO000002775	22 mM glucose	Medium supplement	True
growth_protocol	glucose 120 mM		Cells were grown in TB7 supplemented with <Supp> 22 mM glucose </Supp> until OD600 ~ 1.8 . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE97406	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GSM2564006	K100Q rep 3		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8. PGCGROWTHCONDITIONS	SRR5416998	MCO000002775	22 mM glucose	Medium supplement	True
characteristics	glucose 120 mM		media : <Gtype> Tryptone </Gtype> broth buffered to pH 7 supplemented with <Supp> 22 mM glucose </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE97406	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GSM2564006	K100Q rep 3		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose PGCGROWTHCONDITIONS	SRR5416998	MCO000002775	22 mM glucose	Medium supplement	True
growth_protocol	glucose 120 mM		Cells were grown in TB7 supplemented with <Supp> 22 mM glucose </Supp> until OD600 ~ 1.8 . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE97406	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GSM2564007	K100R rep 1		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8. PGCGROWTHCONDITIONS	SRR5416999	MCO000002775	22 mM glucose	Medium supplement	True
characteristics	glucose 120 mM		media : <Gtype> Tryptone </Gtype> broth buffered to pH 7 supplemented with <Supp> 22 mM glucose </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE97406	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GSM2564007	K100R rep 1		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose PGCGROWTHCONDITIONS	SRR5416999	MCO000002775	22 mM glucose	Medium supplement	True
growth_protocol	glucose 120 mM		Cells were grown in TB7 supplemented with <Supp> 22 mM glucose </Supp> until OD600 ~ 1.8 . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE97406	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GSM2564008	K100R rep 2		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8. PGCGROWTHCONDITIONS	SRR5417000	MCO000002775	22 mM glucose	Medium supplement	True
characteristics	glucose 120 mM		media : <Gtype> Tryptone </Gtype> broth buffered to pH 7 supplemented with <Supp> 22 mM glucose </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE97406	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GSM2564008	K100R rep 2		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose PGCGROWTHCONDITIONS	SRR5417000	MCO000002775	22 mM glucose	Medium supplement	True
growth_protocol	glucose 120 mM		Cells were grown in TB7 supplemented with <Supp> 22 mM glucose </Supp> until OD600 ~ 1.8 . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE97406	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GSM2564009	K100R rep 3		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8. PGCGROWTHCONDITIONS	SRR5417001	MCO000002775	22 mM glucose	Medium supplement	True
characteristics	glucose 120 mM		media : <Gtype> Tryptone </Gtype> broth buffered to pH 7 supplemented with <Supp> 22 mM glucose </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE97406	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GSM2564009	K100R rep 3		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose PGCGROWTHCONDITIONS	SRR5417001	MCO000002775	22 mM glucose	Medium supplement	True
characteristics	MCO		genotype/variation : <Gtype> wild type </Gtype> 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770989	Ribosome profiling at 37°C in WT cells_1	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type PGCGROWTHCONDITIONS	SRR6001737	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype/variation : <Gtype> wild type </Gtype> 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770991	Ribosome profiling 30 min after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type PGCGROWTHCONDITIONS	SRR6001739	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype/variation : <Gtype> wild type </Gtype> 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770994	Ribosome profiling 4 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type PGCGROWTHCONDITIONS	SRR6001742	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype/variation : <Gtype> wild type </Gtype> 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770995	Ribosome profiling 6 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type PGCGROWTHCONDITIONS	SRR6001743	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype/variation : <Gtype> wild type </Gtype> 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770996	Ribosome profiling 5 min after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type PGCGROWTHCONDITIONS	SRR6001744	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype/variation : <Gtype> wild type </Gtype> 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770997	Ribosome profiling 10 min after shift to 10°C in WT cells_2	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type PGCGROWTHCONDITIONS	SRR6001745	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype/variation : <Gtype> wild type </Gtype> 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770998	Ribosome profiling 15 min after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type PGCGROWTHCONDITIONS	SRR6001746	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype/variation : <Gtype> wild type </Gtype> 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2770999	Ribosome profiling 8 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type PGCGROWTHCONDITIONS	SRR6001747SRR6001748	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype/variation : <Gtype> wild type </Gtype> 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771001	Ribosome profiling at 37°C in WT cells_2	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type PGCGROWTHCONDITIONS	SRR6001751	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype/variation : <Gtype> wild type </Gtype> 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771008	mRNA-seq 4 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type PGCGROWTHCONDITIONS	SRR6001758	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype/variation : <Gtype> wild type </Gtype> 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771010	mRNA-seq 8 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type PGCGROWTHCONDITIONS	SRR6001760SRR6001761	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype/variation : <Gtype> wild type </Gtype> 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771014	DMS-seq 30 min after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type PGCGROWTHCONDITIONS	SRR6001766	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype/variation : <Gtype> wild type </Gtype> 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771015	DMS-seq 6 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type PGCGROWTHCONDITIONS	SRR6001769	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype/variation : <Gtype> wild type </Gtype> 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771016	DMS-seq 8 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type PGCGROWTHCONDITIONS	SRR6001772	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype/variation : <Gtype> wild type </Gtype> 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771019	Total RNA-seq 20 min after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type PGCGROWTHCONDITIONS	SRR6001775	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype/variation : <Gtype> wild type </Gtype> 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771020	Total RNA-seq 4 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type PGCGROWTHCONDITIONS	SRR6001776	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype/variation : <Gtype> wild type </Gtype> 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771021	Total RNA-seq 8 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type PGCGROWTHCONDITIONS	SRR6001777	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype/variation : <Gtype> wild type </Gtype> 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771025	Total RNA-seq before rifampicin treatment -- 2 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type PGCGROWTHCONDITIONS	SRR6001781	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype/variation : <Gtype> wild type </Gtype> 	GPL10328-GPL14548-GPL15010-GPL17439	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE103421	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	GSM2771026	Total RNA-seq after rifampicin treatment -- 4 hr after shift to 10°C in WT cells	29628307	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type PGCGROWTHCONDITIONS	SRR6001782	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype : <Gtype> wild type </Gtype> 	GPL24020	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	GSE103937	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GSM2786596	WT glucose_replicate1	29474582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype: wild type PGCGROWTHCONDITIONS	SRR6048166	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype : <Gtype> wild type </Gtype> 	GPL24020	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	GSE103937	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GSM2786597	WT glucose_replicate2	29474582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype: wild type PGCGROWTHCONDITIONS	SRR6048167	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype : <Gtype> wild type </Gtype> 	GPL24020	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	GSE103937	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GSM2786598	WT glucose_replicate3	29474582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype: wild type PGCGROWTHCONDITIONS	SRR6048168	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype : <Gtype> wild type </Gtype> 	GPL24020	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	GSE103937	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GSM2786599	WT_glycerol_replicate1	29474582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype: wild type PGCGROWTHCONDITIONS	SRR6048169	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype : <Gtype> wild type </Gtype> 	GPL24020	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	GSE103937	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GSM2786600	WT_glycerol_replicate2	29474582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype: wild type PGCGROWTHCONDITIONS	SRR6048170	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype : <Gtype> wild type </Gtype> 	GPL24020	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	GSE103937	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GSM2786601	WT_glycerol_replicate3	29474582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype: wild type PGCGROWTHCONDITIONS	SRR6048171	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype : <Gtype> wild type </Gtype> 	GPL24020	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	GSE103937	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GSM2786602	WT UvsW_replicate1	29474582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype: wild type PGCGROWTHCONDITIONS	SRR6048172	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype : <Gtype> wild type </Gtype> 	GPL24020	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	GSE103937	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GSM2786603	WT UvsW_replicate2	29474582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype: wild type PGCGROWTHCONDITIONS	SRR6048173	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype : <Gtype> wild type </Gtype> 	GPL24020	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	GSE103937	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GSM2786604	WT UvsW_replicate3	29474582	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype: wild type PGCGROWTHCONDITIONS	SRR6048174	MCO000002470	wild type	Genetic background	True
growth_protocol	MCO		<Med> LB medium </Med> at 37ºC with 200rpm agitation . 	GPL24145	GPL24145: Illumina NextSeq 500 (Escherichia coli 042)	GSE105133	Transcriptomic study of single mutants hns, hns2 and double mutans hhahha2 and hnshns2 from enteroaggregative E. coli 042 by RNA-seq	GSM2822965	E. coli 042 WT	2957708531014240	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE105133/GSE105133.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	LB medium at 37ºC with 200rpm agitation. PGCGROWTHCONDITIONS	SRR6188476	MCO000002533	LB medium	Medium	True
characteristics	MCO		genotype : <Gtype> wild type </Gtype> 	GPL24145	GPL24145: Illumina NextSeq 500 (Escherichia coli 042)	GSE105133	Transcriptomic study of single mutants hns, hns2 and double mutans hhahha2 and hnshns2 from enteroaggregative E. coli 042 by RNA-seq	GSM2822965	E. coli 042 WT	2957708531014240	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE105133/GSE105133.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype: wild type PGCGROWTHCONDITIONS	SRR6188476	MCO000002470	wild type	Genetic background	True
growth_protocol	MCO		<Med> LB medium </Med> at 37ºC with 200rpm agitation . 	GPL24145	GPL24145: Illumina NextSeq 500 (Escherichia coli 042)	GSE105133	Transcriptomic study of single mutants hns, hns2 and double mutans hhahha2 and hnshns2 from enteroaggregative E. coli 042 by RNA-seq	GSM2822966	E. coli hhahha2	2957708531014240	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE105133/GSE105133.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	LB medium at 37ºC with 200rpm agitation. PGCGROWTHCONDITIONS	SRR6188477	MCO000002533	LB medium	Medium	True
growth_protocol	MCO		<Med> LB medium </Med> at 37ºC with 200rpm agitation . 	GPL24145	GPL24145: Illumina NextSeq 500 (Escherichia coli 042)	GSE105133	Transcriptomic study of single mutants hns, hns2 and double mutans hhahha2 and hnshns2 from enteroaggregative E. coli 042 by RNA-seq	GSM2822967	E. coli hns	2957708531014240	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE105133/GSE105133.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	LB medium at 37ºC with 200rpm agitation. PGCGROWTHCONDITIONS	SRR6188478	MCO000002533	LB medium	Medium	True
growth_protocol	MCO		<Med> LB medium </Med> at 37ºC with 200rpm agitation . 	GPL24145	GPL24145: Illumina NextSeq 500 (Escherichia coli 042)	GSE105133	Transcriptomic study of single mutants hns, hns2 and double mutans hhahha2 and hnshns2 from enteroaggregative E. coli 042 by RNA-seq	GSM2822968	E. coli hns2	2957708531014240	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE105133/GSE105133.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	LB medium at 37ºC with 200rpm agitation. PGCGROWTHCONDITIONS	SRR6188479	MCO000002533	LB medium	Medium	True
growth_protocol	MCO		<Med> LB medium </Med> at 37ºC with 200rpm agitation . 	GPL24145	GPL24145: Illumina NextSeq 500 (Escherichia coli 042)	GSE105133	Transcriptomic study of single mutants hns, hns2 and double mutans hhahha2 and hnshns2 from enteroaggregative E. coli 042 by RNA-seq	GSM2822969	E. coli hnshns2	2957708531014240	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE105133/GSE105133.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	LB medium at 37ºC with 200rpm agitation. PGCGROWTHCONDITIONS	SRR6188480	MCO000002533	LB medium	Medium	True
characteristics	MCO		genotype : <Gtype> wild type </Gtype> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE111094	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GSM3022135	WT rep1	33149261	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype: wild type PGCGROWTHCONDITIONS	SRR6781997	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype : <Gtype> wild type </Gtype> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE111094	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GSM3022136	WT rep2	33149261	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype: wild type PGCGROWTHCONDITIONS	SRR6781998	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype : <Gtype> wild type </Gtype> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE111094	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GSM3108934	WT-low-ph rep1	33149261	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype: wild type PGCGROWTHCONDITIONS	SRR7057985	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype : <Gtype> wild type </Gtype> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE111094	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GSM3108935	WT-low-ph rep2	33149261	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype: wild type PGCGROWTHCONDITIONS	SRR7057986	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype : <Gtype> wild type </Gtype> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE111094	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GSM3108936	WT-high-ph rep1	33149261	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype: wild type PGCGROWTHCONDITIONS	SRR7057987	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype : <Gtype> wild type </Gtype> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE111094	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GSM3108937	WT-high-ph rep2	33149261	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype: wild type PGCGROWTHCONDITIONS	SRR7057988	MCO000002470	wild type	Genetic background	True
characteristics	MCO		strain : <Gtype> wild type </Gtype> 	GPL16085-GPL21222	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE117737	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GSM3566393	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 4	31308523	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	strain: wild type PGCGROWTHCONDITIONS	SRR8449235	MCO000002470	wild type	Genetic background	True
characteristics	MCO		strain : <Gtype> wild type </Gtype> 	GPL16085-GPL21222	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE117737	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GSM3566394	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 5	31308523	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	strain: wild type PGCGROWTHCONDITIONS	SRR8449236	MCO000002470	wild type	Genetic background	True
characteristics	MCO		strain : <Gtype> wild type </Gtype> 	GPL16085-GPL21222	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE117737	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GSM3566395	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 6	31308523	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	strain: wild type PGCGROWTHCONDITIONS	SRR8449237	MCO000002470	wild type	Genetic background	True
characteristics	MCO		strain : <Gtype> wild type </Gtype> 	GPL16085-GPL21222	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE117737	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GSM3566396	RNA-seq WT log phase related to total SEnd-seq WT stationary phase rep4	31308523	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	strain: wild type PGCGROWTHCONDITIONS	SRR8449238	MCO000002470	wild type	Genetic background	True
characteristics	MCO		media : <Air> anaerobic </Air> <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463579	no3_anaero__1	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: anaerobic M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	SRR8173241	MCO000011680	anaerobic	Aeration	True
characteristics	MCO		media : <Air> anaerobic </Air> <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	GPL21433	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	GSE122295	Expression profiling to identify independent regulatory signals in Escherichia coli	GSM3463580	no3_anaero__2	31797920	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: anaerobic M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	SRR8173242	MCO000011680	anaerobic	Aeration	True
growth_protocol	MCO		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275442	WT_LB_R1	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907640	MCO000002526	M9 minimal medium	Medium	True
growth_protocol	MCO		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275443	WT_LB_R2	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907641	MCO000002526	M9 minimal medium	Medium	True
growth_protocol	MCO		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275444	WT_EtOH_R1	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907642	MCO000002526	M9 minimal medium	Medium	True
growth_protocol	MCO		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275446	BaeR_KO_LB_R1	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907644	MCO000002526	M9 minimal medium	Medium	True
growth_protocol	MCO		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275447	BaeR_KO_ LB_R2	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907645	MCO000002526	M9 minimal medium	Medium	True
growth_protocol	MCO		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275448	BaeR_KO_EtOH_R1	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907646	MCO000002526	M9 minimal medium	Medium	True
growth_protocol	MCO		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275450	CpxR_KO_LB_R1	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907648	MCO000002526	M9 minimal medium	Medium	True
growth_protocol	MCO		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275451	CpxR_KO_LB_R2	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907649	MCO000002526	M9 minimal medium	Medium	True
growth_protocol	MCO		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275454	KdpE_KO_01-KCl_R1	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907652	MCO000002526	M9 minimal medium	Medium	True
growth_protocol	MCO		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275455	KdpE_KO_01-KCl_R2	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907653	MCO000002526	M9 minimal medium	Medium	True
growth_protocol	MCO		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275456	KdpE_KO_115-KCl_R1	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907654	MCO000002526	M9 minimal medium	Medium	True
growth_protocol	MCO		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275457	KdpE_KO_115-KCl_R2	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907655	MCO000002526	M9 minimal medium	Medium	True
growth_protocol	MCO		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275458	WT_01-KCl_R1	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907656	MCO000002526	M9 minimal medium	Medium	True
growth_protocol	MCO		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275459	WT_01-KCl_R2	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907657	MCO000002526	M9 minimal medium	Medium	True
growth_protocol	MCO		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275460	WT_115-KCl_R1	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907658	MCO000002526	M9 minimal medium	Medium	True
growth_protocol	MCO		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275461	WT_115-KCl_R2	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907659	MCO000002526	M9 minimal medium	Medium	True
growth_protocol	MCO		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275462	PhoB_KO_M9_R1	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907660	MCO000002526	M9 minimal medium	Medium	True
characteristics	MCO		media : <Med> M9 minimal medium </Med> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275462	PhoB_KO_M9_R1	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal medium PGCGROWTHCONDITIONS	SRR10907660	MCO000002526	M9 minimal medium	Medium	True
growth_protocol	MCO		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275463	PhoB_KO_M9_R2	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907661	MCO000002526	M9 minimal medium	Medium	True
characteristics	MCO		media : <Med> M9 minimal medium </Med> 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275463	PhoB_KO_M9_R2	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal medium PGCGROWTHCONDITIONS	SRR10907661	MCO000002526	M9 minimal medium	Medium	True
growth_protocol	MCO		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275464	PhoB_KO_M9-P_R1	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907662	MCO000002526	M9 minimal medium	Medium	True
characteristics	MCO		media : <Med> M9 minimal medium </Med> without phosphate 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275464	PhoB_KO_M9-P_R1	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal medium without phosphate PGCGROWTHCONDITIONS	SRR10907662	MCO000002526	M9 minimal medium	Medium	True
growth_protocol	MCO		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275465	PhoB_KO_M9-P_R2	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907663	MCO000002526	M9 minimal medium	Medium	True
characteristics	MCO		media : <Med> M9 minimal medium </Med> without phosphate 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275465	PhoB_KO_M9-P_R2	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal medium without phosphate PGCGROWTHCONDITIONS	SRR10907663	MCO000002526	M9 minimal medium	Medium	True
growth_protocol	MCO		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275466	WT_M9-P_R1	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907664	MCO000002526	M9 minimal medium	Medium	True
characteristics	MCO		media : <Med> M9 minimal medium </Med> without phosphate 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275466	WT_M9-P_R1	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal medium without phosphate PGCGROWTHCONDITIONS	SRR10907664	MCO000002526	M9 minimal medium	Medium	True
growth_protocol	MCO		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275467	WT_M9-P_R2	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907665	MCO000002526	M9 minimal medium	Medium	True
characteristics	MCO		media : <Med> M9 minimal medium </Med> without phosphate 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275467	WT_M9-P_R2	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	media: M9 minimal medium without phosphate PGCGROWTHCONDITIONS	SRR10907665	MCO000002526	M9 minimal medium	Medium	True
growth_protocol	MCO		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275469	ZraR_KO_LB_R2	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907667	MCO000002526	M9 minimal medium	Medium	True
growth_protocol	MCO		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275470	ZraR_KO_ZnCl2_R1	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907668	MCO000002526	M9 minimal medium	Medium	True
growth_protocol	MCO		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275471	ZraR_KO_ZnCl2_R2	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907669	MCO000002526	M9 minimal medium	Medium	True
growth_protocol	MCO		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275472	WT_ZnCl2_R1	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907670	MCO000002526	M9 minimal medium	Medium	True
growth_protocol	MCO		For ethanol sensors ( BaeR and CpxR ) : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium to an OD600 = 0.5 , then ethanol was added to a final concentration of 5 % . Cells were grown for <Supp> 30 min </Supp> in the presence of ethanol before being collected for <Technique> ChIP-exo </Technique> and RNA-seq . For KdpDE : Cells were grown at <Temp> 37 °C </Temp> overnight in liquid Tris maleic <Med> acid minimal medium </Med> ( TMA ) supplemented with 115 mM KCl and 0.4 % w/v Glucose , then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose . Cells were inoculated in TMA with <Supp> 0.1 mM KCl </Supp> and 0.4 % w/v Glucose and collected at an OD600 = 0.5 for <Technique> ChIP-exo </Technique> and RNA-seq analysis . For PhoRB : cells were grown in liquid <Med> M9 minimal medium </Med> until OD600 = 0.5 . Then cells were washed three times with M9 minimal medium without phosphate ( M9-P ; without Na2HPO4 and KH2PO4 ) and incubated in M9-P for 60 min ( about the doubling time of MG1655 in <Med> M9 minimal medium </Med> ) at <Temp> 37 °C </Temp> . For ZraSR : Cells were grown at <Temp> 37 °C </Temp> in liquid LB medium containing 1 mM ZnCl2 . 	GPL24659	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	GSE143855	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GSM4275473	WT_ZnCl2_R2	33172971	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	For ethanol sensors (BaeR and CpxR): Cells were grown at 37 °C in liquid LB medium to an OD600=0.5, then ethanol was added to a final concentration of 5%. Cells were grown for 30 min in the presence of ethanol before being collected for ChIP-exo and RNA-seq. For KdpDE: Cells were grown at 37 °C overnight in liquid Tris maleic acid minimal medium (TMA) supplemented with 115 mM KCl and 0.4 % w/v Glucose, then washed twice with TMA containing 0.1 mM KCl and 0.4 % w/v Glucose. Cells were inoculated in TMA with 0.1 mM KCl and 0.4 % w/v Glucose and collected at an OD600=0.5 for ChIP-exo and RNA-seq analysis. For PhoRB: cells were grown in liquid M9 minimal medium until OD600=0.5. Then cells were washed three times with M9 minimal medium without phosphate (M9-P; without Na2HPO4 and KH2PO4) and incubated in M9-P for 60 min (about the doubling time of MG1655 in M9 minimal medium) at 37 °C. For ZraSR: Cells were grown at 37 °C in liquid LB medium containing 1 mM ZnCl2. PGCGROWTHCONDITIONS	SRR10907671	MCO000002526	M9 minimal medium	Medium	True
characteristics	MCO		growth condition : <Air> anaerobic </Air> 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE43408	Quantitative Different Analysis of antimicrobial peptide LL37 expressed in E.coli Top 10 under aerobic and anaerobic condition.	GSM1217969	pHerd30T-LL37 CK+ anaerobic	23856776	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE43408/GSE43408.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth condition: anaerobic PGCGROWTHCONDITIONS	SRR958660	MCO000011680	anaerobic	Aeration	True
characteristics	MCO		growth condition : <Air> anaerobic </Air> 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE43408	Quantitative Different Analysis of antimicrobial peptide LL37 expressed in E.coli Top 10 under aerobic and anaerobic condition.	GSM1217970	pHerd30T-LL37 induced +anaerobic	23856776	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE43408/GSE43408.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	growth condition: anaerobic PGCGROWTHCONDITIONS	SRR958661	MCO000011680	anaerobic	Aeration	True
characteristics	MCO		treatment : <Phase> stationary phase </Phase> 	GPL17137	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	GSE46737	Genome-scale reconstruction of the sigma factor network in E. coli	GSM1137316	E. coli stationary 1	24461193	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE46737/GSE46737.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: stationary phase PGCGROWTHCONDITIONS	SRR847728	MCO000002866	stationary phase	Growth phase	True
characteristics	MCO		treatment : <Supp> glutamine </Supp> 	GPL17137	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	GSE46737	Genome-scale reconstruction of the sigma factor network in E. coli	GSM1137318	E. coli glutamine 1	24461193	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE46737/GSE46737.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: glutamine PGCGROWTHCONDITIONS	SRR847730	MCO000000836	glutamine	Medium supplement	True
characteristics	MCO		treatment : <Supp> glutamine </Supp> 	GPL17137	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	GSE46737	Genome-scale reconstruction of the sigma factor network in E. coli	GSM1137319	E. coli glutamine 2	24461193	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE46737/GSE46737.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: glutamine PGCGROWTHCONDITIONS	SRR847731	MCO000000836	glutamine	Medium supplement	True
characteristics	MCO		oxygen condition : <Air> anaerobic </Air> 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174828	Mid log_wildtype_glc minimal media_anaerobic rep1	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	oxygen condition: anaerobic PGCGROWTHCONDITIONS	SRR922265	MCO000011680	anaerobic	Aeration	True
characteristics	MCO		oxygen condition : <Air> anaerobic </Air> 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174829	Mid log_wildtype_glc minimal media_anaerobic rep2	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	oxygen condition: anaerobic PGCGROWTHCONDITIONS	SRR922266	MCO000011680	anaerobic	Aeration	True
characteristics	MCO		oxygen condition : <Air> anaerobic </Air> 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174830	Mid log_wildtype_glc minimal media_anaerobic rep3	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	oxygen condition: anaerobic PGCGROWTHCONDITIONS	SRR922267	MCO000011680	anaerobic	Aeration	True
characteristics	MCO		oxygen condition : <Air> anaerobic </Air> 	GPL16227	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	GSE48324	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GSM1174836	Mid log_mntR KO_glc minimal media_anaerobic	24987116	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	oxygen condition: anaerobic PGCGROWTHCONDITIONS	SRR922273	MCO000011680	anaerobic	Aeration	True
characteristics	MCO		genotype/variation : <Gtype> wild type </Gtype> 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE48829	Escherichia coli RNA-Seq	GSM1185375	WTA1	24214998	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48829/GSE48829.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type PGCGROWTHCONDITIONS	SRR933989	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype/variation : <Gtype> wild type </Gtype> 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE48829	Escherichia coli RNA-Seq	GSM1185376	WTB1	24214998	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48829/GSE48829.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type PGCGROWTHCONDITIONS	SRR933990	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype/variation : <Gtype> wild type </Gtype> 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE48829	Escherichia coli RNA-Seq	GSM1185377	WTC3	24214998	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48829/GSE48829.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type PGCGROWTHCONDITIONS	SRR933991	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype/variation : <Gtype> wild type </Gtype> 	GPL14548-GPL18183	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18183: Illumina HiSeq 2000 (Streptococcus pneumoniae)	GSE54199	Transcriptome and marker frequency analysis of E. coli (control vs. Trimethoprim) and S. pneumoniae (control vs. HPUra/Kanamycin)	GSM1310003	EC_Cont1_RNA	24725406	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54199/GSE54199.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type PGCGROWTHCONDITIONS	SRR1124840	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype/variation : <Gtype> wild type </Gtype> 	GPL14548-GPL18183	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18183: Illumina HiSeq 2000 (Streptococcus pneumoniae)	GSE54199	Transcriptome and marker frequency analysis of E. coli (control vs. Trimethoprim) and S. pneumoniae (control vs. HPUra/Kanamycin)	GSM1310004	EC_Cont2_RNA	24725406	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54199/GSE54199.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type PGCGROWTHCONDITIONS	SRR1124841	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype/variation : <Gtype> wild type </Gtype> 	GPL14548-GPL18183	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18183: Illumina HiSeq 2000 (Streptococcus pneumoniae)	GSE54199	Transcriptome and marker frequency analysis of E. coli (control vs. Trimethoprim) and S. pneumoniae (control vs. HPUra/Kanamycin)	GSM1310005	EC_Trim1_RNA	24725406	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54199/GSE54199.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type PGCGROWTHCONDITIONS	SRR1124842	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype/variation : <Gtype> wild type </Gtype> 	GPL14548-GPL18183	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18183: Illumina HiSeq 2000 (Streptococcus pneumoniae)	GSE54199	Transcriptome and marker frequency analysis of E. coli (control vs. Trimethoprim) and S. pneumoniae (control vs. HPUra/Kanamycin)	GSM1310006	EC_Trim2_RNA	24725406	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54199/GSE54199.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type PGCGROWTHCONDITIONS	SRR1124843	MCO000002470	wild type	Genetic background	True
growth_protocol	MCO		To harvest total RNA samples , overnight cultures of <Gtype> wild type </Gtype> MG1655 grown in LB at 37 ˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~ 0.4 for cultures grown in M63 . For samples grown to OD600 of ~ 0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution ( 95 % Ethanol , 5 % acid phenol ) . For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution . 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331409	LB 0.4 B1 TEX neg L1 GA	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	To harvest total RNA samples, overnight cultures of wild type MG1655 grown in LB at 37˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~0.4 for cultures grown in M63. For samples grown to OD600 of ~0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution (95% Ethanol, 5% acid phenol). For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution. PGCGROWTHCONDITIONS	SRR1173965	MCO000002470	wild type	Genetic background	True
growth_protocol	MCO		To harvest total RNA samples , overnight cultures of <Gtype> wild type </Gtype> MG1655 grown in LB at 37 ˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~ 0.4 for cultures grown in M63 . For samples grown to OD600 of ~ 0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution ( 95 % Ethanol , 5 % acid phenol ) . For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution . 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331410	LB 0.4 B1 TEX pos L1 GA	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	To harvest total RNA samples, overnight cultures of wild type MG1655 grown in LB at 37˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~0.4 for cultures grown in M63. For samples grown to OD600 of ~0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution (95% Ethanol, 5% acid phenol). For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution. PGCGROWTHCONDITIONS	SRR1173966	MCO000002470	wild type	Genetic background	True
growth_protocol	MCO		To harvest total RNA samples , overnight cultures of <Gtype> wild type </Gtype> MG1655 grown in LB at 37 ˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~ 0.4 for cultures grown in M63 . For samples grown to OD600 of ~ 0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution ( 95 % Ethanol , 5 % acid phenol ) . For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution . 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331411	LB 0.4 B2 TEX neg L1 HS1	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	To harvest total RNA samples, overnight cultures of wild type MG1655 grown in LB at 37˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~0.4 for cultures grown in M63. For samples grown to OD600 of ~0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution (95% Ethanol, 5% acid phenol). For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution. PGCGROWTHCONDITIONS	SRR1173967	MCO000002470	wild type	Genetic background	True
growth_protocol	MCO		To harvest total RNA samples , overnight cultures of <Gtype> wild type </Gtype> MG1655 grown in LB at 37 ˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~ 0.4 for cultures grown in M63 . For samples grown to OD600 of ~ 0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution ( 95 % Ethanol , 5 % acid phenol ) . For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution . 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331412	LB 0.4 B2 TEX neg L1 HS2	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	To harvest total RNA samples, overnight cultures of wild type MG1655 grown in LB at 37˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~0.4 for cultures grown in M63. For samples grown to OD600 of ~0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution (95% Ethanol, 5% acid phenol). For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution. PGCGROWTHCONDITIONS	SRR1173968	MCO000002470	wild type	Genetic background	True
growth_protocol	MCO		To harvest total RNA samples , overnight cultures of <Gtype> wild type </Gtype> MG1655 grown in LB at 37 ˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~ 0.4 for cultures grown in M63 . For samples grown to OD600 of ~ 0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution ( 95 % Ethanol , 5 % acid phenol ) . For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution . 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331413	LB 0.4 B2 TEX pos L1 HS1	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	To harvest total RNA samples, overnight cultures of wild type MG1655 grown in LB at 37˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~0.4 for cultures grown in M63. For samples grown to OD600 of ~0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution (95% Ethanol, 5% acid phenol). For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution. PGCGROWTHCONDITIONS	SRR1173969	MCO000002470	wild type	Genetic background	True
growth_protocol	MCO		To harvest total RNA samples , overnight cultures of <Gtype> wild type </Gtype> MG1655 grown in LB at 37 ˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~ 0.4 for cultures grown in M63 . For samples grown to OD600 of ~ 0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution ( 95 % Ethanol , 5 % acid phenol ) . For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution . 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331414	LB 0.4 B2 TEX pos L1 HS2	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	To harvest total RNA samples, overnight cultures of wild type MG1655 grown in LB at 37˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~0.4 for cultures grown in M63. For samples grown to OD600 of ~0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution (95% Ethanol, 5% acid phenol). For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution. PGCGROWTHCONDITIONS	SRR1173970	MCO000002470	wild type	Genetic background	True
growth_protocol	MCO		To harvest total RNA samples , overnight cultures of <Gtype> wild type </Gtype> MG1655 grown in LB at 37 ˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~ 0.4 for cultures grown in M63 . For samples grown to OD600 of ~ 0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution ( 95 % Ethanol , 5 % acid phenol ) . For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution . 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331415	LB 2.0 B1 TEX neg L1 GA	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	To harvest total RNA samples, overnight cultures of wild type MG1655 grown in LB at 37˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~0.4 for cultures grown in M63. For samples grown to OD600 of ~0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution (95% Ethanol, 5% acid phenol). For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution. PGCGROWTHCONDITIONS	SRR1173971	MCO000002470	wild type	Genetic background	True
growth_protocol	MCO		To harvest total RNA samples , overnight cultures of <Gtype> wild type </Gtype> MG1655 grown in LB at 37 ˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~ 0.4 for cultures grown in M63 . For samples grown to OD600 of ~ 0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution ( 95 % Ethanol , 5 % acid phenol ) . For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution . 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331416	LB 2.0 B1 TEX neg L2 HS2	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	To harvest total RNA samples, overnight cultures of wild type MG1655 grown in LB at 37˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~0.4 for cultures grown in M63. For samples grown to OD600 of ~0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution (95% Ethanol, 5% acid phenol). For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution. PGCGROWTHCONDITIONS	SRR1173972	MCO000002470	wild type	Genetic background	True
growth_protocol	MCO		To harvest total RNA samples , overnight cultures of <Gtype> wild type </Gtype> MG1655 grown in LB at 37 ˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~ 0.4 for cultures grown in M63 . For samples grown to OD600 of ~ 0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution ( 95 % Ethanol , 5 % acid phenol ) . For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution . 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331417	LB 2.0 B1 TEX pos L1 GA	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	To harvest total RNA samples, overnight cultures of wild type MG1655 grown in LB at 37˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~0.4 for cultures grown in M63. For samples grown to OD600 of ~0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution (95% Ethanol, 5% acid phenol). For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution. PGCGROWTHCONDITIONS	SRR1173973	MCO000002470	wild type	Genetic background	True
growth_protocol	MCO		To harvest total RNA samples , overnight cultures of <Gtype> wild type </Gtype> MG1655 grown in LB at 37 ˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~ 0.4 for cultures grown in M63 . For samples grown to OD600 of ~ 0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution ( 95 % Ethanol , 5 % acid phenol ) . For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution . 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331418	LB 2.0 B1 TEX pos L2 HS2	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	To harvest total RNA samples, overnight cultures of wild type MG1655 grown in LB at 37˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~0.4 for cultures grown in M63. For samples grown to OD600 of ~0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution (95% Ethanol, 5% acid phenol). For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution. PGCGROWTHCONDITIONS	SRR1173974	MCO000002470	wild type	Genetic background	True
growth_protocol	MCO		To harvest total RNA samples , overnight cultures of <Gtype> wild type </Gtype> MG1655 grown in LB at 37 ˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~ 0.4 for cultures grown in M63 . For samples grown to OD600 of ~ 0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution ( 95 % Ethanol , 5 % acid phenol ) . For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution . 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331419	LB 2.0 B2 TEX neg L1 HS1	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	To harvest total RNA samples, overnight cultures of wild type MG1655 grown in LB at 37˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~0.4 for cultures grown in M63. For samples grown to OD600 of ~0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution (95% Ethanol, 5% acid phenol). For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution. PGCGROWTHCONDITIONS	SRR1173975	MCO000002470	wild type	Genetic background	True
growth_protocol	MCO		To harvest total RNA samples , overnight cultures of <Gtype> wild type </Gtype> MG1655 grown in LB at 37 ˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~ 0.4 for cultures grown in M63 . For samples grown to OD600 of ~ 0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution ( 95 % Ethanol , 5 % acid phenol ) . For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution . 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331420	LB 2.0 B2 TEX neg L1 HS2	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	To harvest total RNA samples, overnight cultures of wild type MG1655 grown in LB at 37˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~0.4 for cultures grown in M63. For samples grown to OD600 of ~0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution (95% Ethanol, 5% acid phenol). For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution. PGCGROWTHCONDITIONS	SRR1173976	MCO000002470	wild type	Genetic background	True
growth_protocol	MCO		To harvest total RNA samples , overnight cultures of <Gtype> wild type </Gtype> MG1655 grown in LB at 37 ˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~ 0.4 for cultures grown in M63 . For samples grown to OD600 of ~ 0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution ( 95 % Ethanol , 5 % acid phenol ) . For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution . 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331421	LB 2.0 B2 TEX neg L2 HS2	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	To harvest total RNA samples, overnight cultures of wild type MG1655 grown in LB at 37˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~0.4 for cultures grown in M63. For samples grown to OD600 of ~0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution (95% Ethanol, 5% acid phenol). For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution. PGCGROWTHCONDITIONS	SRR1173977	MCO000002470	wild type	Genetic background	True
growth_protocol	MCO		To harvest total RNA samples , overnight cultures of <Gtype> wild type </Gtype> MG1655 grown in LB at 37 ˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~ 0.4 for cultures grown in M63 . For samples grown to OD600 of ~ 0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution ( 95 % Ethanol , 5 % acid phenol ) . For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution . 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331422	LB 2.0 B2 TEX pos L1 HS1	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	To harvest total RNA samples, overnight cultures of wild type MG1655 grown in LB at 37˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~0.4 for cultures grown in M63. For samples grown to OD600 of ~0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution (95% Ethanol, 5% acid phenol). For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution. PGCGROWTHCONDITIONS	SRR1173978	MCO000002470	wild type	Genetic background	True
growth_protocol	MCO		To harvest total RNA samples , overnight cultures of <Gtype> wild type </Gtype> MG1655 grown in LB at 37 ˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~ 0.4 for cultures grown in M63 . For samples grown to OD600 of ~ 0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution ( 95 % Ethanol , 5 % acid phenol ) . For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution . 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331423	LB 2.0 B2 TEX pos L1 HS2	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	To harvest total RNA samples, overnight cultures of wild type MG1655 grown in LB at 37˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~0.4 for cultures grown in M63. For samples grown to OD600 of ~0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution (95% Ethanol, 5% acid phenol). For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution. PGCGROWTHCONDITIONS	SRR1173979	MCO000002470	wild type	Genetic background	True
growth_protocol	MCO		To harvest total RNA samples , overnight cultures of <Gtype> wild type </Gtype> MG1655 grown in LB at 37 ˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~ 0.4 for cultures grown in M63 . For samples grown to OD600 of ~ 0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution ( 95 % Ethanol , 5 % acid phenol ) . For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution . 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331424	LB 2.0 B2 TEX pos L2 HS2	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	To harvest total RNA samples, overnight cultures of wild type MG1655 grown in LB at 37˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~0.4 for cultures grown in M63. For samples grown to OD600 of ~0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution (95% Ethanol, 5% acid phenol). For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution. PGCGROWTHCONDITIONS	SRR1173980	MCO000002470	wild type	Genetic background	True
growth_protocol	MCO		To harvest total RNA samples , overnight cultures of <Gtype> wild type </Gtype> MG1655 grown in LB at 37 ˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~ 0.4 for cultures grown in M63 . For samples grown to OD600 of ~ 0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution ( 95 % Ethanol , 5 % acid phenol ) . For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution . 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331426	M63 0.4 B1 TEX pos L1 GA	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	To harvest total RNA samples, overnight cultures of wild type MG1655 grown in LB at 37˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~0.4 for cultures grown in M63. For samples grown to OD600 of ~0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution (95% Ethanol, 5% acid phenol). For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution. PGCGROWTHCONDITIONS	SRR1173982	MCO000002470	wild type	Genetic background	True
growth_protocol	MCO		To harvest total RNA samples , overnight cultures of <Gtype> wild type </Gtype> MG1655 grown in LB at 37 ˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~ 0.4 for cultures grown in M63 . For samples grown to OD600 of ~ 0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution ( 95 % Ethanol , 5 % acid phenol ) . For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution . 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331427	M63 0.4 B2 TEX neg L1 HS1	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	To harvest total RNA samples, overnight cultures of wild type MG1655 grown in LB at 37˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~0.4 for cultures grown in M63. For samples grown to OD600 of ~0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution (95% Ethanol, 5% acid phenol). For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution. PGCGROWTHCONDITIONS	SRR1173983	MCO000002470	wild type	Genetic background	True
growth_protocol	MCO		To harvest total RNA samples , overnight cultures of <Gtype> wild type </Gtype> MG1655 grown in LB at 37 ˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~ 0.4 for cultures grown in M63 . For samples grown to OD600 of ~ 0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution ( 95 % Ethanol , 5 % acid phenol ) . For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution . 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331428	M63 0.4 B2 TEX neg L1 HS2	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	To harvest total RNA samples, overnight cultures of wild type MG1655 grown in LB at 37˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~0.4 for cultures grown in M63. For samples grown to OD600 of ~0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution (95% Ethanol, 5% acid phenol). For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution. PGCGROWTHCONDITIONS	SRR1173984	MCO000002470	wild type	Genetic background	True
growth_protocol	MCO		To harvest total RNA samples , overnight cultures of <Gtype> wild type </Gtype> MG1655 grown in LB at 37 ˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~ 0.4 for cultures grown in M63 . For samples grown to OD600 of ~ 0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution ( 95 % Ethanol , 5 % acid phenol ) . For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution . 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331429	M63 0.4 B2 TEX pos L1 HS1	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	To harvest total RNA samples, overnight cultures of wild type MG1655 grown in LB at 37˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~0.4 for cultures grown in M63. For samples grown to OD600 of ~0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution (95% Ethanol, 5% acid phenol). For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution. PGCGROWTHCONDITIONS	SRR1173985	MCO000002470	wild type	Genetic background	True
growth_protocol	MCO		To harvest total RNA samples , overnight cultures of <Gtype> wild type </Gtype> MG1655 grown in LB at 37 ˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~ 0.4 for cultures grown in M63 . For samples grown to OD600 of ~ 0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution ( 95 % Ethanol , 5 % acid phenol ) . For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution . 	GPL15010-GPL17024	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	GSE55199	Identification and validation of antisense RNAs in Escherichia coli	GSM1331430	M63 0.4 B2 TEX pos L1 HS2	25266388	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	To harvest total RNA samples, overnight cultures of wild type MG1655 grown in LB at 37˚C were diluted back 1:500 in either fresh LB or M63 minimal glucose medium and allowed to grow until the cultures reached an OD600 of ~ 0.4 and 2.0 for cultures grown in LB and an OD600 of ~0.4 for cultures grown in M63. For samples grown to OD600 of ~0.4 a total volume of 25 ml of cells were harvested and combined with 5 ml of stop solution (95% Ethanol, 5% acid phenol). For samples grown to OD600 of 2.0 a total volume of 5 ml of cells were harvested and combined with 1 ml of stop solution. PGCGROWTHCONDITIONS	SRR1173986	MCO000002470	wild type	Genetic background	True
source_name	MCO		<Gtype> WT </Gtype> _ <Supp> glucose </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602347	WT glucose 1	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	WT_glucose PGCGROWTHCONDITIONS	SRR1787590	MCO000000245	glucose	Medium supplement	True
characteristics	MCO		carbon source : <Supp> glucose </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602347	WT glucose 1	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	carbon source: glucose PGCGROWTHCONDITIONS	SRR1787590	MCO000000245	glucose	Medium supplement	True
source_name	MCO		<Gtype> WT </Gtype> _ <Supp> glucose </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602348	WT glucose 2	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	WT_glucose PGCGROWTHCONDITIONS	SRR1787591	MCO000000245	glucose	Medium supplement	True
characteristics	MCO		carbon source : <Supp> glucose </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602348	WT glucose 2	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	carbon source: glucose PGCGROWTHCONDITIONS	SRR1787591	MCO000000245	glucose	Medium supplement	True
characteristics	MCO		carbon source : <Supp> fructose </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602349	WT fructose 1	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	carbon source: fructose PGCGROWTHCONDITIONS	SRR1787592	MCO000000848	fructose	Medium supplement	True
characteristics	MCO		carbon source : <Supp> fructose </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602350	WT fructose 2	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	carbon source: fructose PGCGROWTHCONDITIONS	SRR1787593	MCO000000848	fructose	Medium supplement	True
source_name	MCO		<Gtype> WT </Gtype> _ <Supp> acetate </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602351	WT acetate 1	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	WT_acetate PGCGROWTHCONDITIONS	SRR1787594	MCO000000910	acetate	Medium supplement	True
characteristics	MCO		carbon source : <Supp> acetate </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602351	WT acetate 1	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	carbon source: acetate PGCGROWTHCONDITIONS	SRR1787594	MCO000000910	acetate	Medium supplement	True
source_name	MCO		<Gtype> WT </Gtype> _ <Supp> acetate </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602352	WT acetate 2	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	WT_acetate PGCGROWTHCONDITIONS	SRR1787595	MCO000000910	acetate	Medium supplement	True
characteristics	MCO		carbon source : <Supp> acetate </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602352	WT acetate 2	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	carbon source: acetate PGCGROWTHCONDITIONS	SRR1787595	MCO000000910	acetate	Medium supplement	True
source_name	MCO		<Gtype> Δcra </Gtype> _ <Supp> glucose </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602353	Δcra glucose 1	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Δcra_glucose PGCGROWTHCONDITIONS	SRR1787596	MCO000000245	glucose	Medium supplement	True
characteristics	MCO		carbon source : <Supp> glucose </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602353	Δcra glucose 1	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	carbon source: glucose PGCGROWTHCONDITIONS	SRR1787596	MCO000000245	glucose	Medium supplement	True
source_name	MCO		<Gtype> Δcra </Gtype> _ <Supp> glucose </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602354	Δcra glucose 2	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Δcra_glucose PGCGROWTHCONDITIONS	SRR1787597	MCO000000245	glucose	Medium supplement	True
characteristics	MCO		carbon source : <Supp> glucose </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602354	Δcra glucose 2	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	carbon source: glucose PGCGROWTHCONDITIONS	SRR1787597	MCO000000245	glucose	Medium supplement	True
characteristics	MCO		carbon source : <Supp> fructose </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602355	Δcra fructose 1	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	carbon source: fructose PGCGROWTHCONDITIONS	SRR1787598	MCO000000848	fructose	Medium supplement	True
characteristics	MCO		carbon source : <Supp> fructose </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602356	Δcra fructose 2	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	carbon source: fructose PGCGROWTHCONDITIONS	SRR1787599	MCO000000848	fructose	Medium supplement	True
source_name	MCO		<Gtype> Δcra </Gtype> _ <Supp> acetate </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602357	Δcra acetate 1	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Δcra_acetate PGCGROWTHCONDITIONS	SRR1787600	MCO000000910	acetate	Medium supplement	True
characteristics	MCO		carbon source : <Supp> acetate </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602357	Δcra acetate 1	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	carbon source: acetate PGCGROWTHCONDITIONS	SRR1787600	MCO000000910	acetate	Medium supplement	True
source_name	MCO		<Gtype> Δcra </Gtype> _ <Supp> acetate </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602358	Δcra acetate 2	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Δcra_acetate PGCGROWTHCONDITIONS	SRR1787601	MCO000000910	acetate	Medium supplement	True
characteristics	MCO		carbon source : <Supp> acetate </Supp> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE65642	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GSM1602358	Δcra acetate 2	29394395	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	carbon source: acetate PGCGROWTHCONDITIONS	SRR1787601	MCO000000910	acetate	Medium supplement	True
growth_protocol	MCO		E. coli K-12 MG1655 WT , gadE , gadW and gadX mutant cells were grown to <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) <Air> aerobically </Air> ( <Agit> 250 rpm </Agit> ) at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> at <pH> pH 5.5 </pH> . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623160	WT pH5.5 1	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5. PGCGROWTHCONDITIONS	SRR1824557	MCO000003211	pH 5.5	pH	True
growth_protocol	MCO		E. coli K-12 MG1655 WT , gadE , gadW and gadX mutant cells were grown to <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) <Air> aerobically </Air> ( <Agit> 250 rpm </Agit> ) at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> at <pH> pH 5.5 </pH> . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623161	WT pH5.5 2	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5. PGCGROWTHCONDITIONS	SRR1824558	MCO000003211	pH 5.5	pH	True
growth_protocol	MCO		E. coli K-12 MG1655 WT , gadE , gadW and gadX mutant cells were grown to <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) <Air> aerobically </Air> ( <Agit> 250 rpm </Agit> ) at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> at <pH> pH 5.5 </pH> . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623162	ΔgadE pH5.5 1	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5. PGCGROWTHCONDITIONS	SRR1824559	MCO000003211	pH 5.5	pH	True
growth_protocol	MCO		E. coli K-12 MG1655 WT , gadE , gadW and gadX mutant cells were grown to <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) <Air> aerobically </Air> ( <Agit> 250 rpm </Agit> ) at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> at <pH> pH 5.5 </pH> . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623163	ΔgadE pH5.5 2	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5. PGCGROWTHCONDITIONS	SRR1824560	MCO000003211	pH 5.5	pH	True
growth_protocol	MCO		E. coli K-12 MG1655 WT , gadE , gadW and gadX mutant cells were grown to <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) <Air> aerobically </Air> ( <Agit> 250 rpm </Agit> ) at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> at <pH> pH 5.5 </pH> . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623164	ΔgadW pH5.5 1	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5. PGCGROWTHCONDITIONS	SRR1824561	MCO000003211	pH 5.5	pH	True
growth_protocol	MCO		E. coli K-12 MG1655 WT , gadE , gadW and gadX mutant cells were grown to <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) <Air> aerobically </Air> ( <Agit> 250 rpm </Agit> ) at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> at <pH> pH 5.5 </pH> . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623165	ΔgadW pH5.5 2	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5. PGCGROWTHCONDITIONS	SRR1824562	MCO000003211	pH 5.5	pH	True
growth_protocol	MCO		E. coli K-12 MG1655 WT , gadE , gadW and gadX mutant cells were grown to <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) <Air> aerobically </Air> ( <Agit> 250 rpm </Agit> ) at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> at <pH> pH 5.5 </pH> . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623166	ΔgadX pH5.5 1	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5. PGCGROWTHCONDITIONS	SRR1824563	MCO000003211	pH 5.5	pH	True
growth_protocol	MCO		E. coli K-12 MG1655 WT , gadE , gadW and gadX mutant cells were grown to <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) <Air> aerobically </Air> ( <Agit> 250 rpm </Agit> ) at <Temp> 37 °C </Temp> in <Med> M9 minimal media </Med> supplemented with <Supp> 0.2 % glucose </Supp> at <pH> pH 5.5 </pH> . 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE66481	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GSM1623167	ΔgadX pH5.5 2	26258987	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) aerobically (250 rpm) at 37°C in M9 minimal media supplemented with 0.2% glucose at pH 5.5. PGCGROWTHCONDITIONS	SRR1824564	MCO000003211	pH 5.5	pH	True
characteristics	MCO		genotype : <Gtype> wild type </Gtype> 	GPL21021	GPL21021: Illumina HiSeq 2500 (Escherichia coli O157:H7 str. EDL933)	GSE73969	RNA-seq to profile the H-NS transcriptome in EHEC O157:H7 strain EDL933	GSM1906887	wt_1	2717363528288207	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73969/GSE73969.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype: wild type PGCGROWTHCONDITIONS	SRR2637695	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype : <Gtype> wild type </Gtype> 	GPL21021	GPL21021: Illumina HiSeq 2500 (Escherichia coli O157:H7 str. EDL933)	GSE73969	RNA-seq to profile the H-NS transcriptome in EHEC O157:H7 strain EDL933	GSM1906888	wt_2	2717363528288207	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73969/GSE73969.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype: wild type PGCGROWTHCONDITIONS	SRR2637696	MCO000002470	wild type	Genetic background	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968346	WTRep1_0min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982421	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968346	WTRep1_0min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982421	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968347	WTRep1_2min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982422	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968347	WTRep1_2min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982422	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968348	WTRep1_4min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982423	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968348	WTRep1_4min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982423	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968349	WTRep1_6min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982424	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968349	WTRep1_6min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982424	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968350	WTRep1_8min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982425	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968350	WTRep1_8min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982425	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968351	WTRep1_10min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982426	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968351	WTRep1_10min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982426	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968352	WTRep1_15min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982427	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968352	WTRep1_15min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982427	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968353	WTRep1_20min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982428	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968353	WTRep1_20min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982428	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968354	WTRep2_0min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982429	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968354	WTRep2_0min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982429	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968355	WTRep2_2min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982430	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968355	WTRep2_2min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982430	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968356	WTRep2_4min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982431	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968356	WTRep2_4min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982431	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968357	WTRep2_6min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982432	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968357	WTRep2_6min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982432	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968358	WTRep2_8min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982433	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968358	WTRep2_8min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982433	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968359	WTRep2_10min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982434	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968359	WTRep2_10min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982434	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968360	WTRep2_15min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982435	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968360	WTRep2_15min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982435	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968361	WTRep2_20min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982436	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968361	WTRep2_20min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982436	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968362	WTKasRep1_0min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982437	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968362	WTKasRep1_0min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982437	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968364	WTKasRep1_4min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982439	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968364	WTKasRep1_4min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982439	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968368	WTKasRep1_15min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982443	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968368	WTKasRep1_15min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982443	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968369	WTKasRep1_20min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982444	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968369	WTKasRep1_20min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982444	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968370	WTKasRep2_0min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982445	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968370	WTKasRep2_0min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982445	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968371	WTKasRep2_2min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982446	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968371	WTKasRep2_2min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982446	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968372	WTKasRep2_4min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982447	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968372	WTKasRep2_4min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982447	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968374	WTKasRep2_8min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982449	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968374	WTKasRep2_8min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982449	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968377	WTKasRep2_20min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982452	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968377	WTKasRep2_20min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982452	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968378	MutRep1_0min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982453	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968378	MutRep1_0min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982453	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968379	MutRep1_2min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982454	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968379	MutRep1_2min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982454	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968380	MutRep1_4min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982455	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968380	MutRep1_4min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982455	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968381	MutRep1_6min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982456	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968381	MutRep1_6min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982456	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968382	MutRep1_8min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982457	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968382	MutRep1_8min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982457	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968383	MutRep1_10min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982458	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968383	MutRep1_10min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982458	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968384	MutRep1_15min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982459	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968384	MutRep1_15min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982459	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968385	MutRep1_20min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982460	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968385	MutRep1_20min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982460	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968386	MutRep2_0min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982461	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968386	MutRep2_0min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982461	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968387	MutRep2_2min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982462	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968387	MutRep2_2min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982462	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968388	MutRep2_4min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982463	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968388	MutRep2_4min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982463	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968389	MutRep2_6min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982464	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968389	MutRep2_6min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982464	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968390	MutRep2_8min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982465	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968390	MutRep2_8min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982465	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968391	MutRep2_10min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982466	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968391	MutRep2_10min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982466	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968392	MutRep2_15min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982467	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968392	MutRep2_15min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982467	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968393	MutRep2_20min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982468	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968393	MutRep2_20min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982468	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968394	neo_0min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982469	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968394	neo_0min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982469	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968395	neo_1min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982470	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968395	neo_1min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982470	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968396	neo_2min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982471	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968396	neo_2min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982471	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968397	neo_4min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982472	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968397	neo_4min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982472	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968398	neo_6min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982473	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968398	neo_6min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982473	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968399	neo_8min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982474	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968399	neo_8min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982474	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968400	neo_10min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982475	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968400	neo_10min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982475	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968401	neo_15min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982476	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968401	neo_15min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982476	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968402	bla_0min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982477	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968402	bla_0min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982477	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968403	bla_1min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982478	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968403	bla_1min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982478	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968404	bla_2min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982479	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968404	bla_2min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982479	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968405	bla_4min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982480	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968405	bla_4min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982480	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968406	bla_6min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982481	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968406	bla_6min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982481	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968407	bla_8min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982482	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968407	bla_8min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982482	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968408	bla_10min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982483	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968408	bla_10min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982483	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968409	bla_15min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982484	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968409	bla_15min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982484	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968410	mMaple3_0min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982485	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968410	mMaple3_0min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982485	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968411	mMaple3_1min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982486	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968411	mMaple3_1min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982486	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968412	mMaple3_2min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982487	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968412	mMaple3_2min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982487	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968413	mMaple3_4min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982488	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968413	mMaple3_4min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982488	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968414	mMaple3_6min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982489	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968414	mMaple3_6min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982489	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968415	mMaple3_8min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982490	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968415	mMaple3_8min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982490	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968416	mMaple3_10min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982491	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968416	mMaple3_10min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982491	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968417	mMaple3_15min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982492	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968417	mMaple3_15min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982492	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968418	phoA_0min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982493	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968418	phoA_0min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982493	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968419	phoA_1min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982494	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968419	phoA_1min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982494	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968420	phoA_2min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982495	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968420	phoA_2min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982495	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968421	phoA_4min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982496	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968421	phoA_4min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982496	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968422	phoA_6min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982497	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968422	phoA_6min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982497	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968423	phoA_8min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982498	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968423	phoA_8min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982498	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968424	phoA_10min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982499	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968424	phoA_10min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982499	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968425	phoA_15min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982500	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968425	phoA_15min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982500	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968426	lacZ_0min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982501	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968426	lacZ_0min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982501	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968427	lacZ_1min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982502	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968427	lacZ_1min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982502	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968428	lacZ_2min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982503	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968428	lacZ_2min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982503	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968429	lacZ_4min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982504	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968429	lacZ_4min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982504	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968430	lacZ_6min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982505	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968430	lacZ_6min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982505	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968431	lacZ_8min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982506	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968431	lacZ_8min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982506	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968432	lacZ_10min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982507	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968432	lacZ_10min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982507	MCO000000828	rifampicin	Medium supplement	True
treatment_protocol	MCO		Cells were treated with <Supp> rifampicin </Supp> before sample collection . In some cases , kasugamycin was added 15 minutes before the rifampicin addition . 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968433	lacZ_15min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition. PGCGROWTHCONDITIONS	SRR2982508	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		treatment : <Supp> rifampicin </Supp> 	GPL14548-GPL21222	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	GSE75818	Spatial organization shapes the turnover of a bacterial transcriptome	GSM1968433	lacZ_15min	27198188	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	treatment: rifampicin PGCGROWTHCONDITIONS	SRR2982508	MCO000000828	rifampicin	Medium supplement	True
characteristics	MCO		genotype : <Gtype> wild type </Gtype> 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE76167	Mechanisms of nickel toxicity in bacteria	GSM1975603	Rodrigue_1-WT-phiNi-1	2737513027668277	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE76167/GSE76167.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype: wild type PGCGROWTHCONDITIONS	SRR3033275SRR3033276SRR3033277SRR3033278SRR3033279	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype : <Gtype> wild type </Gtype> 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE76167	Mechanisms of nickel toxicity in bacteria	GSM1975604	Rodrigue_6-WT-phiNi-2	2737513027668277	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE76167/GSE76167.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype: wild type PGCGROWTHCONDITIONS	SRR3033280SRR3033281SRR3033282SRR3033283	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype : <Gtype> wild type </Gtype> 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE76167	Mechanisms of nickel toxicity in bacteria	GSM1975605	Rodrigue_9-WT-phiNi-3	2737513027668277	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE76167/GSE76167.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype: wild type PGCGROWTHCONDITIONS	SRR3033284SRR3033285SRR3033286SRR3033287	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype : <Gtype> wild type </Gtype> 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE76167	Mechanisms of nickel toxicity in bacteria	GSM1975606	Rodrigue_2-WT-Ni-1	2737513027668277	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE76167/GSE76167.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype: wild type PGCGROWTHCONDITIONS	SRR3033288SRR3033289SRR3033290SRR3033291SRR3033292	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype : <Gtype> wild type </Gtype> 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE76167	Mechanisms of nickel toxicity in bacteria	GSM1975607	Rodrigue_5-WT-Ni-2	2737513027668277	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE76167/GSE76167.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype: wild type PGCGROWTHCONDITIONS	SRR3033293SRR3033294SRR3033295SRR3033296	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype : <Gtype> wild type </Gtype> 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE76167	Mechanisms of nickel toxicity in bacteria	GSM1975608	Rodrigue_10-WT-Ni-3	2737513027668277	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE76167/GSE76167.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype: wild type PGCGROWTHCONDITIONS	SRR3033297SRR3033298SRR3033299SRR3033300SRR3033301	MCO000002470	wild type	Genetic background	True
growth_protocol	MCO		Escherichia coli strains E.coli C ( DSMZ 4860 ) , E. coli Crooks ( DSMZ 1576 ) , E. coli DH5α ( DSMZ 6897 ) E. coli W ( DSMZ 1116 ) , E. coli W3110 ( DSMZ 5911 ) were obtained from DSMZ-German Collection of Microorganism and Cell Cultures ; E. coli BL21 ( DE3 ) was purchased as competent cells from Agilent ( Agilent Technologies Inc. , USA ) , E. coli K-12 MG1655 ( ATCC 700926 ) . All strains were cultured in <Med> M9 minimal medium </Med> ( 1 ) containing Na2HPO4 x 7H2O ( 6.8 g ) , KH2PO4 ( 3 g ) , NaCl ( 0.5 g ) , NH4Cl ( 1 g ) , MgSO4 ( 2 mmol ) , CaCl2 ( 0.1 mmol ) , trace elements , Wolf 's vitamin solution ( 2 ) and glucose ( 2 g L-1 ) . Anoxic <Med> M9 minimal media </Med> with <Supp> glucose </Supp> was obtained by flushing solution with oxygen free nitrogen ( 95 % ) . Overnight cultures from single colonies of each of seven E. coli strains were diluted to a starting optical density ( OD600 ) of 0.01 . Cultures were grown in 250 ml flasks or 300 ml oxygen-free sealed bottles containing 50 ml <Med> glucose-M9 minimal media </Med> in a shaking incubator at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> . 	GPL14548-GPL15010-GPL21530-GPL21531-GPL21532-GPL21533-GPL21534	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21530: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. W3110). GPL21531: Illumina HiSeq 2000 (Escherichia coli W). GPL21532: Illumina HiSeq 2000 (Escherichia coli C). GPL21533: Illumina HiSeq 2000 (Escherichia coli BL21). GPL21534: Illumina HiSeq 2000 (Escherichia coli DH5[alpha])	GSE78756	Quantifying variation within the bacterial species E. coli	GSM2075722	Crooks_aero	27667363	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE78756/GSE78756.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Escherichia coli strains E.coli C (DSMZ 4860), E. coli Crooks (DSMZ 1576), E. coli DH5α (DSMZ 6897) E. coli W (DSMZ 1116), E. coli W3110 (DSMZ 5911) were obtained from DSMZ-German Collection of Microorganism and Cell Cultures; E. coli BL21 (DE3) was purchased as competent cells from Agilent (Agilent Technologies Inc., USA), E. coli K-12 MG1655 (ATCC 700926). All strains were cultured in M9 minimal medium (1) containing Na2HPO4 x 7H2O (6.8 g), KH2PO4 (3 g), NaCl (0.5 g), NH4Cl (1 g), MgSO4 (2 mmol), CaCl2 (0.1 mmol), trace elements, Wolf’s vitamin solution (2) and glucose (2 g L-1). Anoxic M9 minimal media with glucose was obtained by flushing solution with oxygen free nitrogen (95%). Overnight cultures from single colonies of each of seven E. coli strains were diluted to a starting optical density (OD600) of 0.01. Cultures were grown in 250 ml flasks or 300 ml oxygen-free sealed bottles containing 50 ml glucose-M9 minimal media in a shaking incubator at 37°C and 250 rpm. PGCGROWTHCONDITIONS	SRR3194453	MCO000002526	M9 minimal medium	Medium	True
growth_protocol	MCO		Escherichia coli strains E.coli C ( DSMZ 4860 ) , E. coli Crooks ( DSMZ 1576 ) , E. coli DH5α ( DSMZ 6897 ) E. coli W ( DSMZ 1116 ) , E. coli W3110 ( DSMZ 5911 ) were obtained from DSMZ-German Collection of Microorganism and Cell Cultures ; E. coli BL21 ( DE3 ) was purchased as competent cells from Agilent ( Agilent Technologies Inc. , USA ) , E. coli K-12 MG1655 ( ATCC 700926 ) . All strains were cultured in <Med> M9 minimal medium </Med> ( 1 ) containing Na2HPO4 x 7H2O ( 6.8 g ) , KH2PO4 ( 3 g ) , NaCl ( 0.5 g ) , NH4Cl ( 1 g ) , MgSO4 ( 2 mmol ) , CaCl2 ( 0.1 mmol ) , trace elements , Wolf 's vitamin solution ( 2 ) and glucose ( 2 g L-1 ) . Anoxic <Med> M9 minimal media </Med> with <Supp> glucose </Supp> was obtained by flushing solution with oxygen free nitrogen ( 95 % ) . Overnight cultures from single colonies of each of seven E. coli strains were diluted to a starting optical density ( OD600 ) of 0.01 . Cultures were grown in 250 ml flasks or 300 ml oxygen-free sealed bottles containing 50 ml <Med> glucose-M9 minimal media </Med> in a shaking incubator at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> . 	GPL14548-GPL15010-GPL21530-GPL21531-GPL21532-GPL21533-GPL21534	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21530: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. W3110). GPL21531: Illumina HiSeq 2000 (Escherichia coli W). GPL21532: Illumina HiSeq 2000 (Escherichia coli C). GPL21533: Illumina HiSeq 2000 (Escherichia coli BL21). GPL21534: Illumina HiSeq 2000 (Escherichia coli DH5[alpha])	GSE78756	Quantifying variation within the bacterial species E. coli	GSM2075722	Crooks_aero	27667363	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE78756/GSE78756.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Escherichia coli strains E.coli C (DSMZ 4860), E. coli Crooks (DSMZ 1576), E. coli DH5α (DSMZ 6897) E. coli W (DSMZ 1116), E. coli W3110 (DSMZ 5911) were obtained from DSMZ-German Collection of Microorganism and Cell Cultures; E. coli BL21 (DE3) was purchased as competent cells from Agilent (Agilent Technologies Inc., USA), E. coli K-12 MG1655 (ATCC 700926). All strains were cultured in M9 minimal medium (1) containing Na2HPO4 x 7H2O (6.8 g), KH2PO4 (3 g), NaCl (0.5 g), NH4Cl (1 g), MgSO4 (2 mmol), CaCl2 (0.1 mmol), trace elements, Wolf’s vitamin solution (2) and glucose (2 g L-1). Anoxic M9 minimal media with glucose was obtained by flushing solution with oxygen free nitrogen (95%). Overnight cultures from single colonies of each of seven E. coli strains were diluted to a starting optical density (OD600) of 0.01. Cultures were grown in 250 ml flasks or 300 ml oxygen-free sealed bottles containing 50 ml glucose-M9 minimal media in a shaking incubator at 37°C and 250 rpm. PGCGROWTHCONDITIONS	SRR3194453	MCO000000245	glucose	Medium supplement	True
growth_protocol	MCO		Escherichia coli strains E.coli C ( DSMZ 4860 ) , E. coli Crooks ( DSMZ 1576 ) , E. coli DH5α ( DSMZ 6897 ) E. coli W ( DSMZ 1116 ) , E. coli W3110 ( DSMZ 5911 ) were obtained from DSMZ-German Collection of Microorganism and Cell Cultures ; E. coli BL21 ( DE3 ) was purchased as competent cells from Agilent ( Agilent Technologies Inc. , USA ) , E. coli K-12 MG1655 ( ATCC 700926 ) . All strains were cultured in <Med> M9 minimal medium </Med> ( 1 ) containing Na2HPO4 x 7H2O ( 6.8 g ) , KH2PO4 ( 3 g ) , NaCl ( 0.5 g ) , NH4Cl ( 1 g ) , MgSO4 ( 2 mmol ) , CaCl2 ( 0.1 mmol ) , trace elements , Wolf 's vitamin solution ( 2 ) and glucose ( 2 g L-1 ) . Anoxic <Med> M9 minimal media </Med> with <Supp> glucose </Supp> was obtained by flushing solution with oxygen free nitrogen ( 95 % ) . Overnight cultures from single colonies of each of seven E. coli strains were diluted to a starting optical density ( OD600 ) of 0.01 . Cultures were grown in 250 ml flasks or 300 ml oxygen-free sealed bottles containing 50 ml <Med> glucose-M9 minimal media </Med> in a shaking incubator at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> . 	GPL14548-GPL15010-GPL21530-GPL21531-GPL21532-GPL21533-GPL21534	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21530: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. W3110). GPL21531: Illumina HiSeq 2000 (Escherichia coli W). GPL21532: Illumina HiSeq 2000 (Escherichia coli C). GPL21533: Illumina HiSeq 2000 (Escherichia coli BL21). GPL21534: Illumina HiSeq 2000 (Escherichia coli DH5[alpha])	GSE78756	Quantifying variation within the bacterial species E. coli	GSM2075723	Crooks_anaero	27667363	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE78756/GSE78756.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Escherichia coli strains E.coli C (DSMZ 4860), E. coli Crooks (DSMZ 1576), E. coli DH5α (DSMZ 6897) E. coli W (DSMZ 1116), E. coli W3110 (DSMZ 5911) were obtained from DSMZ-German Collection of Microorganism and Cell Cultures; E. coli BL21 (DE3) was purchased as competent cells from Agilent (Agilent Technologies Inc., USA), E. coli K-12 MG1655 (ATCC 700926). All strains were cultured in M9 minimal medium (1) containing Na2HPO4 x 7H2O (6.8 g), KH2PO4 (3 g), NaCl (0.5 g), NH4Cl (1 g), MgSO4 (2 mmol), CaCl2 (0.1 mmol), trace elements, Wolf’s vitamin solution (2) and glucose (2 g L-1). Anoxic M9 minimal media with glucose was obtained by flushing solution with oxygen free nitrogen (95%). Overnight cultures from single colonies of each of seven E. coli strains were diluted to a starting optical density (OD600) of 0.01. Cultures were grown in 250 ml flasks or 300 ml oxygen-free sealed bottles containing 50 ml glucose-M9 minimal media in a shaking incubator at 37°C and 250 rpm. PGCGROWTHCONDITIONS	SRR3194455SRR3194456	MCO000002526	M9 minimal medium	Medium	True
growth_protocol	MCO		Escherichia coli strains E.coli C ( DSMZ 4860 ) , E. coli Crooks ( DSMZ 1576 ) , E. coli DH5α ( DSMZ 6897 ) E. coli W ( DSMZ 1116 ) , E. coli W3110 ( DSMZ 5911 ) were obtained from DSMZ-German Collection of Microorganism and Cell Cultures ; E. coli BL21 ( DE3 ) was purchased as competent cells from Agilent ( Agilent Technologies Inc. , USA ) , E. coli K-12 MG1655 ( ATCC 700926 ) . All strains were cultured in <Med> M9 minimal medium </Med> ( 1 ) containing Na2HPO4 x 7H2O ( 6.8 g ) , KH2PO4 ( 3 g ) , NaCl ( 0.5 g ) , NH4Cl ( 1 g ) , MgSO4 ( 2 mmol ) , CaCl2 ( 0.1 mmol ) , trace elements , Wolf 's vitamin solution ( 2 ) and glucose ( 2 g L-1 ) . Anoxic <Med> M9 minimal media </Med> with <Supp> glucose </Supp> was obtained by flushing solution with oxygen free nitrogen ( 95 % ) . Overnight cultures from single colonies of each of seven E. coli strains were diluted to a starting optical density ( OD600 ) of 0.01 . Cultures were grown in 250 ml flasks or 300 ml oxygen-free sealed bottles containing 50 ml <Med> glucose-M9 minimal media </Med> in a shaking incubator at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> . 	GPL14548-GPL15010-GPL21530-GPL21531-GPL21532-GPL21533-GPL21534	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21530: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. W3110). GPL21531: Illumina HiSeq 2000 (Escherichia coli W). GPL21532: Illumina HiSeq 2000 (Escherichia coli C). GPL21533: Illumina HiSeq 2000 (Escherichia coli BL21). GPL21534: Illumina HiSeq 2000 (Escherichia coli DH5[alpha])	GSE78756	Quantifying variation within the bacterial species E. coli	GSM2075723	Crooks_anaero	27667363	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE78756/GSE78756.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	Escherichia coli strains E.coli C (DSMZ 4860), E. coli Crooks (DSMZ 1576), E. coli DH5α (DSMZ 6897) E. coli W (DSMZ 1116), E. coli W3110 (DSMZ 5911) were obtained from DSMZ-German Collection of Microorganism and Cell Cultures; E. coli BL21 (DE3) was purchased as competent cells from Agilent (Agilent Technologies Inc., USA), E. coli K-12 MG1655 (ATCC 700926). All strains were cultured in M9 minimal medium (1) containing Na2HPO4 x 7H2O (6.8 g), KH2PO4 (3 g), NaCl (0.5 g), NH4Cl (1 g), MgSO4 (2 mmol), CaCl2 (0.1 mmol), trace elements, Wolf’s vitamin solution (2) and glucose (2 g L-1). Anoxic M9 minimal media with glucose was obtained by flushing solution with oxygen free nitrogen (95%). Overnight cultures from single colonies of each of seven E. coli strains were diluted to a starting optical density (OD600) of 0.01. Cultures were grown in 250 ml flasks or 300 ml oxygen-free sealed bottles containing 50 ml glucose-M9 minimal media in a shaking incubator at 37°C and 250 rpm. PGCGROWTHCONDITIONS	SRR3194455SRR3194456	MCO000000245	glucose	Medium supplement	True
growth_protocol	MCO		LB medium , 180 rpm shaking , at <Temp> 37 °C </Temp> , between exponential and <Phase> stationary phase </Phase> 	GPL23073	GPL23073: Illumina MiSeq (Escherichia coli O157:H7 str. EDL933)	GSE94984	Differentiation of ncRNAs from small mRNAs in Escherichia coli O157:H7 EDL933 (EHEC) by combined RNAseq and RIBOseq – ryhB encodes the regulatory RNA RyhB and a peptide, RyhP	GSM2493797	EHEC in LB Experiment 2 [RNA-Seq]	28245801	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE94984/GSE94984.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	LB medium, 180 rpm shaking, at 37°C, between exponential and stationary phase PGCGROWTHCONDITIONS	SRR5266619	MCO000002866	stationary phase	Growth phase	True
source_name	MCO		biomass collected in the transition between exponential to <Phase> stationary phase </Phase> 	GPL23073	GPL23073: Illumina MiSeq (Escherichia coli O157:H7 str. EDL933)	GSE94984	Differentiation of ncRNAs from small mRNAs in Escherichia coli O157:H7 EDL933 (EHEC) by combined RNAseq and RIBOseq – ryhB encodes the regulatory RNA RyhB and a peptide, RyhP	GSM2493797	EHEC in LB Experiment 2 [RNA-Seq]	28245801	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE94984/GSE94984.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	biomass collected in the transition between exponential to stationary phase PGCGROWTHCONDITIONS	SRR5266619	MCO000002866	stationary phase	Growth phase	True
characteristics	MCO		genotype/variation : <Gtype> wild type </Gtype> 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE95318	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GSM2507165	WTA_time0	28351917	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type PGCGROWTHCONDITIONS	SRR5282299	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype/variation : <Gtype> wild type </Gtype> 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE95318	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GSM2507166	WTA_time2.5	28351917	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type PGCGROWTHCONDITIONS	SRR5282300	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype/variation : <Gtype> wild type </Gtype> 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE95318	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GSM2507167	WTA_time5	28351917	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type PGCGROWTHCONDITIONS	SRR5282301	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype/variation : <Gtype> wild type </Gtype> 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE95318	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GSM2507168	WTA_time7.5	28351917	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type PGCGROWTHCONDITIONS	SRR5282302	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype/variation : <Gtype> wild type </Gtype> 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE95318	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GSM2507169	WTA_time10	28351917	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type PGCGROWTHCONDITIONS	SRR5282303	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype/variation : <Gtype> wild type </Gtype> 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE95318	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GSM2507170	WTA_time20	28351917	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type PGCGROWTHCONDITIONS	SRR5282304	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype/variation : <Gtype> wild type </Gtype> 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE95318	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GSM2507171	WTB_time0	28351917	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type PGCGROWTHCONDITIONS	SRR5282305	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype/variation : <Gtype> wild type </Gtype> 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE95318	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GSM2507172	WTB_time2.5	28351917	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type PGCGROWTHCONDITIONS	SRR5282306	MCO000002470	wild type	Genetic background	True
characteristics	MCO		genotype/variation : <Gtype> wild type </Gtype> 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE95318	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GSM2507173	WTB_time7.5	28351917	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	genotype/variation: wild type PGCGROWTHCONDITIONS	SRR5282307	MCO000002470	wild type	Genetic background	True
characteristics	MCO	wild type	genotype : <Gtype> wildtype </Gtype> 	GPL21222-GPL21726	GPL21222: Illumina NextSeq 500 (Escherichia coli). GPL21726: Ion Torrent Proton (Escherichia coli)	GSE104504	Crosstalk between global regulators CRP and FIS in E. coli.	GSM2802566	wt.rep1.me	29205228	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE104504/GSE104504.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: wildtype PGCGROWTHCONDITIONS	SRR6125557	MCO000002470	wildtype	Genetic background	True
characteristics	MCO	wild type	genotype : <Gtype> wildtype </Gtype> 	GPL21222-GPL21726	GPL21222: Illumina NextSeq 500 (Escherichia coli). GPL21726: Ion Torrent Proton (Escherichia coli)	GSE104504	Crosstalk between global regulators CRP and FIS in E. coli.	GSM2802567	wt.rep2.me	29205228	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE104504/GSE104504.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: wildtype PGCGROWTHCONDITIONS	SRR6125558	MCO000002470	wildtype	Genetic background	True
source_name	MCO	exponential phase	bacteria grown at 37 ° C with shaking until <Phase> log phase </Phase> 	GPL10328	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	GSE36248	Transcriptome mapping of blaCMY-2 positive IncA/C plasmid pAR060302	GSM885047	no treatment		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE36248/GSE36248.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	bacteria grown at 37° C with shaking until log phase PGCGROWTHCONDITIONS	SRR427120	MCO000002864	log phase	Growth phase	True
growth_protocol	MCO	agitation at 250 rpm	Cells were grown in a 250 ml fermenter containing 100 ml LB medium supplemented with 3 g/L glucose , <Supp> 0.1 mM IPTG , </Supp> and 50 μg/mL antibiotics . The fermentors were operated at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> with aeration ( 200 mL/min ) . Flow rate was 1.162 ml/min ( dilution rate 0,7 / h ) . The pellets were used for RNA . 	GPL16760	GPL16760: Illumina Genome Analyzer II (Escherichia coli BL21(DE3))	GSE44928	Physiology study of Escherichia coli harboring high intracellular ATP driven by artificial Pck expression	GSM1094082	BL21_2		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE44928/GSE44928.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Cells were grown in a 250 ml fermenter containing 100 ml LB medium supplemented  with 3 g/L glucose, 0.1 mM IPTG, and 50 μg/mL antibiotics. The fermentors were operated at 37 °C and 250 rpm with  aeration (200 mL/min). Flow rate was 1.162ml/min(dilution rate 0,7/h). The pellets were used for RNA. PGCGROWTHCONDITIONS	SRR771533	MCO000011588	250 rpm	Agitation speed	True
growth_protocol	MCO	agitation at 250 rpm	Cells were grown in a 250 ml fermenter containing 100 ml LB medium supplemented with 3 g/L glucose , <Supp> 0.1 mM IPTG , </Supp> and 50 μg/mL antibiotics . The fermentors were operated at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> with aeration ( 200 mL/min ) . Flow rate was 1.162 ml/min ( dilution rate 0,7 / h ) . The pellets were used for RNA . 	GPL16760	GPL16760: Illumina Genome Analyzer II (Escherichia coli BL21(DE3))	GSE44928	Physiology study of Escherichia coli harboring high intracellular ATP driven by artificial Pck expression	GSM1094083	PCK over		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE44928/GSE44928.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Cells were grown in a 250 ml fermenter containing 100 ml LB medium supplemented  with 3 g/L glucose, 0.1 mM IPTG, and 50 μg/mL antibiotics. The fermentors were operated at 37 °C and 250 rpm with  aeration (200 mL/min). Flow rate was 1.162ml/min(dilution rate 0,7/h). The pellets were used for RNA. PGCGROWTHCONDITIONS	SRR771534	MCO000011588	250 rpm	Agitation speed	True
characteristics	MCO	wild type	genotype : <Gtype> wt </Gtype> 	GPL18814	GPL18814: Illumina HiSeq 2000 (Escherichia coli BW38028)	GSE58556	RNA sequencing based analysis of the bacterial transcriptome	GSM1413874	WT_glucose_log	25483350	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE58556/GSE58556.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: wt PGCGROWTHCONDITIONS	SRR1411272	MCO000002470	wt	Genetic background	True
characteristics	MCO	wild type	strain : <Gtype> wt </Gtype> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE64848	Integrated analysis of molecular and systems level function of the Crp regulon [RNA-Seq]	GSM1581598	RNAseq_wt_fructose_NH4Cl_O2_1	29771928	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE64848/GSE64848.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	strain: wt PGCGROWTHCONDITIONS	SRR1751336SRR1751337SRR1751338	MCO000002470	wt	Genetic background	True
characteristics	MCO	wild type	strain : <Gtype> wt </Gtype> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE64848	Integrated analysis of molecular and systems level function of the Crp regulon [RNA-Seq]	GSM1581599	RNAseq_wt_fructose_NH4Cl_O2_2	29771928	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE64848/GSE64848.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	strain: wt PGCGROWTHCONDITIONS	SRR1751339SRR1751340SRR1751341	MCO000002470	wt	Genetic background	True
characteristics	MCO	wild type	strain : <Gtype> wt </Gtype> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE64848	Integrated analysis of molecular and systems level function of the Crp regulon [RNA-Seq]	GSM1581600	RNAseq_wt_glucose_NH4Cl_O2_1	29771928	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE64848/GSE64848.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	strain: wt PGCGROWTHCONDITIONS	SRR1751342SRR1751343	MCO000002470	wt	Genetic background	True
characteristics	MCO	wild type	strain : <Gtype> wt </Gtype> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE64848	Integrated analysis of molecular and systems level function of the Crp regulon [RNA-Seq]	GSM1581601	RNAseq_wt_glucose_NH4Cl_O2_2	29771928	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE64848/GSE64848.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	strain: wt PGCGROWTHCONDITIONS	SRR1751344SRR1751345	MCO000002470	wt	Genetic background	True
characteristics	MCO	wild type	strain : <Gtype> wt </Gtype> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE64848	Integrated analysis of molecular and systems level function of the Crp regulon [RNA-Seq]	GSM1581602	RNAseq_wt_glucose_NH4Cl_O2_3	29771928	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE64848/GSE64848.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	strain: wt PGCGROWTHCONDITIONS	SRR1751346	MCO000002470	wt	Genetic background	True
characteristics	MCO	wild type	strain : <Gtype> wt </Gtype> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE64848	Integrated analysis of molecular and systems level function of the Crp regulon [RNA-Seq]	GSM1581603	RNAseq_wt_glycerol_NH4Cl_O2_1	29771928	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE64848/GSE64848.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	strain: wt PGCGROWTHCONDITIONS	SRR1751347SRR1751348SRR1751349	MCO000002470	wt	Genetic background	True
characteristics	MCO	wild type	strain : <Gtype> wt </Gtype> 	GPL16085	GPL16085: Illumina MiSeq (Escherichia coli)	GSE64848	Integrated analysis of molecular and systems level function of the Crp regulon [RNA-Seq]	GSM1581604	RNAseq_wt_glycerol_NH4Cl_O2_2	29771928	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE64848/GSE64848.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	strain: wt PGCGROWTHCONDITIONS	SRR1751350SRR1751351SRR1751352	MCO000002470	wt	Genetic background	True
characteristics	MCO	wild type	genotype : <Gtype> wildtype </Gtype> 	GPL14548	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	GSE65244	Temporal gene expression in Escherichia coli	GSM1590712	Wt – 60 min		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65244/GSE65244.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	genotype: wildtype PGCGROWTHCONDITIONS	SRR1771414	MCO000002470	wildtype	Genetic background	True
growth_protocol	MCO	minimal defined medium	Glycerol stocks of E. coli K12 strain MG1655 were inoculated into LB media grown at 37 ℃ with constant agitation overnight . Cultures were diluted 1:100 into fresh <Med> minimal medium </Med> and then cultured at 37 ℃ to mid-exponential phase ( OD600 nm ~ 0.6 ) . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE67218	Transcriptional expression level of E. coli at 37 ℃ in LB media	GSM1642593	RNA-seq 37C LB rep1		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE67218/GSE67218.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Glycerol stocks of E. coli K12 strain MG1655 were inoculated into LB media  grown at 37 ℃ with constant agitation overnight. Cultures were diluted 1:100 into fresh minimal medium and then cultured at 37 ℃ to mid-exponential phase (OD600 nm ~ 0.6). PGCGROWTHCONDITIONS	SRR1927169	MCO000011586	minimal medium	Medium	True
growth_protocol	MCO	minimal defined medium	Glycerol stocks of E. coli K12 strain MG1655 were inoculated into LB media grown at 37 ℃ with constant agitation overnight . Cultures were diluted 1:100 into fresh <Med> minimal medium </Med> and then cultured at 37 ℃ to mid-exponential phase ( OD600 nm ~ 0.6 ) . 	GPL17439	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	GSE67218	Transcriptional expression level of E. coli at 37 ℃ in LB media	GSM1642594	RNA-seq 37C LB rep2		http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE67218/GSE67218.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Glycerol stocks of E. coli K12 strain MG1655 were inoculated into LB media  grown at 37 ℃ with constant agitation overnight. Cultures were diluted 1:100 into fresh minimal medium and then cultured at 37 ℃ to mid-exponential phase (OD600 nm ~ 0.6). PGCGROWTHCONDITIONS	SRR1927170	MCO000011586	minimal medium	Medium	True
characteristics	MCO	exponential phase	growth phase : <Phase> log phase </Phase> 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE76167	Mechanisms of nickel toxicity in bacteria	GSM1975603	Rodrigue_1-WT-phiNi-1	2737513027668277	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE76167/GSE76167.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	growth phase: log phase PGCGROWTHCONDITIONS	SRR3033275SRR3033276SRR3033277SRR3033278SRR3033279	MCO000002864	log phase	Growth phase	True
characteristics	MCO	exponential phase	growth phase : <Phase> log phase </Phase> 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE76167	Mechanisms of nickel toxicity in bacteria	GSM1975604	Rodrigue_6-WT-phiNi-2	2737513027668277	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE76167/GSE76167.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	growth phase: log phase PGCGROWTHCONDITIONS	SRR3033280SRR3033281SRR3033282SRR3033283	MCO000002864	log phase	Growth phase	True
characteristics	MCO	exponential phase	growth phase : <Phase> log phase </Phase> 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE76167	Mechanisms of nickel toxicity in bacteria	GSM1975605	Rodrigue_9-WT-phiNi-3	2737513027668277	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE76167/GSE76167.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	growth phase: log phase PGCGROWTHCONDITIONS	SRR3033284SRR3033285SRR3033286SRR3033287	MCO000002864	log phase	Growth phase	True
characteristics	MCO	exponential phase	growth phase : <Phase> log phase </Phase> 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE76167	Mechanisms of nickel toxicity in bacteria	GSM1975606	Rodrigue_2-WT-Ni-1	2737513027668277	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE76167/GSE76167.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	growth phase: log phase PGCGROWTHCONDITIONS	SRR3033288SRR3033289SRR3033290SRR3033291SRR3033292	MCO000002864	log phase	Growth phase	True
characteristics	MCO	exponential phase	growth phase : <Phase> log phase </Phase> 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE76167	Mechanisms of nickel toxicity in bacteria	GSM1975607	Rodrigue_5-WT-Ni-2	2737513027668277	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE76167/GSE76167.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	growth phase: log phase PGCGROWTHCONDITIONS	SRR3033293SRR3033294SRR3033295SRR3033296	MCO000002864	log phase	Growth phase	True
characteristics	MCO	exponential phase	growth phase : <Phase> log phase </Phase> 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE76167	Mechanisms of nickel toxicity in bacteria	GSM1975608	Rodrigue_10-WT-Ni-3	2737513027668277	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE76167/GSE76167.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	growth phase: log phase PGCGROWTHCONDITIONS	SRR3033297SRR3033298SRR3033299SRR3033300SRR3033301	MCO000002864	log phase	Growth phase	True
growth_protocol	MCO	agitation at 250 rpm	Escherichia coli strains E.coli C ( DSMZ 4860 ) , E. coli Crooks ( DSMZ 1576 ) , E. coli DH5α ( DSMZ 6897 ) E. coli W ( DSMZ 1116 ) , E. coli W3110 ( DSMZ 5911 ) were obtained from DSMZ-German Collection of Microorganism and Cell Cultures ; E. coli BL21 ( DE3 ) was purchased as competent cells from Agilent ( Agilent Technologies Inc. , USA ) , E. coli K-12 MG1655 ( ATCC 700926 ) . All strains were cultured in <Med> M9 minimal medium </Med> ( 1 ) containing Na2HPO4 x 7H2O ( 6.8 g ) , KH2PO4 ( 3 g ) , NaCl ( 0.5 g ) , NH4Cl ( 1 g ) , MgSO4 ( 2 mmol ) , CaCl2 ( 0.1 mmol ) , trace elements , Wolf 's vitamin solution ( 2 ) and glucose ( 2 g L-1 ) . Anoxic <Med> M9 minimal media </Med> with <Supp> glucose </Supp> was obtained by flushing solution with oxygen free nitrogen ( 95 % ) . Overnight cultures from single colonies of each of seven E. coli strains were diluted to a starting optical density ( OD600 ) of 0.01 . Cultures were grown in 250 ml flasks or 300 ml oxygen-free sealed bottles containing 50 ml <Med> glucose-M9 minimal media </Med> in a shaking incubator at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> . 	GPL14548-GPL15010-GPL21530-GPL21531-GPL21532-GPL21533-GPL21534	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21530: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. W3110). GPL21531: Illumina HiSeq 2000 (Escherichia coli W). GPL21532: Illumina HiSeq 2000 (Escherichia coli C). GPL21533: Illumina HiSeq 2000 (Escherichia coli BL21). GPL21534: Illumina HiSeq 2000 (Escherichia coli DH5[alpha])	GSE78756	Quantifying variation within the bacterial species E. coli	GSM2075722	Crooks_aero	27667363	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE78756/GSE78756.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Escherichia coli strains E.coli C (DSMZ 4860), E. coli Crooks (DSMZ 1576), E. coli DH5α (DSMZ 6897) E. coli W (DSMZ 1116), E. coli W3110 (DSMZ 5911) were obtained from DSMZ-German Collection of Microorganism and Cell Cultures; E. coli BL21 (DE3) was purchased as competent cells from Agilent (Agilent Technologies Inc., USA), E. coli K-12 MG1655 (ATCC 700926). All strains were cultured in M9 minimal medium (1) containing Na2HPO4 x 7H2O (6.8 g), KH2PO4 (3 g), NaCl (0.5 g), NH4Cl (1 g), MgSO4 (2 mmol), CaCl2 (0.1 mmol), trace elements, Wolf’s vitamin solution (2) and glucose (2 g L-1). Anoxic M9 minimal media with glucose was obtained by flushing solution with oxygen free nitrogen (95%). Overnight cultures from single colonies of each of seven E. coli strains were diluted to a starting optical density (OD600) of 0.01. Cultures were grown in 250 ml flasks or 300 ml oxygen-free sealed bottles containing 50 ml glucose-M9 minimal media in a shaking incubator at 37°C and 250 rpm. PGCGROWTHCONDITIONS	SRR3194453	MCO000011588	250 rpm	Agitation speed	True
growth_protocol	MCO	agitation at 250 rpm	Escherichia coli strains E.coli C ( DSMZ 4860 ) , E. coli Crooks ( DSMZ 1576 ) , E. coli DH5α ( DSMZ 6897 ) E. coli W ( DSMZ 1116 ) , E. coli W3110 ( DSMZ 5911 ) were obtained from DSMZ-German Collection of Microorganism and Cell Cultures ; E. coli BL21 ( DE3 ) was purchased as competent cells from Agilent ( Agilent Technologies Inc. , USA ) , E. coli K-12 MG1655 ( ATCC 700926 ) . All strains were cultured in <Med> M9 minimal medium </Med> ( 1 ) containing Na2HPO4 x 7H2O ( 6.8 g ) , KH2PO4 ( 3 g ) , NaCl ( 0.5 g ) , NH4Cl ( 1 g ) , MgSO4 ( 2 mmol ) , CaCl2 ( 0.1 mmol ) , trace elements , Wolf 's vitamin solution ( 2 ) and glucose ( 2 g L-1 ) . Anoxic <Med> M9 minimal media </Med> with <Supp> glucose </Supp> was obtained by flushing solution with oxygen free nitrogen ( 95 % ) . Overnight cultures from single colonies of each of seven E. coli strains were diluted to a starting optical density ( OD600 ) of 0.01 . Cultures were grown in 250 ml flasks or 300 ml oxygen-free sealed bottles containing 50 ml <Med> glucose-M9 minimal media </Med> in a shaking incubator at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> . 	GPL14548-GPL15010-GPL21530-GPL21531-GPL21532-GPL21533-GPL21534	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21530: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. W3110). GPL21531: Illumina HiSeq 2000 (Escherichia coli W). GPL21532: Illumina HiSeq 2000 (Escherichia coli C). GPL21533: Illumina HiSeq 2000 (Escherichia coli BL21). GPL21534: Illumina HiSeq 2000 (Escherichia coli DH5[alpha])	GSE78756	Quantifying variation within the bacterial species E. coli	GSM2075723	Crooks_anaero	27667363	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE78756/GSE78756.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Escherichia coli strains E.coli C (DSMZ 4860), E. coli Crooks (DSMZ 1576), E. coli DH5α (DSMZ 6897) E. coli W (DSMZ 1116), E. coli W3110 (DSMZ 5911) were obtained from DSMZ-German Collection of Microorganism and Cell Cultures; E. coli BL21 (DE3) was purchased as competent cells from Agilent (Agilent Technologies Inc., USA), E. coli K-12 MG1655 (ATCC 700926). All strains were cultured in M9 minimal medium (1) containing Na2HPO4 x 7H2O (6.8 g), KH2PO4 (3 g), NaCl (0.5 g), NH4Cl (1 g), MgSO4 (2 mmol), CaCl2 (0.1 mmol), trace elements, Wolf’s vitamin solution (2) and glucose (2 g L-1). Anoxic M9 minimal media with glucose was obtained by flushing solution with oxygen free nitrogen (95%). Overnight cultures from single colonies of each of seven E. coli strains were diluted to a starting optical density (OD600) of 0.01. Cultures were grown in 250 ml flasks or 300 ml oxygen-free sealed bottles containing 50 ml glucose-M9 minimal media in a shaking incubator at 37°C and 250 rpm. PGCGROWTHCONDITIONS	SRR3194455SRR3194456	MCO000011588	250 rpm	Agitation speed	True
growth_protocol	MCO	agitation at 250 rpm	Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . For culture tube assays ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) , cells were diluted 658-fold ( 4.56 µL into 3 mL ) into EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE88835	Genetic circuit 0x58	GSM2349915	Tube state 1 (IPTG-/aTc-/Ara-)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR4427755	MCO000011588	250 rpm	Agitation speed	True
growth_protocol	MCO	agitation at 250 rpm	Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . For culture tube assays ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) , cells were diluted 658-fold ( 4.56 µL into 3 mL ) into EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE88835	Genetic circuit 0x58	GSM2349916	Tube state 2 (IPTG+/aTc-/Ara-)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR4427756	MCO000011588	250 rpm	Agitation speed	True
growth_protocol	MCO	agitation at 250 rpm	Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . For culture tube assays ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) , cells were diluted 658-fold ( 4.56 µL into 3 mL ) into EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE88835	Genetic circuit 0x58	GSM2349917	Tube state 3 (IPTG-/aTc+/Ara-)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR4427757	MCO000011588	250 rpm	Agitation speed	True
growth_protocol	MCO	agitation at 250 rpm	Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . For culture tube assays ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) , cells were diluted 658-fold ( 4.56 µL into 3 mL ) into EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE88835	Genetic circuit 0x58	GSM2349918	Tube state 4 (IPTG+/aTc+/Ara-)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR4427758	MCO000011588	250 rpm	Agitation speed	True
growth_protocol	MCO	agitation at 250 rpm	Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . For culture tube assays ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) , cells were diluted 658-fold ( 4.56 µL into 3 mL ) into EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE88835	Genetic circuit 0x58	GSM2349919	Tube state 5 (IPTG-/aTc-/Ara+)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR4427759	MCO000011588	250 rpm	Agitation speed	True
growth_protocol	MCO	agitation at 250 rpm	Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . For culture tube assays ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) , cells were diluted 658-fold ( 4.56 µL into 3 mL ) into EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE88835	Genetic circuit 0x58	GSM2349920	Tube state 6 (IPTG+/aTc-/Ara+)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR4427760	MCO000011588	250 rpm	Agitation speed	True
growth_protocol	MCO	agitation at 250 rpm	Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . For culture tube assays ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) , cells were diluted 658-fold ( 4.56 µL into 3 mL ) into EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE88835	Genetic circuit 0x58	GSM2349921	Tube state 7 (IPTG-/aTc+/Ara+)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR4427761	MCO000011588	250 rpm	Agitation speed	True
growth_protocol	MCO	agitation at 250 rpm	Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . For culture tube assays ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) , cells were diluted 658-fold ( 4.56 µL into 3 mL ) into EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE88835	Genetic circuit 0x58	GSM2349922	Tube state 8 (IPTG+/aTc+/Ara+)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR4427762	MCO000011588	250 rpm	Agitation speed	True
growth_protocol	MCO	agitation at 250 rpm	Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . For culture tube assays ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) , cells were diluted 658-fold ( 4.56 µL into 3 mL ) into EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE88835	Genetic circuit 0x58	GSM2349923	Flask state 1 (IPTG-/aTc-/Ara-)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR4427763	MCO000011588	250 rpm	Agitation speed	True
growth_protocol	MCO	agitation at 250 rpm	Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . For culture tube assays ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) , cells were diluted 658-fold ( 4.56 µL into 3 mL ) into EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE88835	Genetic circuit 0x58	GSM2349924	Flask state 2 (IPTG+/aTc-/Ara-)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR4427764	MCO000011588	250 rpm	Agitation speed	True
growth_protocol	MCO	agitation at 250 rpm	Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . For culture tube assays ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) , cells were diluted 658-fold ( 4.56 µL into 3 mL ) into EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE88835	Genetic circuit 0x58	GSM2349925	Flask state 3 (IPTG-/aTc+/Ara-)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR4427765	MCO000011588	250 rpm	Agitation speed	True
growth_protocol	MCO	agitation at 250 rpm	Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . For culture tube assays ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) , cells were diluted 658-fold ( 4.56 µL into 3 mL ) into EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE88835	Genetic circuit 0x58	GSM2349926	Flask state 4 (IPTG+/aTc+/Ara-)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR4427766	MCO000011588	250 rpm	Agitation speed	True
growth_protocol	MCO	agitation at 250 rpm	Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . For culture tube assays ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) , cells were diluted 658-fold ( 4.56 µL into 3 mL ) into EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE88835	Genetic circuit 0x58	GSM2349927	Flask state 5 (IPTG-/aTc-/Ara+)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR4427767	MCO000011588	250 rpm	Agitation speed	True
growth_protocol	MCO	agitation at 250 rpm	Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . For culture tube assays ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) , cells were diluted 658-fold ( 4.56 µL into 3 mL ) into EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE88835	Genetic circuit 0x58	GSM2349928	Flask state 6 (IPTG+/aTc-/Ara+)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR4427768	MCO000011588	250 rpm	Agitation speed	True
growth_protocol	MCO	agitation at 250 rpm	Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . For culture tube assays ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) , cells were diluted 658-fold ( 4.56 µL into 3 mL ) into EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE88835	Genetic circuit 0x58	GSM2349929	Flask state 7 (IPTG-/aTc+/Ara+)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR4427769	MCO000011588	250 rpm	Agitation speed	True
growth_protocol	MCO	agitation at 250 rpm	Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . For culture tube assays ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) , cells were diluted 658-fold ( 4.56 µL into 3 mL ) into EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE88835	Genetic circuit 0x58	GSM2349930	Flask state 8 (IPTG+/aTc+/Ara+)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. For culture tube assays (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059), cells were diluted 658-fold (4.56 µL into 3 mL) into EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes and Erlenmeyer flasks were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR4427770	MCO000011588	250 rpm	Agitation speed	True
growth_protocol	MCO	agitation at 250 rpm	Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . Cells were diluted 658-fold ( 4.56 µL into 3 mL ) into culture tubes ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) containing EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE98890	Genetic circuit 0x58 replicates and modified	GSM2757255	0x58 replicate 2 state 1 (IPTG-/aTc-/Ara-)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR5985582	MCO000011588	250 rpm	Agitation speed	True
growth_protocol	MCO	agitation at 250 rpm	Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . Cells were diluted 658-fold ( 4.56 µL into 3 mL ) into culture tubes ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) containing EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE98890	Genetic circuit 0x58 replicates and modified	GSM2757256	0x58 replicate 2 state 2 (IPTG+/aTc-/Ara-)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR5985583	MCO000011588	250 rpm	Agitation speed	True
growth_protocol	MCO	agitation at 250 rpm	Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . Cells were diluted 658-fold ( 4.56 µL into 3 mL ) into culture tubes ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) containing EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE98890	Genetic circuit 0x58 replicates and modified	GSM2757257	0x58 replicate 2 state 3 (IPTG-/aTc+/Ara-)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR5985584	MCO000011588	250 rpm	Agitation speed	True
growth_protocol	MCO	agitation at 250 rpm	Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . Cells were diluted 658-fold ( 4.56 µL into 3 mL ) into culture tubes ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) containing EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE98890	Genetic circuit 0x58 replicates and modified	GSM2757258	0x58 replicate 2 state 4 (IPTG+/aTc+/Ara-)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR5985585	MCO000011588	250 rpm	Agitation speed	True
growth_protocol	MCO	agitation at 250 rpm	Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . Cells were diluted 658-fold ( 4.56 µL into 3 mL ) into culture tubes ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) containing EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE98890	Genetic circuit 0x58 replicates and modified	GSM2757259	0x58 replicate 2 state 5 (IPTG-/aTc-/Ara+)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR5985586	MCO000011588	250 rpm	Agitation speed	True
growth_protocol	MCO	agitation at 250 rpm	Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . Cells were diluted 658-fold ( 4.56 µL into 3 mL ) into culture tubes ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) containing EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE98890	Genetic circuit 0x58 replicates and modified	GSM2757260	0x58 replicate 2 state 6 (IPTG+/aTc-/Ara+)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR5985587	MCO000011588	250 rpm	Agitation speed	True
growth_protocol	MCO	agitation at 250 rpm	Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . Cells were diluted 658-fold ( 4.56 µL into 3 mL ) into culture tubes ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) containing EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE98890	Genetic circuit 0x58 replicates and modified	GSM2757261	0x58 replicate 2 state 7 (IPTG-/aTc+/Ara+)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR5985588	MCO000011588	250 rpm	Agitation speed	True
growth_protocol	MCO	agitation at 250 rpm	Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . Cells were diluted 658-fold ( 4.56 µL into 3 mL ) into culture tubes ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) containing EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE98890	Genetic circuit 0x58 replicates and modified	GSM2757262	0x58 replicate 2 state 8 (IPTG+/aTc+/Ara+)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR5985589	MCO000011588	250 rpm	Agitation speed	True
growth_protocol	MCO	agitation at 250 rpm	Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . Cells were diluted 658-fold ( 4.56 µL into 3 mL ) into culture tubes ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) containing EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE98890	Genetic circuit 0x58 replicates and modified	GSM2757263	0x58 replicate 3 state 1 (IPTG-/aTc-/Ara-)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR5985590	MCO000011588	250 rpm	Agitation speed	True
growth_protocol	MCO	agitation at 250 rpm	Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . Cells were diluted 658-fold ( 4.56 µL into 3 mL ) into culture tubes ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) containing EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE98890	Genetic circuit 0x58 replicates and modified	GSM2757264	0x58 replicate 3 state 2 (IPTG+/aTc-/Ara-)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR5985591	MCO000011588	250 rpm	Agitation speed	True
growth_protocol	MCO	agitation at 250 rpm	Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . Cells were diluted 658-fold ( 4.56 µL into 3 mL ) into culture tubes ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) containing EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE98890	Genetic circuit 0x58 replicates and modified	GSM2757265	0x58 replicate 3 state 3 (IPTG-/aTc+/Ara-)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR5985592	MCO000011588	250 rpm	Agitation speed	True
growth_protocol	MCO	agitation at 250 rpm	Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . Cells were diluted 658-fold ( 4.56 µL into 3 mL ) into culture tubes ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) containing EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE98890	Genetic circuit 0x58 replicates and modified	GSM2757266	0x58 replicate 3 state 4 (IPTG+/aTc+/Ara-)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR5985593	MCO000011588	250 rpm	Agitation speed	True
growth_protocol	MCO	agitation at 250 rpm	Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . Cells were diluted 658-fold ( 4.56 µL into 3 mL ) into culture tubes ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) containing EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE98890	Genetic circuit 0x58 replicates and modified	GSM2757267	0x58 replicate 3 state 5 (IPTG-/aTc-/Ara+)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR5985594	MCO000011588	250 rpm	Agitation speed	True
growth_protocol	MCO	agitation at 250 rpm	Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . Cells were diluted 658-fold ( 4.56 µL into 3 mL ) into culture tubes ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) containing EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE98890	Genetic circuit 0x58 replicates and modified	GSM2757268	0x58 replicate 3 state 6 (IPTG+/aTc-/Ara+)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR5985595	MCO000011588	250 rpm	Agitation speed	True
growth_protocol	MCO	agitation at 250 rpm	Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . Cells were diluted 658-fold ( 4.56 µL into 3 mL ) into culture tubes ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) containing EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE98890	Genetic circuit 0x58 replicates and modified	GSM2757269	0x58 replicate 3 state 7 (IPTG-/aTc+/Ara+)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR5985596	MCO000011588	250 rpm	Agitation speed	True
growth_protocol	MCO	agitation at 250 rpm	Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . Cells were diluted 658-fold ( 4.56 µL into 3 mL ) into culture tubes ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) containing EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE98890	Genetic circuit 0x58 replicates and modified	GSM2757270	0x58 replicate 3 state 8 (IPTG+/aTc+/Ara+)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR5985597	MCO000011588	250 rpm	Agitation speed	True
growth_protocol	MCO	agitation at 250 rpm	Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . Cells were diluted 658-fold ( 4.56 µL into 3 mL ) into culture tubes ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) containing EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE98890	Genetic circuit 0x58 replicates and modified	GSM2757272	Control pAN1201 replicate 1 (IPTG-/aTc-/Ara-)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR5985599	MCO000011588	250 rpm	Agitation speed	True
growth_protocol	MCO	agitation at 250 rpm	Individual colonies were inoculated into MOPS EZ Rich Defined Medium ( Teknova , CA , M2105 ) with 0.2 % glycerol carbon source and 50 μg/mL kanamycin ( Gold Biotechnology , MO , K-120-5 ) and grown overnight for <Supp> 16 hours </Supp> at <Temp> 37 °C </Temp> and 1000 RPM in V-bottom 96-well plates ( Nunc , Roskilde , Denmark , 249952 ) in an ELMI Digital Thermos Microplates shaker incubator ( Elmi Ltd , Riga , Latvia ) . The following day , cultures were diluted 178-fold ( two serial dilutions of 15 µL into 185 µL ) into EZ Rich glycerol with kanamycin , and grown under the same ELMI shaker incubator conditions for three hours . Cells were diluted 658-fold ( 4.56 µL into 3 mL ) into culture tubes ( Falcon 14 mL round-bottom polypropylene tubes ; Corning , MA , 352059 ) containing EZ Rich glycerol with kanamycin and inducers . For Erlenmeyer flask assays ( Pyrex 250 mL ; Cole-Palmer , IL , 4980-250 ) , cells were diluted 658-fold ( 76 µL into 50 mL ) into EZ Rich glycerol with kanamycin and inducers . Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG , 10 ng/mL aTc , and 5 mM L-arabinose . Culture tubes were then grown in an Innova 44 shaker ( Eppendorf , CT ) at <Temp> 37 °C </Temp> and <Agit> 250 rpm </Agit> for five hours . 	GPL18133	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	GSE98890	Genetic circuit 0x58 replicates and modified	GSM2757273	Control pAN1201 replicate 2 (IPTG-/aTc-/Ara-)	29122925	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	Individual colonies were inoculated into MOPS EZ Rich Defined Medium (Teknova, CA, M2105) with 0.2% glycerol carbon source and 50 μg/mL kanamycin (Gold Biotechnology, MO, K-120-5) and grown overnight for 16 hours at 37 °C and 1000 RPM in V-bottom 96-well plates (Nunc, Roskilde, Denmark, 249952) in an ELMI Digital Thermos Microplates shaker incubator (Elmi Ltd, Riga, Latvia). The following day, cultures were diluted 178-fold (two serial dilutions of 15 µL into 185 µL) into EZ Rich glycerol with kanamycin, and grown under the same ELMI shaker incubator conditions for three hours. Cells were diluted 658-fold (4.56 µL into 3 mL) into culture tubes (Falcon 14 mL round-bottom polypropylene tubes; Corning, MA, 352059) containing EZ Rich glycerol with kanamycin and inducers. For Erlenmeyer flask assays (Pyrex 250 mL; Cole-Palmer, IL, 4980-250), cells were diluted 658-fold (76 µL into 50 mL) into EZ Rich glycerol with kanamycin and inducers. Eight inducer combinations were used that cover the presence or absence of 0.5 mM IPTG, 10 ng/mL aTc, and 5 mM L-arabinose. Culture tubes were then grown in an Innova 44 shaker (Eppendorf, CT) at 37 °C and 250 rpm for five hours. PGCGROWTHCONDITIONS	SRR5985600	MCO000011588	250 rpm	Agitation speed	True