SRR	GSE	GSM	GPL	PMID	GSM_NAME	GSE_NAME	GPL_NAME	BANGLINE	SOURCE_TEXT_CTRL	FULL_TEXT	TERM_NAME	TERM_TYPE	REPO_FILE	CASE_MATCH	SET	SORT	SOURCE	TERM_ID
SRR6001737	GSE103421	GSM2770989	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling at 37°C in WT cells_1	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	MOPS medium	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	MOPS rich medium	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003160
SRR6001739	GSE103421	GSM2770991	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling 30 min after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	MOPS medium	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	MOPS rich medium	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003160
SRR6001742	GSE103421	GSM2770994	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	MOPS medium	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	MOPS rich medium	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003160
SRR6001743	GSE103421	GSM2770995	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling 6 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	MOPS medium	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	MOPS rich medium	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003160
SRR6001744	GSE103421	GSM2770996	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling 5 min after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	MOPS medium	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	MOPS rich medium	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003160
SRR6001745	GSE103421	GSM2770997	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling 10 min after shift to 10°C in WT cells_2	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	MOPS medium	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	MOPS rich medium	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003160
SRR6001746	GSE103421	GSM2770998	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling 15 min after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	MOPS medium	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	MOPS rich medium	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003160
SRR6001747SRR6001748	GSE103421	GSM2770999	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling 8 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	MOPS medium	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	MOPS rich medium	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003160
SRR6001749SRR6001750	GSE103421	GSM2771000	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling 8 hr after shift to 10°C in ∆cspABEG cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	MOPS medium	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	MOPS rich medium	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003160
SRR6001751	GSE103421	GSM2771001	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling at 37°C in WT cells_2	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	MOPS medium	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	MOPS rich medium	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003160
SRR6001752	GSE103421	GSM2771002	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling at 37°C in ∆cspABCEG cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	MOPS medium	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	MOPS rich medium	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003160
SRR6001758	GSE103421	GSM2771008	GPL10328-GPL14548-GPL15010-GPL17439	29628307	mRNA-seq 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	MOPS medium	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	MOPS rich medium	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003160
SRR6001760SRR6001761	GSE103421	GSM2771010	GPL10328-GPL14548-GPL15010-GPL17439	29628307	mRNA-seq 8 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	MOPS medium	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	MOPS rich medium	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003160
SRR6001762SRR6001763	GSE103421	GSM2771011	GPL10328-GPL14548-GPL15010-GPL17439	29628307	mRNA-seq 8 hr after shift to 10°C in ∆cspABEG cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	MOPS medium	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	MOPS rich medium	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003160
SRR6001766	GSE103421	GSM2771014	GPL10328-GPL14548-GPL15010-GPL17439	29628307	DMS-seq 30 min after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	MOPS medium	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	MOPS rich medium	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003160
SRR6001769	GSE103421	GSM2771015	GPL10328-GPL14548-GPL15010-GPL17439	29628307	DMS-seq 6 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	MOPS medium	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	MOPS rich medium	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003160
SRR6001772	GSE103421	GSM2771016	GPL10328-GPL14548-GPL15010-GPL17439	29628307	DMS-seq 8 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	MOPS medium	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	MOPS rich medium	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003160
SRR6001773	GSE103421	GSM2771017	GPL10328-GPL14548-GPL15010-GPL17439	29628307	DMS-seq 8 hr after shift to 10°C in ∆cspABEG cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	MOPS medium	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	MOPS rich medium	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003160
SRR6001774	GSE103421	GSM2771018	GPL10328-GPL14548-GPL15010-GPL17439	29628307	DMS-seq 8 hr after shift to 10°C in ∆cspBG cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	MOPS medium	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	MOPS rich medium	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003160
SRR6001775	GSE103421	GSM2771019	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq 20 min after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	MOPS medium	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	MOPS rich medium	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003160
SRR6001776	GSE103421	GSM2771020	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	MOPS medium	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	MOPS rich medium	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003160
SRR6001777	GSE103421	GSM2771021	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq 8 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	MOPS medium	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	MOPS rich medium	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003160
SRR6001778	GSE103421	GSM2771022	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq 20 min after shift to 10°C in ∆rnr cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	MOPS medium	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	MOPS rich medium	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003160
SRR6001779	GSE103421	GSM2771023	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq 4 hr after shift to 10°C in ∆rnr cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	MOPS medium	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	MOPS rich medium	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003160
SRR6001780	GSE103421	GSM2771024	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq 8 hr after shift to 10°C in ∆rnr cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	MOPS medium	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	MOPS rich medium	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003160
SRR6001781	GSE103421	GSM2771025	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq before rifampicin treatment -- 2 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	MOPS medium	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	MOPS rich medium	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003160
SRR6001782	GSE103421	GSM2771026	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq after rifampicin treatment -- 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	MOPS medium	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	MOPS rich medium	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003160
SRR6001783	GSE103421	GSM2771027	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq before rifampicin treatment -- 2 hr after shift to 10°C in ∆rnr cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	MOPS medium	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	MOPS rich medium	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003160
SRR6001784	GSE103421	GSM2771028	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq after rifampicin treatment -- 4 hr after shift to 10°C in ∆rnr cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	MOPS medium	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	MOPS rich medium	100	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003160
SRR6001737	GSE103421	GSM2770989	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling at 37°C in WT cells_1	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR6001739	GSE103421	GSM2770991	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling 30 min after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR6001742	GSE103421	GSM2770994	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR6001743	GSE103421	GSM2770995	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling 6 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR6001744	GSE103421	GSM2770996	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling 5 min after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR6001745	GSE103421	GSM2770997	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling 10 min after shift to 10°C in WT cells_2	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR6001746	GSE103421	GSM2770998	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling 15 min after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR6001747SRR6001748	GSE103421	GSM2770999	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling 8 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR6001749SRR6001750	GSE103421	GSM2771000	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling 8 hr after shift to 10°C in ∆cspABEG cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR6001751	GSE103421	GSM2771001	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling at 37°C in WT cells_2	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR6001752	GSE103421	GSM2771002	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling at 37°C in ∆cspABCEG cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR6001758	GSE103421	GSM2771008	GPL10328-GPL14548-GPL15010-GPL17439	29628307	mRNA-seq 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR6001760SRR6001761	GSE103421	GSM2771010	GPL10328-GPL14548-GPL15010-GPL17439	29628307	mRNA-seq 8 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR6001762SRR6001763	GSE103421	GSM2771011	GPL10328-GPL14548-GPL15010-GPL17439	29628307	mRNA-seq 8 hr after shift to 10°C in ∆cspABEG cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR6001766	GSE103421	GSM2771014	GPL10328-GPL14548-GPL15010-GPL17439	29628307	DMS-seq 30 min after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR6001769	GSE103421	GSM2771015	GPL10328-GPL14548-GPL15010-GPL17439	29628307	DMS-seq 6 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR6001772	GSE103421	GSM2771016	GPL10328-GPL14548-GPL15010-GPL17439	29628307	DMS-seq 8 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR6001773	GSE103421	GSM2771017	GPL10328-GPL14548-GPL15010-GPL17439	29628307	DMS-seq 8 hr after shift to 10°C in ∆cspABEG cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR6001774	GSE103421	GSM2771018	GPL10328-GPL14548-GPL15010-GPL17439	29628307	DMS-seq 8 hr after shift to 10°C in ∆cspBG cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR6001775	GSE103421	GSM2771019	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq 20 min after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR6001776	GSE103421	GSM2771020	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR6001777	GSE103421	GSM2771021	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq 8 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR6001778	GSE103421	GSM2771022	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq 20 min after shift to 10°C in ∆rnr cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR6001779	GSE103421	GSM2771023	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq 4 hr after shift to 10°C in ∆rnr cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR6001780	GSE103421	GSM2771024	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq 8 hr after shift to 10°C in ∆rnr cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR6001781	GSE103421	GSM2771025	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq before rifampicin treatment -- 2 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR6001782	GSE103421	GSM2771026	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq after rifampicin treatment -- 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR6001783	GSE103421	GSM2771027	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq before rifampicin treatment -- 2 hr after shift to 10°C in ∆rnr cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR6001784	GSE103421	GSM2771028	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq after rifampicin treatment -- 4 hr after shift to 10°C in ∆rnr cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR8164484	GSE122211	GSM3461164	GPL17024-GPL17439-GPL18995-GPL25769	31797920	MG_glu_1	Expression profiling of E. coli K-12 MG1655	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)	characteristics	media: M9 minimal media w/ 0.2% glucose and 10mM glutamate PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 0.2 % glucose </Supp> and 10mM glutamate 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR8164485	GSE122211	GSM3461165	GPL17024-GPL17439-GPL18995-GPL25769	31797920	MG_glu_2	Expression profiling of E. coli K-12 MG1655	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)	characteristics	media: M9 minimal media w/ 0.2% glucose and 10mM glutamate PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 0.2 % glucose </Supp> and 10mM glutamate 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR8164486	GSE122211	GSM3461166	GPL17024-GPL17439-GPL18995-GPL25769	31797920	MG_glc	Expression profiling of E. coli K-12 MG1655	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)	characteristics	media: M9 minimal media w/ 0.2% glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 0.2 % glucose </Supp> 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR847728	GSE46737	GSM1137316	GPL17137	24461193	E. coli stationary 1	Genome-scale reconstruction of the sigma factor network in E. coli	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE46737/GSE46737.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR847730	GSE46737	GSM1137318	GPL17137	24461193	E. coli glutamine 1	Genome-scale reconstruction of the sigma factor network in E. coli	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE46737/GSE46737.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR847730	GSE46737	GSM1137318	GPL17137	24461193	E. coli glutamine 1	Genome-scale reconstruction of the sigma factor network in E. coli	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	source_name	Cells at mid-log phase (OD600nm 0.5) in W2 media supplemented with 0.2% glucose and 0.2% glutamine PGCGROWTHCONDITIONS	Cells at mid-log phase ( OD600nm 0.5 ) in W2 media supplemented with <Supp> 0.2 % glucose </Supp> and <Supp> 0.2 % glutamine </Supp> 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE46737/GSE46737.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR847731	GSE46737	GSM1137319	GPL17137	24461193	E. coli glutamine 2	Genome-scale reconstruction of the sigma factor network in E. coli	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE46737/GSE46737.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR847731	GSE46737	GSM1137319	GPL17137	24461193	E. coli glutamine 2	Genome-scale reconstruction of the sigma factor network in E. coli	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	source_name	Cells at mid-log phase (OD600nm 0.5) in W2 media supplemented with 0.2% glucose and 0.2% glutamine PGCGROWTHCONDITIONS	Cells at mid-log phase ( OD600nm 0.5 ) in W2 media supplemented with <Supp> 0.2 % glucose </Supp> and <Supp> 0.2 % glutamine </Supp> 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE46737/GSE46737.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR847732	GSE46737	GSM1137320	GPL17137	24461193	E. coli heatshock 1	Genome-scale reconstruction of the sigma factor network in E. coli	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE46737/GSE46737.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR847733	GSE46737	GSM1137321	GPL17137	24461193	E. coli heatshock 2	Genome-scale reconstruction of the sigma factor network in E. coli	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE46737/GSE46737.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR1067773SRR1067774	GSE53767	GSM1300282	GPL14548-GPL18133	24766808	mRNA-seq in rich defined media	Absolute quantification of protein production reveals principles underlying protein synthesis rates	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE53767/GSE53767.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR1168133	GSE54900	GSM1326347	GPL17439	25222563	WT with Fe 1 (RNA-seq)	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR1168134	GSE54900	GSM1326348	GPL17439	25222563	WT with Fe 2 (RNA-seq)	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR1168135	GSE54900	GSM1326349	GPL17439	25222563	WT with DPD 1 (RNA-seq)	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR1168136	GSE54900	GSM1326350	GPL17439	25222563	WT with DPD 2 (RNA-seq)	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR1168137	GSE54900	GSM1326351	GPL17439	25222563	Δfur with Fe 1 (RNA-seq)	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR1168138	GSE54900	GSM1326352	GPL17439	25222563	Δfur with Fe 2 (RNA-seq)	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR1168139	GSE54900	GSM1326353	GPL17439	25222563	Δfur with DPD 1 (RNA-seq)	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR1168140	GSE54900	GSM1326354	GPL17439	25222563	Δfur with DPD 2 (RNA-seq)	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR1411272	GSE58556	GSM1413874	GPL18814	25483350	WT_glucose_log	RNA sequencing based analysis of the bacterial transcriptome	GPL18814: Illumina HiSeq 2000 (Escherichia coli BW38028)	growth_protocol	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	<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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE58556/GSE58556.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR1787590	GSE65642	GSM1602347	GPL16085	29394395	WT glucose 1	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR1787591	GSE65642	GSM1602348	GPL16085	29394395	WT glucose 2	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR1787592	GSE65642	GSM1602349	GPL16085	29394395	WT fructose 1	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR1787593	GSE65642	GSM1602350	GPL16085	29394395	WT fructose 2	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR1787594	GSE65642	GSM1602351	GPL16085	29394395	WT acetate 1	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR1787595	GSE65642	GSM1602352	GPL16085	29394395	WT acetate 2	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR1787596	GSE65642	GSM1602353	GPL16085	29394395	Δcra glucose 1	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR1787597	GSE65642	GSM1602354	GPL16085	29394395	Δcra glucose 2	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR1787598	GSE65642	GSM1602355	GPL16085	29394395	Δcra fructose 1	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR1787599	GSE65642	GSM1602356	GPL16085	29394395	Δcra fructose 2	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR1787600	GSE65642	GSM1602357	GPL16085	29394395	Δcra acetate 1	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR1787601	GSE65642	GSM1602358	GPL16085	29394395	Δcra acetate 2	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR1796598	GSE65711	GSM1603386	GPL16085	26279566	WT PQ 1	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR1796599	GSE65711	GSM1603387	GPL16085	26279566	WT PQ 2	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR1796600	GSE65711	GSM1603388	GPL16085	26279566	ΔoxyR PQ 1	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR1796601	GSE65711	GSM1603389	GPL16085	26279566	ΔoxyR PQ 2	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR1796603	GSE65711	GSM1603391	GPL16085	26279566	ΔsoxR PQ 2	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR1796604	GSE65711	GSM1603392	GPL16085	26279566	ΔsoxS PQ 1	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR1796605	GSE65711	GSM1603393	GPL16085	26279566	ΔsoxS PQ 2	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR1824557	GSE66481	GSM1623160	GPL16085	26258987	WT pH5.5 1	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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> . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR1824558	GSE66481	GSM1623161	GPL16085	26258987	WT pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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> . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR1824559	GSE66481	GSM1623162	GPL16085	26258987	ΔgadE pH5.5 1	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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> . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR1824560	GSE66481	GSM1623163	GPL16085	26258987	ΔgadE pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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> . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR1824561	GSE66481	GSM1623164	GPL16085	26258987	ΔgadW pH5.5 1	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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> . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR1824562	GSE66481	GSM1623165	GPL16085	26258987	ΔgadW pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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> . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR1824563	GSE66481	GSM1623166	GPL16085	26258987	ΔgadX pH5.5 1	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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> . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR1824564	GSE66481	GSM1623167	GPL16085	26258987	ΔgadX pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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> . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR5186139	GSE77617	GSM2462936	GPL14548-GPL21433	28139975	mRNA-seq 37°C in WT with control plasmid	Operon mRNAs are organized into ORF-centric structures that predict translation efficiency	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21433: Illumina HiSeq 4000 (Escherichia coli)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE77617/GSE77617.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR5186140	GSE77617	GSM2462937	GPL14548-GPL21433	28139975	mRNA-seq 37°C in WT with plasmid expressing mini-ORF CUA	Operon mRNAs are organized into ORF-centric structures that predict translation efficiency	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21433: Illumina HiSeq 4000 (Escherichia coli)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE77617/GSE77617.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR5186141	GSE77617	GSM2462938	GPL14548-GPL21433	28139975	mRNA-seq 37°C in WT with plasmid expressing mini-ORF CUG	Operon mRNAs are organized into ORF-centric structures that predict translation efficiency	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21433: Illumina HiSeq 4000 (Escherichia coli)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE77617/GSE77617.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR4435464	GSE88980	GSM2356687	GPL17439	28526842	WT NaCl 1	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]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88980/GSE88980.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR4435465	GSE88980	GSM2356688	GPL17439	28526842	WT NaCl 2	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]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88980/GSE88980.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR4435466	GSE88980	GSM2356689	GPL17439	28526842	ΔompR NaCl 1	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]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88980/GSE88980.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR4435467	GSE88980	GSM2356690	GPL17439	28526842	ΔompR NaCl 2	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]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88980/GSE88980.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR5121109	GSE92601	GSM2433290	GPL18956	29807996	ORF1_1_IPTG	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR5121110	GSE92601	GSM2433291	GPL18956	29807996	ORF1_1	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR5121111	GSE92601	GSM2433292	GPL18956	29807996	ORF1_2_IPTG	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR5121112	GSE92601	GSM2433293	GPL18956	29807996	ORF1_2	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR5121113	GSE92601	GSM2433294	GPL18956	29807996	Svi3_3_1_IPTG	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR5121114	GSE92601	GSM2433295	GPL18956	29807996	Svi3_3_1	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR5121115	GSE92601	GSM2433296	GPL18956	29807996	Svi3_3_2_IPTG	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR5121116	GSE92601	GSM2433297	GPL18956	29807996	Svi3_3_2	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR5121117	GSE92601	GSM2433298	GPL18956	29807996	WT1_IPTG	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR5121118	GSE92601	GSM2433299	GPL18956	29807996	WT2_IPTG	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	0.2 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	glucose 0.2%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002770
SRR6001737	GSE103421	GSM2770989	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling at 37°C in WT cells_1	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001737	GSE103421	GSM2770989	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling at 37°C in WT cells_1	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	treatment_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001737	GSE103421	GSM2770989	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling at 37°C in WT cells_1	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	characteristics	temperature: 37°C PGCGROWTHCONDITIONS	temperature : <Temp> 37 °C </Temp> 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001739	GSE103421	GSM2770991	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling 30 min after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001739	GSE103421	GSM2770991	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling 30 min after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	treatment_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001742	GSE103421	GSM2770994	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001742	GSE103421	GSM2770994	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	treatment_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001743	GSE103421	GSM2770995	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling 6 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001743	GSE103421	GSM2770995	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling 6 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	treatment_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001744	GSE103421	GSM2770996	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling 5 min after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001744	GSE103421	GSM2770996	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling 5 min after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	treatment_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001745	GSE103421	GSM2770997	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling 10 min after shift to 10°C in WT cells_2	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001745	GSE103421	GSM2770997	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling 10 min after shift to 10°C in WT cells_2	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	treatment_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001746	GSE103421	GSM2770998	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling 15 min after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001746	GSE103421	GSM2770998	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling 15 min after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	treatment_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001747SRR6001748	GSE103421	GSM2770999	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling 8 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001747SRR6001748	GSE103421	GSM2770999	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling 8 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	treatment_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001749SRR6001750	GSE103421	GSM2771000	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling 8 hr after shift to 10°C in ∆cspABEG cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001749SRR6001750	GSE103421	GSM2771000	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling 8 hr after shift to 10°C in ∆cspABEG cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	treatment_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001751	GSE103421	GSM2771001	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling at 37°C in WT cells_2	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001751	GSE103421	GSM2771001	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling at 37°C in WT cells_2	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	treatment_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001751	GSE103421	GSM2771001	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling at 37°C in WT cells_2	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	characteristics	temperature: 37°C PGCGROWTHCONDITIONS	temperature : <Temp> 37 °C </Temp> 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001752	GSE103421	GSM2771002	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling at 37°C in ∆cspABCEG cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001752	GSE103421	GSM2771002	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling at 37°C in ∆cspABCEG cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	treatment_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001752	GSE103421	GSM2771002	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Ribosome profiling at 37°C in ∆cspABCEG cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	characteristics	temperature: 37°C PGCGROWTHCONDITIONS	temperature : <Temp> 37 °C </Temp> 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001758	GSE103421	GSM2771008	GPL10328-GPL14548-GPL15010-GPL17439	29628307	mRNA-seq 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001758	GSE103421	GSM2771008	GPL10328-GPL14548-GPL15010-GPL17439	29628307	mRNA-seq 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	treatment_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001760SRR6001761	GSE103421	GSM2771010	GPL10328-GPL14548-GPL15010-GPL17439	29628307	mRNA-seq 8 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001760SRR6001761	GSE103421	GSM2771010	GPL10328-GPL14548-GPL15010-GPL17439	29628307	mRNA-seq 8 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	treatment_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001762SRR6001763	GSE103421	GSM2771011	GPL10328-GPL14548-GPL15010-GPL17439	29628307	mRNA-seq 8 hr after shift to 10°C in ∆cspABEG cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001762SRR6001763	GSE103421	GSM2771011	GPL10328-GPL14548-GPL15010-GPL17439	29628307	mRNA-seq 8 hr after shift to 10°C in ∆cspABEG cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	treatment_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001766	GSE103421	GSM2771014	GPL10328-GPL14548-GPL15010-GPL17439	29628307	DMS-seq 30 min after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001766	GSE103421	GSM2771014	GPL10328-GPL14548-GPL15010-GPL17439	29628307	DMS-seq 30 min after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	treatment_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001769	GSE103421	GSM2771015	GPL10328-GPL14548-GPL15010-GPL17439	29628307	DMS-seq 6 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001769	GSE103421	GSM2771015	GPL10328-GPL14548-GPL15010-GPL17439	29628307	DMS-seq 6 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	treatment_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001772	GSE103421	GSM2771016	GPL10328-GPL14548-GPL15010-GPL17439	29628307	DMS-seq 8 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001772	GSE103421	GSM2771016	GPL10328-GPL14548-GPL15010-GPL17439	29628307	DMS-seq 8 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	treatment_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001773	GSE103421	GSM2771017	GPL10328-GPL14548-GPL15010-GPL17439	29628307	DMS-seq 8 hr after shift to 10°C in ∆cspABEG cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001773	GSE103421	GSM2771017	GPL10328-GPL14548-GPL15010-GPL17439	29628307	DMS-seq 8 hr after shift to 10°C in ∆cspABEG cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	treatment_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001774	GSE103421	GSM2771018	GPL10328-GPL14548-GPL15010-GPL17439	29628307	DMS-seq 8 hr after shift to 10°C in ∆cspBG cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001774	GSE103421	GSM2771018	GPL10328-GPL14548-GPL15010-GPL17439	29628307	DMS-seq 8 hr after shift to 10°C in ∆cspBG cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	treatment_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001775	GSE103421	GSM2771019	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq 20 min after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001775	GSE103421	GSM2771019	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq 20 min after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	treatment_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001776	GSE103421	GSM2771020	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001776	GSE103421	GSM2771020	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	treatment_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001777	GSE103421	GSM2771021	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq 8 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001777	GSE103421	GSM2771021	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq 8 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	treatment_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001778	GSE103421	GSM2771022	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq 20 min after shift to 10°C in ∆rnr cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001778	GSE103421	GSM2771022	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq 20 min after shift to 10°C in ∆rnr cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	treatment_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001779	GSE103421	GSM2771023	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq 4 hr after shift to 10°C in ∆rnr cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001779	GSE103421	GSM2771023	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq 4 hr after shift to 10°C in ∆rnr cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	treatment_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001780	GSE103421	GSM2771024	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq 8 hr after shift to 10°C in ∆rnr cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001780	GSE103421	GSM2771024	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq 8 hr after shift to 10°C in ∆rnr cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	treatment_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001781	GSE103421	GSM2771025	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq before rifampicin treatment -- 2 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001781	GSE103421	GSM2771025	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq before rifampicin treatment -- 2 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	treatment_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001782	GSE103421	GSM2771026	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq after rifampicin treatment -- 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001782	GSE103421	GSM2771026	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq after rifampicin treatment -- 4 hr after shift to 10°C in WT cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	treatment_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001783	GSE103421	GSM2771027	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq before rifampicin treatment -- 2 hr after shift to 10°C in ∆rnr cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001783	GSE103421	GSM2771027	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq before rifampicin treatment -- 2 hr after shift to 10°C in ∆rnr cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	treatment_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001784	GSE103421	GSM2771028	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq after rifampicin treatment -- 4 hr after shift to 10°C in ∆rnr cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6001784	GSE103421	GSM2771028	GPL10328-GPL14548-GPL15010-GPL17439	29628307	Total RNA-seq after rifampicin treatment -- 4 hr after shift to 10°C in ∆rnr cells	A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation	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)	treatment_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103421/GSE103421.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6305247	GSE107093	GSM2861128	GPL18133	29578536	R2 DH10BGFP_pLys_M1_1	Burden- driven feedback control of gene expression	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6305248	GSE107093	GSM2861129	GPL18133	29578536	R3 DH10BGFP_pSB1C3_1	Burden- driven feedback control of gene expression	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6305251	GSE107093	GSM2861132	GPL18133	29578536	R6 DH10BGFP_pD864_LacZ_1	Burden- driven feedback control of gene expression	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6305256	GSE107093	GSM2861137	GPL18133	29578536	R11 DH10BGFP_pLys_1	Burden- driven feedback control of gene expression	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6305261	GSE107093	GSM2861142	GPL18133	29578536	R16 MG1655GFP_pLys_M1_1	Burden- driven feedback control of gene expression	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6305264	GSE107093	GSM2861145	GPL18133	29578536	R19 MG1655GFP_Lux_1	Burden- driven feedback control of gene expression	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6305271	GSE107093	GSM2861152	GPL18133	29578536	R26 MG1655GFP_Lux_1	Burden- driven feedback control of gene expression	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6305272	GSE107093	GSM2861153	GPL18133	29578536	R27 MG1655GFP_pD864_LacZ_1	Burden- driven feedback control of gene expression	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6305274	GSE107093	GSM2861155	GPL18133	29578536	R29 DH10BGFP_None_1	Burden- driven feedback control of gene expression	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6305278	GSE107093	GSM2861159	GPL18133	29578536	B3 DH10BGFP_pSB1C3_2	Burden- driven feedback control of gene expression	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6305279	GSE107093	GSM2861160	GPL18133	29578536	B4 DH10BGFP_pLys_2	Burden- driven feedback control of gene expression	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6305282	GSE107093	GSM2861163	GPL18133	29578536	B7 DH10BGFP_pD864_2	Burden- driven feedback control of gene expression	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6305284	GSE107093	GSM2861165	GPL18133	29578536	B9 DH10BGFP_pLys_M1_2	Burden- driven feedback control of gene expression	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6305285	GSE107093	GSM2861166	GPL18133	29578536	B10 DH10BGFP_pSB1C3_2	Burden- driven feedback control of gene expression	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6305292	GSE107093	GSM2861173	GPL18133	29578536	B17 MG1655GFP_pSB1C3_2	Burden- driven feedback control of gene expression	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6305297	GSE107093	GSM2861178	GPL18133	29578536	B22 MG1655GFP_pSB1C3_H3_2	Burden- driven feedback control of gene expression	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6305301	GSE107093	GSM2861182	GPL18133	29578536	B26 MG1655GFP_Lux_2	Burden- driven feedback control of gene expression	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6305310	GSE107093	GSM2861191	GPL18133	29578536	G5 DH10BGFP_Lux_3	Burden- driven feedback control of gene expression	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6305311	GSE107093	GSM2861192	GPL18133	29578536	G6 DH10BGFP_pD864_LacZ_3	Burden- driven feedback control of gene expression	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6305326	GSE107093	GSM2861207	GPL18133	29578536	G21 MG1655GFP_pD864_3	Burden- driven feedback control of gene expression	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6305328	GSE107093	GSM2861209	GPL18133	29578536	G23 MG1655GFP_pLys_M1_3	Burden- driven feedback control of gene expression	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6305333	GSE107093	GSM2861214	GPL18133	29578536	G28 MG1655GFP_pD864_3	Burden- driven feedback control of gene expression	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6305334	GSE107093	GSM2861215	GPL18133	29578536	G29 DH10BGFP_None_3	Burden- driven feedback control of gene expression	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107093/GSE107093.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6354578	GSE107301	GSM2870440	GPL15010-GPL21117	29358050	RNA-seq of E. coli wt cells in stationary phase 30°C (30h)	Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21117: Illumina NextSeq 500 (Escherichia coli str. K-12 substr. MG1655)	extract_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107301/GSE107301.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6354578	GSE107301	GSM2870440	GPL15010-GPL21117	29358050	RNA-seq of E. coli wt cells in stationary phase 30°C (30h)	Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21117: Illumina NextSeq 500 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107301/GSE107301.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6354579	GSE107301	GSM2870441	GPL15010-GPL21117	29358050	RNA-seq of E. coli wt cells in stationary phase 30°C (30h) -Replicate 1	Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21117: Illumina NextSeq 500 (Escherichia coli str. K-12 substr. MG1655)	extract_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107301/GSE107301.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6354579	GSE107301	GSM2870441	GPL15010-GPL21117	29358050	RNA-seq of E. coli wt cells in stationary phase 30°C (30h) -Replicate 1	Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21117: Illumina NextSeq 500 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107301/GSE107301.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6322033	GSE107327	GSM2864853	GPL21222	29861158	emptyvec_mRNA_5m_rep1	E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis [RNA-seq]	GPL21222: Illumina NextSeq 500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107327/GSE107327.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6322034	GSE107327	GSM2864854	GPL21222	29861158	emptyvec_mRNA_5m_rep2	E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis [RNA-seq]	GPL21222: Illumina NextSeq 500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107327/GSE107327.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6322035	GSE107327	GSM2864855	GPL21222	29861158	MazF_mRNA_5m_rep1	E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis [RNA-seq]	GPL21222: Illumina NextSeq 500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107327/GSE107327.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6322036	GSE107327	GSM2864856	GPL21222	29861158	MazF_mRNA_5m_rep2	E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis [RNA-seq]	GPL21222: Illumina NextSeq 500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107327/GSE107327.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6449107	GSE108846	GSM2914313	GPL16085	29378945	CF104.3.3_y2	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6449107	GSE108846	GSM2914313	GPL16085	29378945	CF104.3.3_y2	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6449109	GSE108846	GSM2914315	GPL16085	29378945	CF108.4B_y3	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6449109	GSE108846	GSM2914315	GPL16085	29378945	CF108.4B_y3	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6449111	GSE108846	GSM2914317	GPL16085	29378945	CON206.3A_y1	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6449111	GSE108846	GSM2914317	GPL16085	29378945	CON206.3A_y1	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6449112	GSE108846	GSM2914318	GPL16085	29378945	CON206.3A_y2	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6449112	GSE108846	GSM2914318	GPL16085	29378945	CON206.3A_y2	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6449113	GSE108846	GSM2914319	GPL16085	29378945	CON208.3A_y2	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6449113	GSE108846	GSM2914319	GPL16085	29378945	CON208.3A_y2	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6449114	GSE108846	GSM2914320	GPL16085	29378945	CON208.3A_y6	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6449114	GSE108846	GSM2914320	GPL16085	29378945	CON208.3A_y6	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6449115	GSE108846	GSM2914321	GPL16085	29378945	CF104.3.3_u1	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6449115	GSE108846	GSM2914321	GPL16085	29378945	CF104.3.3_u1	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6449116	GSE108846	GSM2914322	GPL16085	29378945	CF104.3.3_u7	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6449116	GSE108846	GSM2914322	GPL16085	29378945	CF104.3.3_u7	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6449117	GSE108846	GSM2914323	GPL16085	29378945	CF108.4B_u1	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6449117	GSE108846	GSM2914323	GPL16085	29378945	CF108.4B_u1	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6449118	GSE108846	GSM2914324	GPL16085	29378945	CF108.4B_u2	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6449118	GSE108846	GSM2914324	GPL16085	29378945	CF108.4B_u2	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6449119	GSE108846	GSM2914325	GPL16085	29378945	CON206.3A_u1	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6449119	GSE108846	GSM2914325	GPL16085	29378945	CON206.3A_u1	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6449120	GSE108846	GSM2914326	GPL16085	29378945	CON206.3A_u2	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6449120	GSE108846	GSM2914326	GPL16085	29378945	CON206.3A_u2	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6449121	GSE108846	GSM2914327	GPL16085	29378945	CON208.3A_u1	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6449121	GSE108846	GSM2914327	GPL16085	29378945	CON208.3A_u1	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6449122	GSE108846	GSM2914328	GPL16085	29378945	CON208.3A_u8	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6449122	GSE108846	GSM2914328	GPL16085	29378945	CON208.3A_u8	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR7217923	GSE114917	GSM3154484	GPL17439	30016375	HP1	Genetic response of E.coli to mild elevated pressure	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE114917/GSE114917.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR7217924	GSE114917	GSM3154485	GPL17439	30016375	HP2	Genetic response of E.coli to mild elevated pressure	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE114917/GSE114917.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR7217925	GSE114917	GSM3154486	GPL17439	30016375	HP3	Genetic response of E.coli to mild elevated pressure	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE114917/GSE114917.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR7217926	GSE114917	GSM3154487	GPL17439	30016375	HP4	Genetic response of E.coli to mild elevated pressure	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE114917/GSE114917.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR7217927	GSE114917	GSM3154488	GPL17439	30016375	LP1	Genetic response of E.coli to mild elevated pressure	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE114917/GSE114917.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR7217928	GSE114917	GSM3154489	GPL17439	30016375	LP2	Genetic response of E.coli to mild elevated pressure	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE114917/GSE114917.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR7217929	GSE114917	GSM3154490	GPL17439	30016375	LP3	Genetic response of E.coli to mild elevated pressure	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE114917/GSE114917.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR7217930	GSE114917	GSM3154491	GPL17439	30016375	LP4	Genetic response of E.coli to mild elevated pressure	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE114917/GSE114917.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR7537397	GSE117326	GSM3291044	GPL25346		envz600	Gene expression profiles in E. coli under different frequency signals	GPL25346: HiSeq X Ten (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117326/GSE117326.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR7537398	GSE117326	GSM3291045	GPL25346		envz900	Gene expression profiles in E. coli under different frequency signals	GPL25346: HiSeq X Ten (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117326/GSE117326.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR7537402	GSE117326	GSM3291049	GPL25346		envz3600	Gene expression profiles in E. coli under different frequency signals	GPL25346: HiSeq X Ten (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117326/GSE117326.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR7537403	GSE117326	GSM3291050	GPL25346		envzM600	Gene expression profiles in E. coli under different frequency signals	GPL25346: HiSeq X Ten (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117326/GSE117326.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR7537404	GSE117326	GSM3291051	GPL25346		envzM900	Gene expression profiles in E. coli under different frequency signals	GPL25346: HiSeq X Ten (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117326/GSE117326.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR7537405	GSE117326	GSM3291052	GPL25346		envzM1200	Gene expression profiles in E. coli under different frequency signals	GPL25346: HiSeq X Ten (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117326/GSE117326.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR7537407	GSE117326	GSM3291054	GPL25346		envzM2400	Gene expression profiles in E. coli under different frequency signals	GPL25346: HiSeq X Ten (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117326/GSE117326.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR7537408	GSE117326	GSM3291055	GPL25346		envzM3600	Gene expression profiles in E. coli under different frequency signals	GPL25346: HiSeq X Ten (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117326/GSE117326.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8449235	GSE117737	GSM3566393	GPL16085-GPL21222	31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 4	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8449235	GSE117737	GSM3566393	GPL16085-GPL21222	31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 4	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8449235	GSE117737	GSM3566393	GPL16085-GPL21222	31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 4	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	treatment_protocol	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	<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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8449235	GSE117737	GSM3566393	GPL16085-GPL21222	31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 4	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	characteristics	treatment: 37°C culture PGCGROWTHCONDITIONS	treatment : <Temp> 37 °C </Temp> culture 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8449236	GSE117737	GSM3566394	GPL16085-GPL21222	31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 5	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8449236	GSE117737	GSM3566394	GPL16085-GPL21222	31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 5	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8449236	GSE117737	GSM3566394	GPL16085-GPL21222	31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 5	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	treatment_protocol	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	<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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8449236	GSE117737	GSM3566394	GPL16085-GPL21222	31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 5	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	characteristics	treatment: 37°C culture PGCGROWTHCONDITIONS	treatment : <Temp> 37 °C </Temp> culture 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8449237	GSE117737	GSM3566395	GPL16085-GPL21222	31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 6	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8449237	GSE117737	GSM3566395	GPL16085-GPL21222	31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 6	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8449237	GSE117737	GSM3566395	GPL16085-GPL21222	31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 6	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	treatment_protocol	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	<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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8449237	GSE117737	GSM3566395	GPL16085-GPL21222	31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 6	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	characteristics	treatment: 37°C culture PGCGROWTHCONDITIONS	treatment : <Temp> 37 °C </Temp> culture 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8449238	GSE117737	GSM3566396	GPL16085-GPL21222	31308523	RNA-seq WT log phase related to total SEnd-seq WT stationary phase rep4	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8449238	GSE117737	GSM3566396	GPL16085-GPL21222	31308523	RNA-seq WT log phase related to total SEnd-seq WT stationary phase rep4	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8449238	GSE117737	GSM3566396	GPL16085-GPL21222	31308523	RNA-seq WT log phase related to total SEnd-seq WT stationary phase rep4	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	treatment_protocol	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	<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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8449238	GSE117737	GSM3566396	GPL16085-GPL21222	31308523	RNA-seq WT log phase related to total SEnd-seq WT stationary phase rep4	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	characteristics	treatment: 37°C culture PGCGROWTHCONDITIONS	treatment : <Temp> 37 °C </Temp> culture 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8164476	GSE122211	GSM3461156	GPL17024-GPL17439-GPL18995-GPL25769	31797920	MG_no_te_1	Expression profiling of E. coli K-12 MG1655	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)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8164477	GSE122211	GSM3461157	GPL17024-GPL17439-GPL18995-GPL25769	31797920	MG_no_te_2	Expression profiling of E. coli K-12 MG1655	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)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8164484	GSE122211	GSM3461164	GPL17024-GPL17439-GPL18995-GPL25769	31797920	MG_glu_1	Expression profiling of E. coli K-12 MG1655	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)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8164485	GSE122211	GSM3461165	GPL17024-GPL17439-GPL18995-GPL25769	31797920	MG_glu_2	Expression profiling of E. coli K-12 MG1655	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)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8164486	GSE122211	GSM3461166	GPL17024-GPL17439-GPL18995-GPL25769	31797920	MG_glc	Expression profiling of E. coli K-12 MG1655	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)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8173227	GSE122295	GSM3463565	GPL21433	31797920	wt_glc__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8173228	GSE122295	GSM3463566	GPL21433	31797920	wt_glc__2	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8173229	GSE122295	GSM3463567	GPL21433	31797920	wt_glc__3	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8173230	GSE122295	GSM3463568	GPL21433	31797920	wt_glc__4	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8173231	GSE122295	GSM3463569	GPL21433	31797920	arg_sbt__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8173232	GSE122295	GSM3463570	GPL21433	31797920	arg_sbt__2	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8173233	GSE122295	GSM3463571	GPL21433	31797920	cytd_rib__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8173234	GSE122295	GSM3463572	GPL21433	31797920	cytd_rib__2	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8173235	GSE122295	GSM3463573	GPL21433	31797920	gth__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8173236	GSE122295	GSM3463574	GPL21433	31797920	gth__2	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8173237	GSE122295	GSM3463575	GPL21433	31797920	leu_glcr__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8173238	GSE122295	GSM3463576	GPL21433	31797920	leu_glcr__2	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8173239	GSE122295	GSM3463577	GPL21433	31797920	met_glc__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8173240	GSE122295	GSM3463578	GPL21433	31797920	met_glc__2	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8173241	GSE122295	GSM3463579	GPL21433	31797920	no3_anaero__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8173242	GSE122295	GSM3463580	GPL21433	31797920	no3_anaero__2	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8173243	GSE122295	GSM3463581	GPL21433	31797920	phe_acgam__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8173244	GSE122295	GSM3463582	GPL21433	31797920	phe_acgam__2	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8173245	GSE122295	GSM3463583	GPL21433	31797920	thm_gal__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8173246	GSE122295	GSM3463584	GPL21433	31797920	thm_gal__2	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8173247	GSE122295	GSM3463585	GPL21433	31797920	tyr_glcn__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8173248	GSE122295	GSM3463586	GPL21433	31797920	tyr_glcn__2	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8173249	GSE122295	GSM3463587	GPL21433	31797920	ura_pyr__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8173250	GSE122295	GSM3463588	GPL21433	31797920	ura_pyr__2	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR9204648	GSE122295	GSM3854833	GPL21433	31797920	wt_glc_5__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR9204649	GSE122295	GSM3854834	GPL21433	31797920	wt_glc_6__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR9204650	GSE122295	GSM3854835	GPL21433	31797920	bw_delpurR_cytd__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR9204651	GSE122295	GSM3854836	GPL21433	31797920	bw_delpurR_cytd__2	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR9204652	GSE122295	GSM3854837	GPL21433	31797920	ade_glc__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR9204653	GSE122295	GSM3854838	GPL21433	31797920	ade_glc__2	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8173221	GSE122296	GSM3463601	GPL16085	31797920	MG1655_1	Expression profiling of multiple Escherichia coli strains on glucose minimal media	GPL16085: Illumina MiSeq (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122296/GSE122296.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8173222	GSE122296	GSM3463602	GPL16085	31797920	MG1655_2	Expression profiling of multiple Escherichia coli strains on glucose minimal media	GPL16085: Illumina MiSeq (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122296/GSE122296.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8309841	GSE123554	GSM3507068	GPL18133		delta-fis rep1	Reconstruction of transcriptional regulatory networks of Fis and H-NS in Escherichia coli from genome wide data analysis	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE123554/GSE123554.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8309842	GSE123554	GSM3507069	GPL18133		delta-fis rep2	Reconstruction of transcriptional regulatory networks of Fis and H-NS in Escherichia coli from genome wide data analysis	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE123554/GSE123554.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8309843	GSE123554	GSM3507070	GPL18133		delta-hns rep1	Reconstruction of transcriptional regulatory networks of Fis and H-NS in Escherichia coli from genome wide data analysis	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE123554/GSE123554.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8309844	GSE123554	GSM3507071	GPL18133		delta-hns rep2	Reconstruction of transcriptional regulatory networks of Fis and H-NS in Escherichia coli from genome wide data analysis	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE123554/GSE123554.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8587784	GSE126710	GSM3611666	GPL26204	31208335	E. coli K-12 MG1655_R1 [MG_1]	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GPL26204: NextSeq 550 (Escherichia coli K-12)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE126710/GSE126710.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8587785	GSE126710	GSM3611667	GPL26204	31208335	E. coli K-12 MG1655_R2 [MG_2]	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GPL26204: NextSeq 550 (Escherichia coli K-12)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE126710/GSE126710.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8587786	GSE126710	GSM3611668	GPL26204	31208335	E. coli K-12 MG1655_R3 [MG_3]	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GPL26204: NextSeq 550 (Escherichia coli K-12)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE126710/GSE126710.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8587787	GSE126710	GSM3611669	GPL26204	31208335	E. coli K-12 MG1655::φO104_R1 [O104_1]	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GPL26204: NextSeq 550 (Escherichia coli K-12)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE126710/GSE126710.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8587788	GSE126710	GSM3611670	GPL26204	31208335	E. coli K-12 MG1655::φO104_R2 [O104_2]	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GPL26204: NextSeq 550 (Escherichia coli K-12)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE126710/GSE126710.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8587789	GSE126710	GSM3611671	GPL26204	31208335	E. coli K-12 MG1655::φO104_R3 [O104_3]	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GPL26204: NextSeq 550 (Escherichia coli K-12)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE126710/GSE126710.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8587790	GSE126710	GSM3611672	GPL26204	31208335	E. coli K-12 MG1655_φPA8_R1 [PA8_1]	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GPL26204: NextSeq 550 (Escherichia coli K-12)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE126710/GSE126710.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8587791	GSE126710	GSM3611673	GPL26204	31208335	E. coli K-12 MG1655_φPA8_R2 [PA8_2]	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GPL26204: NextSeq 550 (Escherichia coli K-12)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE126710/GSE126710.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR8587792	GSE126710	GSM3611674	GPL26204	31208335	E. coli K-12 MG1655_fastφPA8_R3 [PA8_3]	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GPL26204: NextSeq 550 (Escherichia coli K-12)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE126710/GSE126710.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR10907640	GSE143855	GSM4275442	GPL24659	33172971	WT_LB_R1	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR10907641	GSE143855	GSM4275443	GPL24659	33172971	WT_LB_R2	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR10907642	GSE143855	GSM4275444	GPL24659	33172971	WT_EtOH_R1	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR10907644	GSE143855	GSM4275446	GPL24659	33172971	BaeR_KO_LB_R1	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR10907645	GSE143855	GSM4275447	GPL24659	33172971	BaeR_KO_ LB_R2	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR10907646	GSE143855	GSM4275448	GPL24659	33172971	BaeR_KO_EtOH_R1	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR10907648	GSE143855	GSM4275450	GPL24659	33172971	CpxR_KO_LB_R1	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR10907649	GSE143855	GSM4275451	GPL24659	33172971	CpxR_KO_LB_R2	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR10907652	GSE143855	GSM4275454	GPL24659	33172971	KdpE_KO_01-KCl_R1	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR10907653	GSE143855	GSM4275455	GPL24659	33172971	KdpE_KO_01-KCl_R2	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR10907654	GSE143855	GSM4275456	GPL24659	33172971	KdpE_KO_115-KCl_R1	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR10907655	GSE143855	GSM4275457	GPL24659	33172971	KdpE_KO_115-KCl_R2	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR10907656	GSE143855	GSM4275458	GPL24659	33172971	WT_01-KCl_R1	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR10907657	GSE143855	GSM4275459	GPL24659	33172971	WT_01-KCl_R2	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR10907658	GSE143855	GSM4275460	GPL24659	33172971	WT_115-KCl_R1	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR10907659	GSE143855	GSM4275461	GPL24659	33172971	WT_115-KCl_R2	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR10907660	GSE143855	GSM4275462	GPL24659	33172971	PhoB_KO_M9_R1	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR10907661	GSE143855	GSM4275463	GPL24659	33172971	PhoB_KO_M9_R2	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR10907662	GSE143855	GSM4275464	GPL24659	33172971	PhoB_KO_M9-P_R1	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR10907663	GSE143855	GSM4275465	GPL24659	33172971	PhoB_KO_M9-P_R2	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR10907664	GSE143855	GSM4275466	GPL24659	33172971	WT_M9-P_R1	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR10907665	GSE143855	GSM4275467	GPL24659	33172971	WT_M9-P_R2	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR10907667	GSE143855	GSM4275469	GPL24659	33172971	ZraR_KO_LB_R2	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR10907668	GSE143855	GSM4275470	GPL24659	33172971	ZraR_KO_ZnCl2_R1	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR10907669	GSE143855	GSM4275471	GPL24659	33172971	ZraR_KO_ZnCl2_R2	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR10907670	GSE143855	GSM4275472	GPL24659	33172971	WT_ZnCl2_R1	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR10907671	GSE143855	GSM4275473	GPL24659	33172971	WT_ZnCl2_R2	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR364363	GSE33671	GSM832606	GPL10328	22153074	DSP1_AP	Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE33671/GSE33671.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR364364	GSE33671	GSM832607	GPL10328	22153074	DSP1_Total	Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE33671/GSE33671.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR364365	GSE33671	GSM832608	GPL10328	22153074	DSP2_AP	Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE33671/GSE33671.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR364366	GSE33671	GSM832609	GPL10328	22153074	DSP2_Total	Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE33671/GSE33671.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR364367	GSE33671	GSM832610	GPL10328	22153074	DSP3_AP	Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE33671/GSE33671.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR364368	GSE33671	GSM832611	GPL10328	22153074	DSP3_Total	Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE33671/GSE33671.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR364369	GSE33671	GSM832612	GPL10328	22153074	EDC1_AP	Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE33671/GSE33671.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR364370	GSE33671	GSM832613	GPL10328	22153074	EDC1_Total	Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE33671/GSE33671.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR958658	GSE43408	GSM1217967	GPL14548	23856776	pHerd30T CK+aerobic	Quantitative Different Analysis of antimicrobial peptide LL37 expressed in E.coli Top 10 under aerobic and anaerobic condition.	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	treatment_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE43408/GSE43408.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR958659	GSE43408	GSM1217968	GPL14548	23856776	pHerd30T-LL37 induced+aerobic	Quantitative Different Analysis of antimicrobial peptide LL37 expressed in E.coli Top 10 under aerobic and anaerobic condition.	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	treatment_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE43408/GSE43408.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR958660	GSE43408	GSM1217969	GPL14548	23856776	pHerd30T-LL37 CK+ anaerobic	Quantitative Different Analysis of antimicrobial peptide LL37 expressed in E.coli Top 10 under aerobic and anaerobic condition.	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	treatment_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE43408/GSE43408.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR958661	GSE43408	GSM1217970	GPL14548	23856776	pHerd30T-LL37 induced +anaerobic	Quantitative Different Analysis of antimicrobial peptide LL37 expressed in E.coli Top 10 under aerobic and anaerobic condition.	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	treatment_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE43408/GSE43408.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794827	GSE45443	GSM1104381	GPL15010	23716638	pHDB3_1	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794832	GSE45443	GSM1104386	GPL15010	23716638	pLCV1_3	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794833	GSE45443	GSM1104387	GPL15010	23716638	MG1655-aMG_1	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794834	GSE45443	GSM1104388	GPL15010	23716638	MG1655-aMG_2	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794835	GSE45443	GSM1104389	GPL15010	23716638	MG1655-aMG_3	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794836	GSE45443	GSM1104390	GPL15010	23716638	MG1655+aMG_1	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794837	GSE45443	GSM1104391	GPL15010	23716638	MG1655+aMG_2	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794838	GSE45443	GSM1104392	GPL15010	23716638	MG1655+aMG_3	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794839	GSE45443	GSM1104393	GPL15010	23716638	SgrR_1	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794840	GSE45443	GSM1104394	GPL15010	23716638	SgrR_2	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794841	GSE45443	GSM1104395	GPL15010	23716638	SgrR_3	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794842	GSE45443	GSM1104396	GPL15010	23716638	sgrS_T_1	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794843	GSE45443	GSM1104397	GPL15010	23716638	sgrS_T_2	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794844	GSE45443	GSM1104398	GPL15010	23716638	sgrS_T_3	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794845	GSE45443	GSM1104399	GPL15010	23716638	sgrS_un_1	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794846	GSE45443	GSM1104400	GPL15010	23716638	sgrS_un_2	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794847	GSE45443	GSM1104401	GPL15010	23716638	sgrS_un_3	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794848	GSE45443	GSM1104402	GPL15010	23716638	WT_1	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794849	GSE45443	GSM1104403	GPL15010	23716638	WT_2	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794850	GSE45443	GSM1104404	GPL15010	23716638	WT_3	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794851	GSE45443	GSM1104405	GPL15010	23716638	wt_T_1	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794852	GSE45443	GSM1104406	GPL15010	23716638	wt_T_2	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794853	GSE45443	GSM1104407	GPL15010	23716638	wt_T_3	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794854	GSE45443	GSM1104408	GPL15010	23716638	wt_un_1	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794856	GSE45443	GSM1104410	GPL15010	23716638	wt_un_3	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794857	GSE45443	GSM1104411	GPL15010	23716638	CV108_minus_aMG_1	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794858	GSE45443	GSM1104412	GPL15010	23716638	CV108_minus_aMG_2	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794859	GSE45443	GSM1104413	GPL15010	23716638	CV108_minus_aMG_3	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794860	GSE45443	GSM1104414	GPL15010	23716638	CV108_plus_aMG_1	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794861	GSE45443	GSM1104415	GPL15010	23716638	CV108_plus_aMG_2	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794862	GSE45443	GSM1104416	GPL15010	23716638	CV108_plus_aMG_3	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794863	GSE45443	GSM1104417	GPL15010	23716638	MG1655_minus_aMG_1	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794864	GSE45443	GSM1104418	GPL15010	23716638	MG1655_minus_aMG_2	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794865	GSE45443	GSM1104419	GPL15010	23716638	MG1655_minus_aMG_3	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794866	GSE45443	GSM1104420	GPL15010	23716638	MG1655_plus_aMG_1	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794867	GSE45443	GSM1104421	GPL15010	23716638	MG1655_plus_aMG_2	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794868	GSE45443	GSM1104422	GPL15010	23716638	MG1655_plus_aMG_3	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794869	GSE45443	GSM1104423	GPL15010	23716638	WT_minus_2DG_1	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794870	GSE45443	GSM1104424	GPL15010	23716638	WT_minus_2DG_2	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794871	GSE45443	GSM1104425	GPL15010	23716638	WT_minus_2DG_3	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794872	GSE45443	GSM1104426	GPL15010	23716638	WT_plus_2DG_1	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794873	GSE45443	GSM1104427	GPL15010	23716638	WT_plus_2DG_2	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR794874	GSE45443	GSM1104428	GPL15010	23716638	WT_plus_2DG_3	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR922260	GSE48324	GSM1174823	GPL16227	24987116	Mid log_wildtype_glc minimal media_aerobic rep1	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR922261	GSE48324	GSM1174824	GPL16227	24987116	Mid log_wildtype_glc minimal media_aerobic rep2	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR922262	GSE48324	GSM1174825	GPL16227	24987116	Mid log_wildtype_glc minimal media_aerobic rep3	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR922263	GSE48324	GSM1174826	GPL16227	24987116	Mid log_wildtype_glc minimal media + adenine_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR922264	GSE48324	GSM1174827	GPL16227	24987116	Mid log_wildtype_glc minimal media + L-tryptophan_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR922265	GSE48324	GSM1174828	GPL16227	24987116	Mid log_wildtype_glc minimal media_anaerobic rep1	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR922266	GSE48324	GSM1174829	GPL16227	24987116	Mid log_wildtype_glc minimal media_anaerobic rep2	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR922267	GSE48324	GSM1174830	GPL16227	24987116	Mid log_wildtype_glc minimal media_anaerobic rep3	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR922268	GSE48324	GSM1174831	GPL16227	24987116	Mid log_nac KO_glc minimal media_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR922269	GSE48324	GSM1174832	GPL16227	24987116	Mid log_nac KO_glc minimal media + adenine_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR922270	GSE48324	GSM1174833	GPL16227	24987116	Mid log_cra KO_glc minimal media_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR922271	GSE48324	GSM1174834	GPL16227	24987116	Mid log_cra KO_glc minimal media + L-tryptophan_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR922272	GSE48324	GSM1174835	GPL16227	24987116	Mid log_mntR KO_glc minimal media_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR922273	GSE48324	GSM1174836	GPL16227	24987116	Mid log_mntR KO_glc minimal media_anaerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1168133	GSE54900	GSM1326347	GPL17439	25222563	WT with Fe 1 (RNA-seq)	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1168134	GSE54900	GSM1326348	GPL17439	25222563	WT with Fe 2 (RNA-seq)	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1168135	GSE54900	GSM1326349	GPL17439	25222563	WT with DPD 1 (RNA-seq)	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1168136	GSE54900	GSM1326350	GPL17439	25222563	WT with DPD 2 (RNA-seq)	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1168137	GSE54900	GSM1326351	GPL17439	25222563	Δfur with Fe 1 (RNA-seq)	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1168138	GSE54900	GSM1326352	GPL17439	25222563	Δfur with Fe 2 (RNA-seq)	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1168139	GSE54900	GSM1326353	GPL17439	25222563	Δfur with DPD 1 (RNA-seq)	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1168140	GSE54900	GSM1326354	GPL17439	25222563	Δfur with DPD 2 (RNA-seq)	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1211036	GSE56372	GSM1360031	GPL14548	24927582	Wild-type (MG1655) T0 RNA rep 2	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1211037	GSE56372	GSM1360032	GPL14548	24927582	Wild-type (MG1655) T1 RNA rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1211038	GSE56372	GSM1360033	GPL14548	24927582	Wild-type (MG1655) T1 RNA rep 2	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1211039	GSE56372	GSM1360034	GPL14548	24927582	Wild-type (MG1655) T2 RNA rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1211040	GSE56372	GSM1360035	GPL14548	24927582	Wild-type (MG1655) T2 RNA rep 2	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1211041	GSE56372	GSM1360036	GPL14548	24927582	Mutant (EP61) T0 RNA rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1211042	GSE56372	GSM1360037	GPL14548	24927582	Mutant (EP61) T0 RNA rep 2	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1211043	GSE56372	GSM1360038	GPL14548	24927582	Mutant (EP61) T1 RNA rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1211044	GSE56372	GSM1360039	GPL14548	24927582	Mutant (EP61) T1 RNA rep 2	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1211045	GSE56372	GSM1360040	GPL14548	24927582	Mutant (EP61) T2 RNA rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1211046	GSE56372	GSM1360041	GPL14548	24927582	Mutant (EP61) T2 RNA rep 2	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1211047	GSE56372	GSM1360042	GPL14548	24927582	Wild-type (MG1655) T0 RP rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1211048	GSE56372	GSM1360043	GPL14548	24927582	Wild-type (MG1655) T0 RP rep 2	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1211049	GSE56372	GSM1360044	GPL14548	24927582	Wild-type (MG1655) T1 RP rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1211050	GSE56372	GSM1360045	GPL14548	24927582	Wild-type (MG1655) T1 RP rep 2	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1211051	GSE56372	GSM1360046	GPL14548	24927582	Wild-type (MG1655) T2 RP rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1211052	GSE56372	GSM1360047	GPL14548	24927582	Wild-type (MG1655) T2 RP rep 2	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1211053	GSE56372	GSM1360048	GPL14548	24927582	Mutant (EP61) T0 RP rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1211054	GSE56372	GSM1360049	GPL14548	24927582	Mutant (EP61) T0 RP rep 2	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1211055	GSE56372	GSM1360050	GPL14548	24927582	Mutant (EP61) T1 RP rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1211056	GSE56372	GSM1360051	GPL14548	24927582	Mutant (EP61) T1 RP rep 2	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1211057	GSE56372	GSM1360052	GPL14548	24927582	Mutant (EP61) T2 RP rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1211058	GSE56372	GSM1360053	GPL14548	24927582	Mutant (EP61) T2 RP rep 2	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1363864	GSE58285	GSM1405877	GPL14548	25237058	rne wild-type	Direct entry by RNase E is a major pathway for the degradation and processing of RNA in Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE58285/GSE58285.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1363865	GSE58285	GSM1405878	GPL14548	25237058	rne-3071 ts	Direct entry by RNase E is a major pathway for the degradation and processing of RNA in Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE58285/GSE58285.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1363866	GSE58285	GSM1405879	GPL14548	25237058	T170V 0 min	Direct entry by RNase E is a major pathway for the degradation and processing of RNA in Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE58285/GSE58285.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1363867	GSE58285	GSM1405880	GPL14548	25237058	T170V 10 min	Direct entry by RNase E is a major pathway for the degradation and processing of RNA in Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE58285/GSE58285.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1363869	GSE58285	GSM1405882	GPL14548	25237058	rng mutant	Direct entry by RNase E is a major pathway for the degradation and processing of RNA in Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE58285/GSE58285.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1411272	GSE58556	GSM1413874	GPL18814	25483350	WT_glucose_log	RNA sequencing based analysis of the bacterial transcriptome	GPL18814: Illumina HiSeq 2000 (Escherichia coli BW38028)	growth_protocol	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	<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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE58556/GSE58556.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1692165	GSE63817	GSM1558078	GPL14548-GPL18945	26495981	LB mRNA	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE63817/GSE63817.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1692165	GSE63817	GSM1558078	GPL14548-GPL18945	26495981	LB mRNA	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	growth_protocol	E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media PGCGROWTHCONDITIONS	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> 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE63817/GSE63817.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1692166	GSE63817	GSM1558079	GPL14548-GPL18945	26495981	LB RPF	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE63817/GSE63817.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1692166	GSE63817	GSM1558079	GPL14548-GPL18945	26495981	LB RPF	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	growth_protocol	E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media PGCGROWTHCONDITIONS	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> 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE63817/GSE63817.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1692167	GSE63817	GSM1558080	GPL14548-GPL18945	26495981	LB mRNA technical replicate	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE63817/GSE63817.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1692167	GSE63817	GSM1558080	GPL14548-GPL18945	26495981	LB mRNA technical replicate	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	growth_protocol	E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media PGCGROWTHCONDITIONS	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> 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE63817/GSE63817.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1692168	GSE63817	GSM1558081	GPL14548-GPL18945	26495981	LB RPF biological replicate	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE63817/GSE63817.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1692168	GSE63817	GSM1558081	GPL14548-GPL18945	26495981	LB RPF biological replicate	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	growth_protocol	E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media PGCGROWTHCONDITIONS	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> 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE63817/GSE63817.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1692169	GSE63817	GSM1558082	GPL14548-GPL18945	26495981	LB mRNA biological replicate	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE63817/GSE63817.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1692169	GSE63817	GSM1558082	GPL14548-GPL18945	26495981	LB mRNA biological replicate	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	growth_protocol	E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media PGCGROWTHCONDITIONS	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> 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE63817/GSE63817.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1692173	GSE63817	GSM1558086	GPL14548-GPL18945	26495981	AT1 biological replicate	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE63817/GSE63817.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1692173	GSE63817	GSM1558086	GPL14548-GPL18945	26495981	AT1 biological replicate	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	growth_protocol	E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media PGCGROWTHCONDITIONS	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> 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE63817/GSE63817.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1771414	GSE65244	GSM1590712	GPL14548		Wt – 60 min	Temporal gene expression in Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS	<Med> LB medium , </Med> <Temp> 37 °C </Temp> , airated , constant pH 7.5 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65244/GSE65244.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1771419	GSE65244	GSM1590717	GPL14548		Fis – 60 min	Temporal gene expression in Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS	<Med> LB medium , </Med> <Temp> 37 °C </Temp> , airated , constant pH 7.5 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65244/GSE65244.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1771420	GSE65244	GSM1590718	GPL14548		Fis – 120 min	Temporal gene expression in Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS	<Med> LB medium , </Med> <Temp> 37 °C </Temp> , airated , constant pH 7.5 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65244/GSE65244.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1771421	GSE65244	GSM1590719	GPL14548		Fis – 180 min	Temporal gene expression in Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS	<Med> LB medium , </Med> <Temp> 37 °C </Temp> , airated , constant pH 7.5 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65244/GSE65244.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1771422	GSE65244	GSM1590720	GPL14548		Fis – 420 min	Temporal gene expression in Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS	<Med> LB medium , </Med> <Temp> 37 °C </Temp> , airated , constant pH 7.5 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65244/GSE65244.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1771423	GSE65244	GSM1590721	GPL14548		Hns – 60 min	Temporal gene expression in Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS	<Med> LB medium , </Med> <Temp> 37 °C </Temp> , airated , constant pH 7.5 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65244/GSE65244.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1771424	GSE65244	GSM1590722	GPL14548		Hns – 120 min	Temporal gene expression in Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS	<Med> LB medium , </Med> <Temp> 37 °C </Temp> , airated , constant pH 7.5 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65244/GSE65244.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1787590	GSE65642	GSM1602347	GPL16085	29394395	WT glucose 1	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1787591	GSE65642	GSM1602348	GPL16085	29394395	WT glucose 2	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1787592	GSE65642	GSM1602349	GPL16085	29394395	WT fructose 1	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1787593	GSE65642	GSM1602350	GPL16085	29394395	WT fructose 2	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1787594	GSE65642	GSM1602351	GPL16085	29394395	WT acetate 1	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1787595	GSE65642	GSM1602352	GPL16085	29394395	WT acetate 2	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1787596	GSE65642	GSM1602353	GPL16085	29394395	Δcra glucose 1	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1787597	GSE65642	GSM1602354	GPL16085	29394395	Δcra glucose 2	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1787598	GSE65642	GSM1602355	GPL16085	29394395	Δcra fructose 1	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1787599	GSE65642	GSM1602356	GPL16085	29394395	Δcra fructose 2	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1787600	GSE65642	GSM1602357	GPL16085	29394395	Δcra acetate 1	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1787601	GSE65642	GSM1602358	GPL16085	29394395	Δcra acetate 2	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1796598	GSE65711	GSM1603386	GPL16085	26279566	WT PQ 1	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1796599	GSE65711	GSM1603387	GPL16085	26279566	WT PQ 2	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1796600	GSE65711	GSM1603388	GPL16085	26279566	ΔoxyR PQ 1	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1796601	GSE65711	GSM1603389	GPL16085	26279566	ΔoxyR PQ 2	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1796603	GSE65711	GSM1603391	GPL16085	26279566	ΔsoxR PQ 2	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1796604	GSE65711	GSM1603392	GPL16085	26279566	ΔsoxS PQ 1	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1796605	GSE65711	GSM1603393	GPL16085	26279566	ΔsoxS PQ 2	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1824557	GSE66481	GSM1623160	GPL16085	26258987	WT pH5.5 1	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1824558	GSE66481	GSM1623161	GPL16085	26258987	WT pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1824559	GSE66481	GSM1623162	GPL16085	26258987	ΔgadE pH5.5 1	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1824560	GSE66481	GSM1623163	GPL16085	26258987	ΔgadE pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1824561	GSE66481	GSM1623164	GPL16085	26258987	ΔgadW pH5.5 1	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1824562	GSE66481	GSM1623165	GPL16085	26258987	ΔgadW pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1824563	GSE66481	GSM1623166	GPL16085	26258987	ΔgadX pH5.5 1	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR1824564	GSE66481	GSM1623167	GPL16085	26258987	ΔgadX pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547467	GSE73672	GSM1900470	GPL20227	27713404	Parent LB rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547469	GSE73672	GSM1900472	GPL20227	27713404	cysG KO LB rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547471	GSE73672	GSM1900474	GPL20227	27713404	cysH KO LB rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547472	GSE73672	GSM1900475	GPL20227	27713404	cysH KO LB rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547473	GSE73672	GSM1900476	GPL20227	27713404	dcd KO LB rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547474	GSE73672	GSM1900477	GPL20227	27713404	dcd KO LB rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547475	GSE73672	GSM1900478	GPL20227	27713404	fadr KO LB rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547476	GSE73672	GSM1900479	GPL20227	27713404	fadr KO LB rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547477	GSE73672	GSM1900480	GPL20227	27713404	ppk KO LB rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547479	GSE73672	GSM1900482	GPL20227	27713404	wzc KO LB rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547480	GSE73672	GSM1900483	GPL20227	27713404	wzc KO LB rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547482	GSE73672	GSM1900485	GPL20227	27713404	yghD KO LB rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547483	GSE73672	GSM1900486	GPL20227	27713404	fepA KO LB rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547485	GSE73672	GSM1900488	GPL20227	27713404	lacA KO LB rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547487	GSE73672	GSM1900490	GPL20227	27713404	Parent M9 rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547488	GSE73672	GSM1900491	GPL20227	27713404	Parent M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547489	GSE73672	GSM1900492	GPL20227	27713404	dcd KO M9 rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547490	GSE73672	GSM1900493	GPL20227	27713404	dcd KO M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547491	GSE73672	GSM1900494	GPL20227	27713404	fadr KO M9 rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547492	GSE73672	GSM1900495	GPL20227	27713404	fadr KO M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547493	GSE73672	GSM1900496	GPL20227	27713404	ppk KO M9 rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547494	GSE73672	GSM1900497	GPL20227	27713404	ppk KO M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547495	GSE73672	GSM1900498	GPL20227	27713404	wzc KO M9 rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547496	GSE73672	GSM1900499	GPL20227	27713404	wzc KO M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547497	GSE73672	GSM1900500	GPL20227	27713404	yghD KO M9 rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547498	GSE73672	GSM1900501	GPL20227	27713404	yghD KO M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547499	GSE73672	GSM1900502	GPL20227	27713404	fepA KO M9 rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547504	GSE73672	GSM1900507	GPL20227	27713404	WT rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547506	GSE73672	GSM1900509	GPL20227	27713404	mgtA KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547507	GSE73672	GSM1900510	GPL20227	27713404	mgtA KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547510	GSE73672	GSM1900513	GPL20227	27713404	gabT KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547511	GSE73672	GSM1900514	GPL20227	27713404	gabT KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547512	GSE73672	GSM1900515	GPL20227	27713404	sdhC KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547513	GSE73672	GSM1900516	GPL20227	27713404	sdhC KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547515	GSE73672	GSM1900518	GPL20227	27713404	putP KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547517	GSE73672	GSM1900520	GPL20227	27713404	putP KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547518	GSE73672	GSM1900521	GPL20227	27713404	rfbA KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547519	GSE73672	GSM1900522	GPL20227	27713404	rfbA KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547521	GSE73672	GSM1900524	GPL20227	27713404	entF KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547522	GSE73672	GSM1900525	GPL20227	27713404	entF KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547523	GSE73672	GSM1900526	GPL20227	27713404	entF KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547524	GSE73672	GSM1900527	GPL20227	27713404	kefB KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547526	GSE73672	GSM1900529	GPL20227	27713404	kefB KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547527	GSE73672	GSM1900530	GPL20227	27713404	cysA KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547528	GSE73672	GSM1900531	GPL20227	27713404	cysA KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547529	GSE73672	GSM1900532	GPL20227	27713404	cysA KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547531	GSE73672	GSM1900534	GPL20227	27713404	galE KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547533	GSE73672	GSM1900536	GPL20227	27713404	mhpD KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547534	GSE73672	GSM1900537	GPL20227	27713404	mhpD KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547535	GSE73672	GSM1900538	GPL20227	27713404	mhpD KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547536	GSE73672	GSM1900539	GPL20227	27713404	fliY KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547537	GSE73672	GSM1900540	GPL20227	27713404	fliY KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547538	GSE73672	GSM1900541	GPL20227	27713404	fliY KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547539	GSE73672	GSM1900542	GPL20227	27713404	lplA KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547540	GSE73672	GSM1900543	GPL20227	27713404	lplA KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547541	GSE73672	GSM1900544	GPL20227	27713404	lplA KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547542	GSE73672	GSM1900545	GPL20227	27713404	khc KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547543	GSE73672	GSM1900546	GPL20227	27713404	khc KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547544	GSE73672	GSM1900547	GPL20227	27713404	khc KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547545	GSE73672	GSM1900548	GPL20227	27713404	ugpC KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547546	GSE73672	GSM1900549	GPL20227	27713404	ugpC KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547547	GSE73672	GSM1900550	GPL20227	27713404	ugpC KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547548	GSE73672	GSM1900551	GPL20227	27713404	trpD KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547549	GSE73672	GSM1900552	GPL20227	27713404	trpD KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547550	GSE73672	GSM1900553	GPL20227	27713404	trpD KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547551	GSE73672	GSM1900554	GPL20227	27713404	aspC KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547552	GSE73672	GSM1900555	GPL20227	27713404	aspC KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR2547553	GSE73672	GSM1900556	GPL20227	27713404	aspC KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5186139	GSE77617	GSM2462936	GPL14548-GPL21433	28139975	mRNA-seq 37°C in WT with control plasmid	Operon mRNAs are organized into ORF-centric structures that predict translation efficiency	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21433: Illumina HiSeq 4000 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE77617/GSE77617.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5186139	GSE77617	GSM2462936	GPL14548-GPL21433	28139975	mRNA-seq 37°C in WT with control plasmid	Operon mRNAs are organized into ORF-centric structures that predict translation efficiency	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21433: Illumina HiSeq 4000 (Escherichia coli)	treatment_protocol	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	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> ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE77617/GSE77617.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5186140	GSE77617	GSM2462937	GPL14548-GPL21433	28139975	mRNA-seq 37°C in WT with plasmid expressing mini-ORF CUA	Operon mRNAs are organized into ORF-centric structures that predict translation efficiency	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21433: Illumina HiSeq 4000 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE77617/GSE77617.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5186140	GSE77617	GSM2462937	GPL14548-GPL21433	28139975	mRNA-seq 37°C in WT with plasmid expressing mini-ORF CUA	Operon mRNAs are organized into ORF-centric structures that predict translation efficiency	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21433: Illumina HiSeq 4000 (Escherichia coli)	treatment_protocol	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	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> ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE77617/GSE77617.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5186141	GSE77617	GSM2462938	GPL14548-GPL21433	28139975	mRNA-seq 37°C in WT with plasmid expressing mini-ORF CUG	Operon mRNAs are organized into ORF-centric structures that predict translation efficiency	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21433: Illumina HiSeq 4000 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE77617/GSE77617.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5186141	GSE77617	GSM2462938	GPL14548-GPL21433	28139975	mRNA-seq 37°C in WT with plasmid expressing mini-ORF CUG	Operon mRNAs are organized into ORF-centric structures that predict translation efficiency	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21433: Illumina HiSeq 4000 (Escherichia coli)	treatment_protocol	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	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> ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE77617/GSE77617.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR3176282	GSE78041	GSM2065371	GPL21475	27748404	TEX-_E. coli O104:H4	Differential RNA-Seq (dRNA-seq)  of Escherichia coli O104:H4	GPL21475: Illumina HiSeq 2500 (Escherichia coli O104:H4)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE78041/GSE78041.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR3176283	GSE78041	GSM2065372	GPL21475	27748404	TEX+_E. coli O104:H4	Differential RNA-Seq (dRNA-seq)  of Escherichia coli O104:H4	GPL21475: Illumina HiSeq 2500 (Escherichia coli O104:H4)	extract_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE78041/GSE78041.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR3194453	GSE78756	GSM2075722	GPL14548-GPL15010-GPL21530-GPL21531-GPL21532-GPL21533-GPL21534	27667363	Crooks_aero	Quantifying variation within the bacterial species E. coli	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])	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE78756/GSE78756.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR3194455SRR3194456	GSE78756	GSM2075723	GPL14548-GPL15010-GPL21530-GPL21531-GPL21532-GPL21533-GPL21534	27667363	Crooks_anaero	Quantifying variation within the bacterial species E. coli	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])	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE78756/GSE78756.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR3379590	GSE80251	GSM2122743	GPL21726	27645242	Untreated_replicate_1	Genome-wide transcriptome analyses of E. coli treated with ribosome-targeting antibiotics	GPL21726: Ion Torrent Proton (Escherichia coli)	treatment_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80251/GSE80251.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR3379591	GSE80251	GSM2122744	GPL21726	27645242	Untreated_replicate_2	Genome-wide transcriptome analyses of E. coli treated with ribosome-targeting antibiotics	GPL21726: Ion Torrent Proton (Escherichia coli)	treatment_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80251/GSE80251.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR3379592	GSE80251	GSM2122745	GPL21726	27645242	Untreated_replicate_3	Genome-wide transcriptome analyses of E. coli treated with ribosome-targeting antibiotics	GPL21726: Ion Torrent Proton (Escherichia coli)	treatment_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80251/GSE80251.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR3379593	GSE80251	GSM2122746	GPL21726	27645242	Erythromycin_replicate_1	Genome-wide transcriptome analyses of E. coli treated with ribosome-targeting antibiotics	GPL21726: Ion Torrent Proton (Escherichia coli)	treatment_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80251/GSE80251.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR3379594	GSE80251	GSM2122747	GPL21726	27645242	Erythromycin_replicate_2	Genome-wide transcriptome analyses of E. coli treated with ribosome-targeting antibiotics	GPL21726: Ion Torrent Proton (Escherichia coli)	treatment_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80251/GSE80251.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR3379595	GSE80251	GSM2122748	GPL21726	27645242	Erythromycin_replicate_3	Genome-wide transcriptome analyses of E. coli treated with ribosome-targeting antibiotics	GPL21726: Ion Torrent Proton (Escherichia coli)	treatment_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80251/GSE80251.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR3379596	GSE80251	GSM2122749	GPL21726	27645242	Clindamycin_replicate_1	Genome-wide transcriptome analyses of E. coli treated with ribosome-targeting antibiotics	GPL21726: Ion Torrent Proton (Escherichia coli)	treatment_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80251/GSE80251.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR3379597	GSE80251	GSM2122750	GPL21726	27645242	Clindamycin_replicate_2	Genome-wide transcriptome analyses of E. coli treated with ribosome-targeting antibiotics	GPL21726: Ion Torrent Proton (Escherichia coli)	treatment_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80251/GSE80251.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR3379598	GSE80251	GSM2122751	GPL21726	27645242	Clindamycin_replicate_3	Genome-wide transcriptome analyses of E. coli treated with ribosome-targeting antibiotics	GPL21726: Ion Torrent Proton (Escherichia coli)	treatment_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80251/GSE80251.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR3403686	GSE80451	GSM2127617	GPL14548	28103245	Aerobic 1	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	<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. 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80451/GSE80451.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR3403687	GSE80451	GSM2127618	GPL14548	28103245	Aerobic 2	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	<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. 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80451/GSE80451.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR3403688	GSE80451	GSM2127619	GPL14548	28103245	Aerobic 3	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	<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. 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80451/GSE80451.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR3584193SRR3584194SRR3584195	GSE81584	GSM2157648	GPL14548		MG1655_1	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	extract_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE81584/GSE81584.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR3584196SRR3584197SRR3584198	GSE81584	GSM2157649	GPL14548		MG1655_2	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	extract_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE81584/GSE81584.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR3584199SRR3584200	GSE81584	GSM2157650	GPL14548		MG1655_3	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	extract_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE81584/GSE81584.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR3584201SRR3584202	GSE81584	GSM2157651	GPL14548		mfd_1	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	extract_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE81584/GSE81584.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR3584203SRR3584204	GSE81584	GSM2157652	GPL14548		mfd_2	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	extract_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE81584/GSE81584.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR3584205SRR3584206SRR3584207	GSE81584	GSM2157653	GPL14548		mfd_3	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	extract_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE81584/GSE81584.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR3584208SRR3584209	GSE81584	GSM2157654	GPL14548		MG1655_vector_1	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	extract_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE81584/GSE81584.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR3584210SRR3584211	GSE81584	GSM2157655	GPL14548		MG1655_vector_2	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	extract_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE81584/GSE81584.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR3584212SRR3584213SRR3584214	GSE81584	GSM2157656	GPL14548		MFD++_1	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	extract_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE81584/GSE81584.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR3584215SRR3584216SRR3584217	GSE81584	GSM2157657	GPL14548		MFD++_2	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	extract_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE81584/GSE81584.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4255368	GSE87071	GSM2321583	GPL14548		10J.0	The Escherichia coli nucleoid is shaped around replication and transcription [RNA-Seq]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	extract_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE87071/GSE87071.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4255368	GSE87071	GSM2321583	GPL14548		10J.0	The Escherichia coli nucleoid is shaped around replication and transcription [RNA-Seq]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE87071/GSE87071.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4255369	GSE87071	GSM2321584	GPL14548		11K.60	The Escherichia coli nucleoid is shaped around replication and transcription [RNA-Seq]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	extract_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE87071/GSE87071.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4255369	GSE87071	GSM2321584	GPL14548		11K.60	The Escherichia coli nucleoid is shaped around replication and transcription [RNA-Seq]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE87071/GSE87071.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4255370	GSE87071	GSM2321585	GPL14548		12L.120	The Escherichia coli nucleoid is shaped around replication and transcription [RNA-Seq]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	extract_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE87071/GSE87071.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4255370	GSE87071	GSM2321585	GPL14548		12L.120	The Escherichia coli nucleoid is shaped around replication and transcription [RNA-Seq]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE87071/GSE87071.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4255371	GSE87071	GSM2321586	GPL14548		7G.0	The Escherichia coli nucleoid is shaped around replication and transcription [RNA-Seq]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	extract_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE87071/GSE87071.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4255371	GSE87071	GSM2321586	GPL14548		7G.0	The Escherichia coli nucleoid is shaped around replication and transcription [RNA-Seq]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 ) . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE87071/GSE87071.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4421263	GSE88725	GSM2344783	GPL14548	28301469	WT_exp1_mRNA	Global analysis of translation termination in E. coli using release factor manipulations	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88725/GSE88725.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4421264	GSE88725	GSM2344784	GPL14548	28301469	WT_exp2_mRNA	Global analysis of translation termination in E. coli using release factor manipulations	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88725/GSE88725.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4421265SRR4421266	GSE88725	GSM2344785	GPL14548	28301469	WT_exp3_mRNA	Global analysis of translation termination in E. coli using release factor manipulations	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88725/GSE88725.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4421267	GSE88725	GSM2344786	GPL14548	28301469	WT_exp4_mRNA	Global analysis of translation termination in E. coli using release factor manipulations	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88725/GSE88725.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4421268	GSE88725	GSM2344787	GPL14548	28301469	∆RF3_exp1_mRNA	Global analysis of translation termination in E. coli using release factor manipulations	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88725/GSE88725.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4421269SRR4421270	GSE88725	GSM2344788	GPL14548	28301469	∆RF3_exp3_mRNA	Global analysis of translation termination in E. coli using release factor manipulations	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88725/GSE88725.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4421271	GSE88725	GSM2344789	GPL14548	28301469	RF2*_exp1_mRNA	Global analysis of translation termination in E. coli using release factor manipulations	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88725/GSE88725.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4421272SRR4421273	GSE88725	GSM2344790	GPL14548	28301469	RF2*_exp3_mRNA	Global analysis of translation termination in E. coli using release factor manipulations	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88725/GSE88725.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4421274	GSE88725	GSM2344791	GPL14548	28301469	RF2*∆RF3_exp2_repA_mRNA	Global analysis of translation termination in E. coli using release factor manipulations	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88725/GSE88725.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4421275	GSE88725	GSM2344792	GPL14548	28301469	RF2*∆RF3_exp2_repB_mRNA	Global analysis of translation termination in E. coli using release factor manipulations	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88725/GSE88725.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4421276SRR4421277	GSE88725	GSM2344793	GPL14548	28301469	RF2*∆RF3_exp3_mRNA	Global analysis of translation termination in E. coli using release factor manipulations	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88725/GSE88725.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4421278	GSE88725	GSM2344794	GPL14548	28301469	RF2*∆RF3_exp4_repA_mRNA	Global analysis of translation termination in E. coli using release factor manipulations	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88725/GSE88725.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4421279	GSE88725	GSM2344795	GPL14548	28301469	RF2*∆RF3_exp4_repB_mRNA	Global analysis of translation termination in E. coli using release factor manipulations	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88725/GSE88725.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4421297	GSE88725	GSM2344809	GPL14548	28301469	WT_minimal_mRNA	Global analysis of translation termination in E. coli using release factor manipulations	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88725/GSE88725.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4421298	GSE88725	GSM2344810	GPL14548	28301469	∆RF3_minimal_mRNA	Global analysis of translation termination in E. coli using release factor manipulations	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	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 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88725/GSE88725.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4427755	GSE88835	GSM2349915	GPL18133	29122925	Tube state 1 (IPTG-/aTc-/Ara-)	Genetic circuit 0x58	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4427756	GSE88835	GSM2349916	GPL18133	29122925	Tube state 2 (IPTG+/aTc-/Ara-)	Genetic circuit 0x58	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4427757	GSE88835	GSM2349917	GPL18133	29122925	Tube state 3 (IPTG-/aTc+/Ara-)	Genetic circuit 0x58	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4427758	GSE88835	GSM2349918	GPL18133	29122925	Tube state 4 (IPTG+/aTc+/Ara-)	Genetic circuit 0x58	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4427759	GSE88835	GSM2349919	GPL18133	29122925	Tube state 5 (IPTG-/aTc-/Ara+)	Genetic circuit 0x58	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4427760	GSE88835	GSM2349920	GPL18133	29122925	Tube state 6 (IPTG+/aTc-/Ara+)	Genetic circuit 0x58	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4427761	GSE88835	GSM2349921	GPL18133	29122925	Tube state 7 (IPTG-/aTc+/Ara+)	Genetic circuit 0x58	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4427762	GSE88835	GSM2349922	GPL18133	29122925	Tube state 8 (IPTG+/aTc+/Ara+)	Genetic circuit 0x58	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4427763	GSE88835	GSM2349923	GPL18133	29122925	Flask state 1 (IPTG-/aTc-/Ara-)	Genetic circuit 0x58	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4427764	GSE88835	GSM2349924	GPL18133	29122925	Flask state 2 (IPTG+/aTc-/Ara-)	Genetic circuit 0x58	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4427765	GSE88835	GSM2349925	GPL18133	29122925	Flask state 3 (IPTG-/aTc+/Ara-)	Genetic circuit 0x58	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4427766	GSE88835	GSM2349926	GPL18133	29122925	Flask state 4 (IPTG+/aTc+/Ara-)	Genetic circuit 0x58	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4427767	GSE88835	GSM2349927	GPL18133	29122925	Flask state 5 (IPTG-/aTc-/Ara+)	Genetic circuit 0x58	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4427768	GSE88835	GSM2349928	GPL18133	29122925	Flask state 6 (IPTG+/aTc-/Ara+)	Genetic circuit 0x58	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4427769	GSE88835	GSM2349929	GPL18133	29122925	Flask state 7 (IPTG-/aTc+/Ara+)	Genetic circuit 0x58	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4427770	GSE88835	GSM2349930	GPL18133	29122925	Flask state 8 (IPTG+/aTc+/Ara+)	Genetic circuit 0x58	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88835/GSE88835.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4435464	GSE88980	GSM2356687	GPL17439	28526842	WT NaCl 1	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]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88980/GSE88980.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4435465	GSE88980	GSM2356688	GPL17439	28526842	WT NaCl 2	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]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88980/GSE88980.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4435466	GSE88980	GSM2356689	GPL17439	28526842	ΔompR NaCl 1	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]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88980/GSE88980.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR4435467	GSE88980	GSM2356690	GPL17439	28526842	ΔompR NaCl 2	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]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88980/GSE88980.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071589	GSE90743	GSM2411669	GPL18133	2844739128702020	chemostat STR-PFR culture STR 5min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071590	GSE90743	GSM2411670	GPL18133	2844739128702020	chemostat STR-PFR culture STR 10min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071591	GSE90743	GSM2411671	GPL18133	2844739128702020	chemostat STR-PFR culture STR 25min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071592	GSE90743	GSM2411672	GPL18133	2844739128702020	chemostat STR-PFR culture STR 45min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071593	GSE90743	GSM2411673	GPL18133	2844739128702020	chemostat STR-PFR culture STR 75min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071594	GSE90743	GSM2411674	GPL18133	2844739128702020	chemostat STR-PFR culture STR 120min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071595	GSE90743	GSM2411675	GPL18133	2844739128702020	chemostat STR-PFR culture STR 210min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071596	GSE90743	GSM2411676	GPL18133	2844739128702020	chemostat STR-PFR culture STR 330min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071597	GSE90743	GSM2411677	GPL18133	2844739128702020	chemostat STR-PFR culture STR 25h, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071598	GSE90743	GSM2411678	GPL18133	2844739128702020	chemostat STR-PFR culture STR 26h, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071599	GSE90743	GSM2411679	GPL18133	2844739128702020	chemostat STR-PFR culture STR 28h, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071600	GSE90743	GSM2411680	GPL18133	2844739128702020	chemostat STR culture STR  reference 1, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071601	GSE90743	GSM2411681	GPL18133	2844739128702020	chemostat STR culture STR  reference 2, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071602	GSE90743	GSM2411682	GPL18133	2844739128702020	chemostat STR culture STR  reference 3, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071603	GSE90743	GSM2411683	GPL18133	2844739128702020	chemostat STR-PFR culture PFR P5 5min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071604	GSE90743	GSM2411684	GPL18133	2844739128702020	chemostat STR-PFR culture PFR P5 10min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071605	GSE90743	GSM2411685	GPL18133	2844739128702020	chemostat STR-PFR culture PFR P5 25min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071606	GSE90743	GSM2411686	GPL18133	2844739128702020	chemostat STR-PFR culture PFR P3 25min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071607	GSE90743	GSM2411687	GPL18133	2844739128702020	chemostat STR-PFR culture PFR P1 25min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071608	GSE90743	GSM2411688	GPL18133	2844739128702020	chemostat STR-PFR culture PFR P5 45min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071609	GSE90743	GSM2411689	GPL18133	2844739128702020	chemostat STR-PFR culture PFR P5 120min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071610	GSE90743	GSM2411690	GPL18133	2844739128702020	chemostat STR-PFR culture PFR P3 120min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071611	GSE90743	GSM2411691	GPL18133	2844739128702020	chemostat STR-PFR culture PFR P1 120min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071612	GSE90743	GSM2411692	GPL18133	2844739128702020	chemostat STR-PFR culture PFR P5 210min, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071613	GSE90743	GSM2411693	GPL18133	2844739128702020	chemostat STR-PFR culture PFR P5 25h, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071614	GSE90743	GSM2411694	GPL18133	2844739128702020	chemostat STR-PFR culture PFR P3 28h, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071615	GSE90743	GSM2411695	GPL18133	2844739128702020	chemostat STR-PFR culture PFR P5 28h, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071616	GSE90743	GSM2411696	GPL18133	2844739128702020	chemostat STR-PFR culture PFR P1 28h, rep1	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071617	GSE90743	GSM2411697	GPL18133	2844739128702020	chemostat STR-PFR culture STR 5min, rep2	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071618	GSE90743	GSM2411698	GPL18133	2844739128702020	chemostat STR-PFR culture STR 10min, rep2	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071619	GSE90743	GSM2411699	GPL18133	2844739128702020	chemostat STR-PFR culture STR 25min, rep2	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071620	GSE90743	GSM2411700	GPL18133	2844739128702020	chemostat STR-PFR culture STR 45min, rep2	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071621	GSE90743	GSM2411701	GPL18133	2844739128702020	chemostat STR-PFR culture STR 75min, rep2	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071622	GSE90743	GSM2411702	GPL18133	2844739128702020	chemostat STR-PFR culture STR 120min, rep2	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071623	GSE90743	GSM2411703	GPL18133	2844739128702020	chemostat STR-PFR culture STR 210min, rep2	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071624	GSE90743	GSM2411704	GPL18133	2844739128702020	chemostat STR-PFR culture STR 330min, rep2	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071625	GSE90743	GSM2411705	GPL18133	2844739128702020	chemostat STR-PFR culture STR 25h, rep2	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071626	GSE90743	GSM2411706	GPL18133	2844739128702020	chemostat STR-PFR culture STR 26h, rep2	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071627	GSE90743	GSM2411707	GPL18133	2844739128702020	chemostat STR-PFR culture STR 28h, rep2	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071628	GSE90743	GSM2411708	GPL18133	2844739128702020	chemostat STR culture STR reference 1 , rep2	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071629	GSE90743	GSM2411709	GPL18133	2844739128702020	chemostat STR culture STR reference 2 , rep2	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071630	GSE90743	GSM2411710	GPL18133	2844739128702020	chemostat STR culture STR reference 3 , rep2	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071631	GSE90743	GSM2411711	GPL18133	2844739128702020	chemostat STR-PFR culture PFR P5 5min, rep2	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071632	GSE90743	GSM2411712	GPL18133	2844739128702020	chemostat STR-PFR culture PFR P5 10min, rep2	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071633	GSE90743	GSM2411713	GPL18133	2844739128702020	chemostat STR-PFR culture PFR P5 25min, rep2	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071634	GSE90743	GSM2411714	GPL18133	2844739128702020	chemostat STR-PFR culture PFR P3 25min, rep2	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071635	GSE90743	GSM2411715	GPL18133	2844739128702020	chemostat STR-PFR culture PFR P1 25min, rep2	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071636	GSE90743	GSM2411716	GPL18133	2844739128702020	chemostat STR-PFR culture PFR P5 45min, rep2	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071637	GSE90743	GSM2411717	GPL18133	2844739128702020	chemostat STR-PFR culture PFR P5 75min, rep2	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071638	GSE90743	GSM2411718	GPL18133	2844739128702020	chemostat STR-PFR culture PFR P5 120min, rep2	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071639	GSE90743	GSM2411719	GPL18133	2844739128702020	chemostat STR-PFR culture PFR P3 120min, rep2	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071640	GSE90743	GSM2411720	GPL18133	2844739128702020	chemostat STR-PFR culture PFR P1 120min, rep2	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071641	GSE90743	GSM2411721	GPL18133	2844739128702020	chemostat STR-PFR culture PFR P5 210min, rep2	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071642	GSE90743	GSM2411722	GPL18133	2844739128702020	chemostat STR-PFR culture PFR P5 330min, rep2	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071643	GSE90743	GSM2411723	GPL18133	2844739128702020	chemostat STR-PFR culture PFR P5 25h, rep2	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071644	GSE90743	GSM2411724	GPL18133	2844739128702020	chemostat STR-PFR culture PFR P5 26h, rep2	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071645	GSE90743	GSM2411725	GPL18133	2844739128702020	chemostat STR-PFR culture PFR P5 28h, rep2	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071646	GSE90743	GSM2411726	GPL18133	2844739128702020	chemostat STR-PFR culture PFR P3 28h, rep2	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5071647	GSE90743	GSM2411727	GPL18133	2844739128702020	chemostat STR-PFR culture PFR P1 28h, rep2	RNA-seq of Escherichia coli under fluctuating ammonia availability (limitation-depletion)	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90743/GSE90743.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5143857	GSE93125	GSM2445135	GPL18133	28959742	Eco_TolC_0min_A	Transcriptomal changes of Escherichia coli TolC grown with the biofilm inhibitor Carolacton	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS	E. coli TolC cells were grown o/n in LB medium at <Temp> 37 °C </Temp> and 200 rpm . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE93125/GSE93125.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5143858	GSE93125	GSM2445138	GPL18133	28959742	Eco_TolC_0min_B	Transcriptomal changes of Escherichia coli TolC grown with the biofilm inhibitor Carolacton	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS	E. coli TolC cells were grown o/n in LB medium at <Temp> 37 °C </Temp> and 200 rpm . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE93125/GSE93125.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5143859	GSE93125	GSM2445140	GPL18133	28959742	Eco_TolC_5min_control_A	Transcriptomal changes of Escherichia coli TolC grown with the biofilm inhibitor Carolacton	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS	E. coli TolC cells were grown o/n in LB medium at <Temp> 37 °C </Temp> and 200 rpm . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE93125/GSE93125.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5143860	GSE93125	GSM2445142	GPL18133	28959742	Eco_TolC_5min_control_B	Transcriptomal changes of Escherichia coli TolC grown with the biofilm inhibitor Carolacton	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS	E. coli TolC cells were grown o/n in LB medium at <Temp> 37 °C </Temp> and 200 rpm . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE93125/GSE93125.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5143861	GSE93125	GSM2445144	GPL18133	28959742	Eco_TolC_5min_Carolacton_A	Transcriptomal changes of Escherichia coli TolC grown with the biofilm inhibitor Carolacton	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS	E. coli TolC cells were grown o/n in LB medium at <Temp> 37 °C </Temp> and 200 rpm . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE93125/GSE93125.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5143862	GSE93125	GSM2445145	GPL18133	28959742	Eco_TolC_5min_Carolacton_B	Transcriptomal changes of Escherichia coli TolC grown with the biofilm inhibitor Carolacton	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS	E. coli TolC cells were grown o/n in LB medium at <Temp> 37 °C </Temp> and 200 rpm . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE93125/GSE93125.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5143863	GSE93125	GSM2445147	GPL18133	28959742	Eco_TolC_15min_control_A	Transcriptomal changes of Escherichia coli TolC grown with the biofilm inhibitor Carolacton	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS	E. coli TolC cells were grown o/n in LB medium at <Temp> 37 °C </Temp> and 200 rpm . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE93125/GSE93125.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5143864	GSE93125	GSM2445149	GPL18133	28959742	Eco_TolC_15min_control_B	Transcriptomal changes of Escherichia coli TolC grown with the biofilm inhibitor Carolacton	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS	E. coli TolC cells were grown o/n in LB medium at <Temp> 37 °C </Temp> and 200 rpm . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE93125/GSE93125.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5143865	GSE93125	GSM2445151	GPL18133	28959742	Eco_TolC_15min_Carolacton_A	Transcriptomal changes of Escherichia coli TolC grown with the biofilm inhibitor Carolacton	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS	E. coli TolC cells were grown o/n in LB medium at <Temp> 37 °C </Temp> and 200 rpm . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE93125/GSE93125.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5143866	GSE93125	GSM2445153	GPL18133	28959742	Eco_TolC_15min_Carolacton_B	Transcriptomal changes of Escherichia coli TolC grown with the biofilm inhibitor Carolacton	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS	E. coli TolC cells were grown o/n in LB medium at <Temp> 37 °C </Temp> and 200 rpm . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE93125/GSE93125.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5143868	GSE93125	GSM2445155	GPL18133	28959742	Eco_TolC_30min_control_A	Transcriptomal changes of Escherichia coli TolC grown with the biofilm inhibitor Carolacton	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS	E. coli TolC cells were grown o/n in LB medium at <Temp> 37 °C </Temp> and 200 rpm . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE93125/GSE93125.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5143869	GSE93125	GSM2445157	GPL18133	28959742	Eco_TolC_30min_control_B	Transcriptomal changes of Escherichia coli TolC grown with the biofilm inhibitor Carolacton	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS	E. coli TolC cells were grown o/n in LB medium at <Temp> 37 °C </Temp> and 200 rpm . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE93125/GSE93125.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5143870	GSE93125	GSM2445159	GPL18133	28959742	Eco_TolC_30min_Carolacton_A	Transcriptomal changes of Escherichia coli TolC grown with the biofilm inhibitor Carolacton	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS	E. coli TolC cells were grown o/n in LB medium at <Temp> 37 °C </Temp> and 200 rpm . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE93125/GSE93125.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5143871	GSE93125	GSM2445161	GPL18133	28959742	Eco_TolC_30min_Carolacton_B	Transcriptomal changes of Escherichia coli TolC grown with the biofilm inhibitor Carolacton	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	E. coli TolC cells were grown o/n in LB medium at 37°C and 200 rpm. PGCGROWTHCONDITIONS	E. coli TolC cells were grown o/n in LB medium at <Temp> 37 °C </Temp> and 200 rpm . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE93125/GSE93125.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5266619	GSE94984	GSM2493797	GPL23073	28245801	EHEC in LB Experiment 2 [RNA-Seq]	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	GPL23073: Illumina MiSeq (Escherichia coli O157:H7 str. EDL933)	growth_protocol	LB medium, 180 rpm shaking, at 37°C, between exponential and stationary phase PGCGROWTHCONDITIONS	LB medium , 180 rpm shaking , at <Temp> 37 °C </Temp> , between exponential and <Phase> stationary phase </Phase> 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE94984/GSE94984.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5304286	GSE95575	GSM2516609	GPL15010	29338696	1A_MG_t0	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5304287	GSE95575	GSM2516610	GPL15010	29338696	2A_MG_t10	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5304288	GSE95575	GSM2516611	GPL15010	29338696	3A_MG_t30	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5304289	GSE95575	GSM2516612	GPL15010	29338696	4A_MG_t60	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5304290	GSE95575	GSM2516613	GPL15010	29338696	5A_MG+Hg_t10	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5304291	GSE95575	GSM2516614	GPL15010	29338696	6A_MG+Hg_t30	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5304292	GSE95575	GSM2516615	GPL15010	29338696	7A_MG+Hg_t60	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5304293	GSE95575	GSM2516616	GPL15010	29338696	8A_MG+PMA_t10	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5304294	GSE95575	GSM2516617	GPL15010	29338696	9A_MG+PMA_t30	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5304295	GSE95575	GSM2516618	GPL15010	29338696	10A_MG+PMA_t60	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5304296	GSE95575	GSM2516619	GPL15010	29338696	1B_MG_t0	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5304297	GSE95575	GSM2516620	GPL15010	29338696	2B_MG_t10	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5304298	GSE95575	GSM2516621	GPL15010	29338696	3B_MG_t30	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5304299	GSE95575	GSM2516622	GPL15010	29338696	4B_MG_t60	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5304300	GSE95575	GSM2516623	GPL15010	29338696	5B_MG+Hg_t10	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5304301	GSE95575	GSM2516624	GPL15010	29338696	6B_MG+Hg_t30	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5304302	GSE95575	GSM2516625	GPL15010	29338696	7B_MG+Hg_t60	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5304303	GSE95575	GSM2516626	GPL15010	29338696	8B_MG+PMA_t10	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5304304	GSE95575	GSM2516627	GPL15010	29338696	9B_MG+PMA_t30	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5304305	GSE95575	GSM2516628	GPL15010	29338696	10B_MG+PMA_t60	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5304306	GSE95575	GSM2516629	GPL15010	29338696	1C_MG_t0	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5304307	GSE95575	GSM2516630	GPL15010	29338696	2C_MG_t10	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5304308	GSE95575	GSM2516631	GPL15010	29338696	3C_MG_t30	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5304309	GSE95575	GSM2516632	GPL15010	29338696	4C_MG_t60	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5304310	GSE95575	GSM2516633	GPL15010	29338696	5C_MG+Hg_t10	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5304311	GSE95575	GSM2516634	GPL15010	29338696	6C_MG+Hg_t30	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5304312	GSE95575	GSM2516635	GPL15010	29338696	7C_MG+Hg_t60	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5304313	GSE95575	GSM2516636	GPL15010	29338696	8C_MG+PMA_t10	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5304314	GSE95575	GSM2516637	GPL15010	29338696	9C_MG+PMA_t30	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5304315	GSE95575	GSM2516638	GPL15010	29338696	10C_MG+PMA_t60	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5985582	GSE98890	GSM2757255	GPL18133	29122925	0x58 replicate 2 state 1 (IPTG-/aTc-/Ara-)	Genetic circuit 0x58 replicates and modified	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5985583	GSE98890	GSM2757256	GPL18133	29122925	0x58 replicate 2 state 2 (IPTG+/aTc-/Ara-)	Genetic circuit 0x58 replicates and modified	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5985584	GSE98890	GSM2757257	GPL18133	29122925	0x58 replicate 2 state 3 (IPTG-/aTc+/Ara-)	Genetic circuit 0x58 replicates and modified	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5985585	GSE98890	GSM2757258	GPL18133	29122925	0x58 replicate 2 state 4 (IPTG+/aTc+/Ara-)	Genetic circuit 0x58 replicates and modified	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5985586	GSE98890	GSM2757259	GPL18133	29122925	0x58 replicate 2 state 5 (IPTG-/aTc-/Ara+)	Genetic circuit 0x58 replicates and modified	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5985587	GSE98890	GSM2757260	GPL18133	29122925	0x58 replicate 2 state 6 (IPTG+/aTc-/Ara+)	Genetic circuit 0x58 replicates and modified	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5985588	GSE98890	GSM2757261	GPL18133	29122925	0x58 replicate 2 state 7 (IPTG-/aTc+/Ara+)	Genetic circuit 0x58 replicates and modified	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5985589	GSE98890	GSM2757262	GPL18133	29122925	0x58 replicate 2 state 8 (IPTG+/aTc+/Ara+)	Genetic circuit 0x58 replicates and modified	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5985590	GSE98890	GSM2757263	GPL18133	29122925	0x58 replicate 3 state 1 (IPTG-/aTc-/Ara-)	Genetic circuit 0x58 replicates and modified	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5985591	GSE98890	GSM2757264	GPL18133	29122925	0x58 replicate 3 state 2 (IPTG+/aTc-/Ara-)	Genetic circuit 0x58 replicates and modified	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5985592	GSE98890	GSM2757265	GPL18133	29122925	0x58 replicate 3 state 3 (IPTG-/aTc+/Ara-)	Genetic circuit 0x58 replicates and modified	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5985593	GSE98890	GSM2757266	GPL18133	29122925	0x58 replicate 3 state 4 (IPTG+/aTc+/Ara-)	Genetic circuit 0x58 replicates and modified	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5985594	GSE98890	GSM2757267	GPL18133	29122925	0x58 replicate 3 state 5 (IPTG-/aTc-/Ara+)	Genetic circuit 0x58 replicates and modified	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5985595	GSE98890	GSM2757268	GPL18133	29122925	0x58 replicate 3 state 6 (IPTG+/aTc-/Ara+)	Genetic circuit 0x58 replicates and modified	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5985596	GSE98890	GSM2757269	GPL18133	29122925	0x58 replicate 3 state 7 (IPTG-/aTc+/Ara+)	Genetic circuit 0x58 replicates and modified	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5985597	GSE98890	GSM2757270	GPL18133	29122925	0x58 replicate 3 state 8 (IPTG+/aTc+/Ara+)	Genetic circuit 0x58 replicates and modified	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5985599	GSE98890	GSM2757272	GPL18133	29122925	Control pAN1201 replicate 1 (IPTG-/aTc-/Ara-)	Genetic circuit 0x58 replicates and modified	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR5985600	GSE98890	GSM2757273	GPL18133	29122925	Control pAN1201 replicate 2 (IPTG-/aTc-/Ara-)	Genetic circuit 0x58 replicates and modified	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	37 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE98890/GSE98890.soft.gz	35.7 C	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003199
SRR6048166	GSE103937	GSM2786596	GPL24020	29474582	WT glucose_replicate1	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	treatment_protocol	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	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 	IPTG was	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	iptg	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002105
SRR6048167	GSE103937	GSM2786597	GPL24020	29474582	WT glucose_replicate2	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	treatment_protocol	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	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 	IPTG was	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	iptg	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002105
SRR6048168	GSE103937	GSM2786598	GPL24020	29474582	WT glucose_replicate3	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	treatment_protocol	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	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 	IPTG was	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	iptg	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002105
SRR6048169	GSE103937	GSM2786599	GPL24020	29474582	WT_glycerol_replicate1	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	treatment_protocol	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	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 	IPTG was	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	iptg	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002105
SRR6048170	GSE103937	GSM2786600	GPL24020	29474582	WT_glycerol_replicate2	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	treatment_protocol	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	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 	IPTG was	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	iptg	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002105
SRR6048171	GSE103937	GSM2786601	GPL24020	29474582	WT_glycerol_replicate3	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	treatment_protocol	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	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 	IPTG was	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	iptg	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002105
SRR6048172	GSE103937	GSM2786602	GPL24020	29474582	WT UvsW_replicate1	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	treatment_protocol	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	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 	IPTG was	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	iptg	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002105
SRR6048173	GSE103937	GSM2786603	GPL24020	29474582	WT UvsW_replicate2	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	treatment_protocol	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	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 	IPTG was	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	iptg	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002105
SRR6048174	GSE103937	GSM2786604	GPL24020	29474582	WT UvsW_replicate3	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	treatment_protocol	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	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 	IPTG was	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	iptg	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002105
SRR6048175	GSE103937	GSM2786605	GPL24020	29474582	∆rho UvsW_replicate1	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	treatment_protocol	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	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 	IPTG was	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	iptg	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002105
SRR6048176	GSE103937	GSM2786606	GPL24020	29474582	∆rho UvsW_replicate2	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	treatment_protocol	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	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 	IPTG was	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	iptg	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002105
SRR6048177	GSE103937	GSM2786607	GPL24020	29474582	∆rho UvsW_replicate3	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	treatment_protocol	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	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 	IPTG was	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	iptg	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002105
SRR6048178	GSE103937	GSM2786608	GPL24020	29474582	∆nusG UvsW_replicate1	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	treatment_protocol	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	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 	IPTG was	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	iptg	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002105
SRR6048179	GSE103937	GSM2786609	GPL24020	29474582	∆nusG UvsW_replicate2	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	treatment_protocol	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	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 	IPTG was	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	iptg	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002105
SRR6048180	GSE103937	GSM2786610	GPL24020	29474582	∆nusG UvsW_replicate3	Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli	GPL24020: Illumina NextSeq 500 (Escherichia coli K-12)	treatment_protocol	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	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 	IPTG was	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE103937/GSE103937.soft.gz	iptg	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002105
SRR6125551	GSE104504	GSM2802560	GPL21222-GPL21726	29205228	fis.rep1.me	Crosstalk between global regulators CRP and FIS in E. coli.	GPL21222: Illumina NextSeq 500 (Escherichia coli). GPL21726: Ion Torrent Proton (Escherichia coli)	characteristics	growth phase: Mid exponential PGCGROWTHCONDITIONS	growth phase : <Anti> Mid </Anti> <Phase> exponential </Phase> 	exponential	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE104504/GSE104504.soft.gz	exponential phase	100	79	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002864
SRR6125552	GSE104504	GSM2802561	GPL21222-GPL21726	29205228	fis.rep2.me	Crosstalk between global regulators CRP and FIS in E. coli.	GPL21222: Illumina NextSeq 500 (Escherichia coli). GPL21726: Ion Torrent Proton (Escherichia coli)	characteristics	growth phase: Mid exponential PGCGROWTHCONDITIONS	growth phase : <Anti> Mid </Anti> <Phase> exponential </Phase> 	exponential	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE104504/GSE104504.soft.gz	exponential phase	100	79	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002864
SRR6125556	GSE104504	GSM2802565	GPL21222-GPL21726	29205228	cya.rep2.me	Crosstalk between global regulators CRP and FIS in E. coli.	GPL21222: Illumina NextSeq 500 (Escherichia coli). GPL21726: Ion Torrent Proton (Escherichia coli)	characteristics	growth phase: Mid exponential PGCGROWTHCONDITIONS	growth phase : <Anti> Mid </Anti> <Phase> exponential </Phase> 	exponential	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE104504/GSE104504.soft.gz	exponential phase	100	79	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002864
SRR6125557	GSE104504	GSM2802566	GPL21222-GPL21726	29205228	wt.rep1.me	Crosstalk between global regulators CRP and FIS in E. coli.	GPL21222: Illumina NextSeq 500 (Escherichia coli). GPL21726: Ion Torrent Proton (Escherichia coli)	characteristics	growth phase: Mid exponential PGCGROWTHCONDITIONS	growth phase : <Anti> Mid </Anti> <Phase> exponential </Phase> 	exponential	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE104504/GSE104504.soft.gz	exponential phase	100	79	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002864
SRR6125558	GSE104504	GSM2802567	GPL21222-GPL21726	29205228	wt.rep2.me	Crosstalk between global regulators CRP and FIS in E. coli.	GPL21222: Illumina NextSeq 500 (Escherichia coli). GPL21726: Ion Torrent Proton (Escherichia coli)	characteristics	growth phase: Mid exponential PGCGROWTHCONDITIONS	growth phase : <Anti> Mid </Anti> <Phase> exponential </Phase> 	exponential	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE104504/GSE104504.soft.gz	exponential phase	100	79	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002864
SRR1173965	GSE55199	GSM1331409	GPL15010-GPL17024	25266388	LB 0.4 B1 TEX neg L1 GA	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	characteristics	growth phase: exponential PGCGROWTHCONDITIONS	growth phase : <Phase> exponential </Phase> 	exponential	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	exponential phase	100	79	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002864
SRR1173966	GSE55199	GSM1331410	GPL15010-GPL17024	25266388	LB 0.4 B1 TEX pos L1 GA	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	characteristics	growth phase: exponential PGCGROWTHCONDITIONS	growth phase : <Phase> exponential </Phase> 	exponential	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	exponential phase	100	79	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002864
SRR1173967	GSE55199	GSM1331411	GPL15010-GPL17024	25266388	LB 0.4 B2 TEX neg L1 HS1	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	characteristics	growth phase: exponential PGCGROWTHCONDITIONS	growth phase : <Phase> exponential </Phase> 	exponential	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	exponential phase	100	79	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002864
SRR1173968	GSE55199	GSM1331412	GPL15010-GPL17024	25266388	LB 0.4 B2 TEX neg L1 HS2	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	characteristics	growth phase: exponential PGCGROWTHCONDITIONS	growth phase : <Phase> exponential </Phase> 	exponential	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	exponential phase	100	79	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002864
SRR1173969	GSE55199	GSM1331413	GPL15010-GPL17024	25266388	LB 0.4 B2 TEX pos L1 HS1	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	characteristics	growth phase: exponential PGCGROWTHCONDITIONS	growth phase : <Phase> exponential </Phase> 	exponential	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	exponential phase	100	79	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002864
SRR1173970	GSE55199	GSM1331414	GPL15010-GPL17024	25266388	LB 0.4 B2 TEX pos L1 HS2	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	characteristics	growth phase: exponential PGCGROWTHCONDITIONS	growth phase : <Phase> exponential </Phase> 	exponential	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	exponential phase	100	79	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002864
SRR1173982	GSE55199	GSM1331426	GPL15010-GPL17024	25266388	M63 0.4 B1 TEX pos L1 GA	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	characteristics	growth phase: exponential PGCGROWTHCONDITIONS	growth phase : <Phase> exponential </Phase> 	exponential	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	exponential phase	100	79	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002864
SRR1173983	GSE55199	GSM1331427	GPL15010-GPL17024	25266388	M63 0.4 B2 TEX neg L1 HS1	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	characteristics	growth phase: exponential PGCGROWTHCONDITIONS	growth phase : <Phase> exponential </Phase> 	exponential	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	exponential phase	100	79	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002864
SRR1173984	GSE55199	GSM1331428	GPL15010-GPL17024	25266388	M63 0.4 B2 TEX neg L1 HS2	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	characteristics	growth phase: exponential PGCGROWTHCONDITIONS	growth phase : <Phase> exponential </Phase> 	exponential	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	exponential phase	100	79	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002864
SRR1173985	GSE55199	GSM1331429	GPL15010-GPL17024	25266388	M63 0.4 B2 TEX pos L1 HS1	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	characteristics	growth phase: exponential PGCGROWTHCONDITIONS	growth phase : <Phase> exponential </Phase> 	exponential	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	exponential phase	100	79	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002864
SRR1173986	GSE55199	GSM1331430	GPL15010-GPL17024	25266388	M63 0.4 B2 TEX pos L1 HS2	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	characteristics	growth phase: exponential PGCGROWTHCONDITIONS	growth phase : <Phase> exponential </Phase> 	exponential	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	exponential phase	100	79	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002864
SRR6354578	GSE107301	GSM2870440	GPL15010-GPL21117	29358050	RNA-seq of E. coli wt cells in stationary phase 30°C (30h)	Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21117: Illumina NextSeq 500 (Escherichia coli str. K-12 substr. MG1655)	characteristics	growth condition: MM + 0.12% casaminoacids +0.4% glucose at 30°C PGCGROWTHCONDITIONS	growth condition : <Supp> MM + 0.12 % casaminoacids +0.4 % glucose </Supp> at <Temp> 30 °C </Temp> 	30 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107301/GSE107301.soft.gz	30.0 C	100	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002695
SRR6354579	GSE107301	GSM2870441	GPL15010-GPL21117	29358050	RNA-seq of E. coli wt cells in stationary phase 30°C (30h) -Replicate 1	Multiscale structuring of the E. coli chromosome by nucleoid-associated and condensin proteins	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL21117: Illumina NextSeq 500 (Escherichia coli str. K-12 substr. MG1655)	characteristics	growth condition: MM + 0.12% casaminoacids +0.4% glucose at 30°C PGCGROWTHCONDITIONS	growth condition : <Supp> MM + 0.12 % casaminoacids +0.4 % glucose </Supp> at <Temp> 30 °C </Temp> 	30 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE107301/GSE107301.soft.gz	30.0 C	100	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002695
SRR389819	GSE34449	GSM849370	GPL15010	22232676	E_coli_transcriptome_1	Digital RNA Sequencing Minimizes Sequence-Dependent Bias and Amplification Noise with Optimized Single Molecule Barcodes	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	30 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE34449/GSE34449.soft.gz	30.0 C	100	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002695
SRR389820	GSE34449	GSM849371	GPL15010	22232676	E_coli_transcriptome_2	Digital RNA Sequencing Minimizes Sequence-Dependent Bias and Amplification Noise with Optimized Single Molecule Barcodes	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	30 °C	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE34449/GSE34449.soft.gz	30.0 C	100	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002695
SRR6449107	GSE108846	GSM2914313	GPL16085	29378945	CF104.3.3_y2	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR6449109	GSE108846	GSM2914315	GPL16085	29378945	CF108.4B_y3	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR6449111	GSE108846	GSM2914317	GPL16085	29378945	CON206.3A_y1	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR6449112	GSE108846	GSM2914318	GPL16085	29378945	CON206.3A_y2	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR6449113	GSE108846	GSM2914319	GPL16085	29378945	CON208.3A_y2	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR6449114	GSE108846	GSM2914320	GPL16085	29378945	CON208.3A_y6	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR6449115	GSE108846	GSM2914321	GPL16085	29378945	CF104.3.3_u1	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR6449116	GSE108846	GSM2914322	GPL16085	29378945	CF104.3.3_u7	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR6449117	GSE108846	GSM2914323	GPL16085	29378945	CF108.4B_u1	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR6449118	GSE108846	GSM2914324	GPL16085	29378945	CF108.4B_u2	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR6449119	GSE108846	GSM2914325	GPL16085	29378945	CON206.3A_u1	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR6449120	GSE108846	GSM2914326	GPL16085	29378945	CON206.3A_u2	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR6449121	GSE108846	GSM2914327	GPL16085	29378945	CON208.3A_u1	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR6449122	GSE108846	GSM2914328	GPL16085	29378945	CON208.3A_u8	Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE108846/GSE108846.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR8164476	GSE122211	GSM3461156	GPL17024-GPL17439-GPL18995-GPL25769	31797920	MG_no_te_1	Expression profiling of E. coli K-12 MG1655	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)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR8164476	GSE122211	GSM3461156	GPL17024-GPL17439-GPL18995-GPL25769	31797920	MG_no_te_1	Expression profiling of E. coli K-12 MG1655	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)	characteristics	media: M9 minimal media w/ 0.2% glucose w/o trace elements PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / 0.2 % glucose w/o trace elements 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR8164477	GSE122211	GSM3461157	GPL17024-GPL17439-GPL18995-GPL25769	31797920	MG_no_te_2	Expression profiling of E. coli K-12 MG1655	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)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR8164477	GSE122211	GSM3461157	GPL17024-GPL17439-GPL18995-GPL25769	31797920	MG_no_te_2	Expression profiling of E. coli K-12 MG1655	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)	characteristics	media: M9 minimal media w/ 0.2% glucose w/o trace elements PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / 0.2 % glucose w/o trace elements 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR8164484	GSE122211	GSM3461164	GPL17024-GPL17439-GPL18995-GPL25769	31797920	MG_glu_1	Expression profiling of E. coli K-12 MG1655	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)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR8164484	GSE122211	GSM3461164	GPL17024-GPL17439-GPL18995-GPL25769	31797920	MG_glu_1	Expression profiling of E. coli K-12 MG1655	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)	characteristics	media: M9 minimal media w/ 0.2% glucose and 10mM glutamate PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 0.2 % glucose </Supp> and 10mM glutamate 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR8164485	GSE122211	GSM3461165	GPL17024-GPL17439-GPL18995-GPL25769	31797920	MG_glu_2	Expression profiling of E. coli K-12 MG1655	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)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR8164485	GSE122211	GSM3461165	GPL17024-GPL17439-GPL18995-GPL25769	31797920	MG_glu_2	Expression profiling of E. coli K-12 MG1655	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)	characteristics	media: M9 minimal media w/ 0.2% glucose and 10mM glutamate PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 0.2 % glucose </Supp> and 10mM glutamate 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR8164486	GSE122211	GSM3461166	GPL17024-GPL17439-GPL18995-GPL25769	31797920	MG_glc	Expression profiling of E. coli K-12 MG1655	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)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR8164486	GSE122211	GSM3461166	GPL17024-GPL17439-GPL18995-GPL25769	31797920	MG_glc	Expression profiling of E. coli K-12 MG1655	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)	characteristics	media: M9 minimal media w/ 0.2% glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 0.2 % glucose </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR8173227	GSE122295	GSM3463565	GPL21433	31797920	wt_glc__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR8173228	GSE122295	GSM3463566	GPL21433	31797920	wt_glc__2	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR8173229	GSE122295	GSM3463567	GPL21433	31797920	wt_glc__3	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR8173230	GSE122295	GSM3463568	GPL21433	31797920	wt_glc__4	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR8173231	GSE122295	GSM3463569	GPL21433	31797920	arg_sbt__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 4g/L D-sorbitol PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / 4g/L D-sorbitol 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR8173232	GSE122295	GSM3463570	GPL21433	31797920	arg_sbt__2	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 4g/L D-sorbitol PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / 4g/L D-sorbitol 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR8173233	GSE122295	GSM3463571	GPL21433	31797920	cytd_rib__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 4g/L D-ribose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / 4g/L D-ribose 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR8173234	GSE122295	GSM3463572	GPL21433	31797920	cytd_rib__2	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 4g/L D-ribose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / 4g/L D-ribose 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR8173235	GSE122295	GSM3463573	GPL21433	31797920	gth__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR8173236	GSE122295	GSM3463574	GPL21433	31797920	gth__2	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR8173237	GSE122295	GSM3463575	GPL21433	31797920	leu_glcr__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 4g/L glucarate PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / 4g/L glucarate 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR8173238	GSE122295	GSM3463576	GPL21433	31797920	leu_glcr__2	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 4g/L glucarate PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / 4g/L glucarate 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR8173239	GSE122295	GSM3463577	GPL21433	31797920	met_glc__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR8173240	GSE122295	GSM3463578	GPL21433	31797920	met_glc__2	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR8173241	GSE122295	GSM3463579	GPL21433	31797920	no3_anaero__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: anaerobic M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	media : <Air> anaerobic </Air> <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR8173242	GSE122295	GSM3463580	GPL21433	31797920	no3_anaero__2	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: anaerobic M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	media : <Air> anaerobic </Air> <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR8173243	GSE122295	GSM3463581	GPL21433	31797920	phe_acgam__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 4g/L N-acetylglucosamine PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / 4g/L N-acetylglucosamine 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR8173244	GSE122295	GSM3463582	GPL21433	31797920	phe_acgam__2	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 4g/L N-acetylglucosamine PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / 4g/L N-acetylglucosamine 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR8173245	GSE122295	GSM3463583	GPL21433	31797920	thm_gal__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 4g/L galactose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / 4g/L galactose 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR8173246	GSE122295	GSM3463584	GPL21433	31797920	thm_gal__2	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 4g/L galactose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / 4g/L galactose 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR8173247	GSE122295	GSM3463585	GPL21433	31797920	tyr_glcn__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 4g/L D-gluconate PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / 4g/L D-gluconate 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR8173248	GSE122295	GSM3463586	GPL21433	31797920	tyr_glcn__2	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 4g/L D-gluconate PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / 4g/L D-gluconate 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR9204648	GSE122295	GSM3854833	GPL21433	31797920	wt_glc_5__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR9204649	GSE122295	GSM3854834	GPL21433	31797920	wt_glc_6__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR9204650	GSE122295	GSM3854835	GPL21433	31797920	bw_delpurR_cytd__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 2g/L glucose and 1 mM cytidine PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose and 1 mM cytidine </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR9204651	GSE122295	GSM3854836	GPL21433	31797920	bw_delpurR_cytd__2	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 2g/L glucose and 1 mM cytidine PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose and 1 mM cytidine </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR9204652	GSE122295	GSM3854837	GPL21433	31797920	ade_glc__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 2g/L glucose and 100 mg/L adenine PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> and 100 mg/L adenine 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR9204653	GSE122295	GSM3854838	GPL21433	31797920	ade_glc__2	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 2g/L glucose and 100 mg/L adenine PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> and 100 mg/L adenine 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR8173221	GSE122296	GSM3463601	GPL16085	31797920	MG1655_1	Expression profiling of multiple Escherichia coli strains on glucose minimal media	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122296/GSE122296.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR8173222	GSE122296	GSM3463602	GPL16085	31797920	MG1655_2	Expression profiling of multiple Escherichia coli strains on glucose minimal media	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122296/GSE122296.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR8309841	GSE123554	GSM3507068	GPL18133		delta-fis rep1	Reconstruction of transcriptional regulatory networks of Fis and H-NS in Escherichia coli from genome wide data analysis	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE123554/GSE123554.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR8309842	GSE123554	GSM3507069	GPL18133		delta-fis rep2	Reconstruction of transcriptional regulatory networks of Fis and H-NS in Escherichia coli from genome wide data analysis	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE123554/GSE123554.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR8309843	GSE123554	GSM3507070	GPL18133		delta-hns rep1	Reconstruction of transcriptional regulatory networks of Fis and H-NS in Escherichia coli from genome wide data analysis	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE123554/GSE123554.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR8309844	GSE123554	GSM3507071	GPL18133		delta-hns rep2	Reconstruction of transcriptional regulatory networks of Fis and H-NS in Escherichia coli from genome wide data analysis	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE123554/GSE123554.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR9919224	GSE135516	GSM4013462	GPL24377	31651953	WT_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR9919225	GSE135516	GSM4013463	GPL24377	31651953	WT_2	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR9919226	GSE135516	GSM4013464	GPL24377	31651953	WT_H2O2_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR9919227	GSE135516	GSM4013465	GPL24377	31651953	WT_H2O2_2	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR9919228	GSE135516	GSM4013466	GPL24377	31651953	GMOS_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR9919229	GSE135516	GSM4013467	GPL24377	31651953	GMOS_2	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR9919230	GSE135516	GSM4013468	GPL24377	31651953	GMOS_H2O2_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR9919232	GSE135516	GSM4013470	GPL24377	31651953	EC ALE-1_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR9919233	GSE135516	GSM4013471	GPL24377	31651953	EC ALE-1_2	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR9919234	GSE135516	GSM4013472	GPL24377	31651953	EC ALE-1_H2O2_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR9919235	GSE135516	GSM4013473	GPL24377	31651953	EC ALE-1_H2O2_2	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR9919236	GSE135516	GSM4013474	GPL24377	31651953	EC ALE-2_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR9919237	GSE135516	GSM4013475	GPL24377	31651953	EC ALE-2_2	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR9919238	GSE135516	GSM4013476	GPL24377	31651953	EC ALE-2_H2O2_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR9919239	GSE135516	GSM4013477	GPL24377	31651953	EC ALE-2_H2O2_2	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR9919240	GSE135516	GSM4013478	GPL24377	31651953	EC ALE-3_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR9919241	GSE135516	GSM4013479	GPL24377	31651953	EC ALE-3_2	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR9919242	GSE135516	GSM4013480	GPL24377	31651953	EC ALE-3_H2O2_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR9919243	GSE135516	GSM4013481	GPL24377	31651953	EC ALE-3_H2O2_2	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR9919244	GSE135516	GSM4013482	GPL24377	31651953	EC ALE-4_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR9919245	GSE135516	GSM4013483	GPL24377	31651953	EC ALE-4_2	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR9919246	GSE135516	GSM4013484	GPL24377	31651953	EC ALE-4_H2O2_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR9919247	GSE135516	GSM4013485	GPL24377	31651953	EC ALE-4_H2O2_2	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR922260	GSE48324	GSM1174823	GPL16227	24987116	Mid log_wildtype_glc minimal media_aerobic rep1	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR922261	GSE48324	GSM1174824	GPL16227	24987116	Mid log_wildtype_glc minimal media_aerobic rep2	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR922262	GSE48324	GSM1174825	GPL16227	24987116	Mid log_wildtype_glc minimal media_aerobic rep3	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR922263	GSE48324	GSM1174826	GPL16227	24987116	Mid log_wildtype_glc minimal media + adenine_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR922264	GSE48324	GSM1174827	GPL16227	24987116	Mid log_wildtype_glc minimal media + L-tryptophan_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR922265	GSE48324	GSM1174828	GPL16227	24987116	Mid log_wildtype_glc minimal media_anaerobic rep1	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR922266	GSE48324	GSM1174829	GPL16227	24987116	Mid log_wildtype_glc minimal media_anaerobic rep2	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR922267	GSE48324	GSM1174830	GPL16227	24987116	Mid log_wildtype_glc minimal media_anaerobic rep3	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR922268	GSE48324	GSM1174831	GPL16227	24987116	Mid log_nac KO_glc minimal media_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR922269	GSE48324	GSM1174832	GPL16227	24987116	Mid log_nac KO_glc minimal media + adenine_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR922270	GSE48324	GSM1174833	GPL16227	24987116	Mid log_cra KO_glc minimal media_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR922271	GSE48324	GSM1174834	GPL16227	24987116	Mid log_cra KO_glc minimal media + L-tryptophan_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR922272	GSE48324	GSM1174835	GPL16227	24987116	Mid log_mntR KO_glc minimal media_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR922273	GSE48324	GSM1174836	GPL16227	24987116	Mid log_mntR KO_glc minimal media_anaerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR1168133	GSE54900	GSM1326347	GPL17439	25222563	WT with Fe 1 (RNA-seq)	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR1168134	GSE54900	GSM1326348	GPL17439	25222563	WT with Fe 2 (RNA-seq)	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR1168135	GSE54900	GSM1326349	GPL17439	25222563	WT with DPD 1 (RNA-seq)	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR1168136	GSE54900	GSM1326350	GPL17439	25222563	WT with DPD 2 (RNA-seq)	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR1168137	GSE54900	GSM1326351	GPL17439	25222563	Δfur with Fe 1 (RNA-seq)	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR1168138	GSE54900	GSM1326352	GPL17439	25222563	Δfur with Fe 2 (RNA-seq)	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR1168139	GSE54900	GSM1326353	GPL17439	25222563	Δfur with DPD 1 (RNA-seq)	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR1168140	GSE54900	GSM1326354	GPL17439	25222563	Δfur with DPD 2 (RNA-seq)	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR1787590	GSE65642	GSM1602347	GPL16085	29394395	WT glucose 1	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR1787591	GSE65642	GSM1602348	GPL16085	29394395	WT glucose 2	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR1787592	GSE65642	GSM1602349	GPL16085	29394395	WT fructose 1	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR1787593	GSE65642	GSM1602350	GPL16085	29394395	WT fructose 2	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR1787594	GSE65642	GSM1602351	GPL16085	29394395	WT acetate 1	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR1787595	GSE65642	GSM1602352	GPL16085	29394395	WT acetate 2	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR1787596	GSE65642	GSM1602353	GPL16085	29394395	Δcra glucose 1	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR1787597	GSE65642	GSM1602354	GPL16085	29394395	Δcra glucose 2	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR1787598	GSE65642	GSM1602355	GPL16085	29394395	Δcra fructose 1	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR1787599	GSE65642	GSM1602356	GPL16085	29394395	Δcra fructose 2	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR1787600	GSE65642	GSM1602357	GPL16085	29394395	Δcra acetate 1	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR1787601	GSE65642	GSM1602358	GPL16085	29394395	Δcra acetate 2	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR1796598	GSE65711	GSM1603386	GPL16085	26279566	WT PQ 1	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR1796599	GSE65711	GSM1603387	GPL16085	26279566	WT PQ 2	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR1796600	GSE65711	GSM1603388	GPL16085	26279566	ΔoxyR PQ 1	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR1796601	GSE65711	GSM1603389	GPL16085	26279566	ΔoxyR PQ 2	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR1796603	GSE65711	GSM1603391	GPL16085	26279566	ΔsoxR PQ 2	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR1796604	GSE65711	GSM1603392	GPL16085	26279566	ΔsoxS PQ 1	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR1796605	GSE65711	GSM1603393	GPL16085	26279566	ΔsoxS PQ 2	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR1824557	GSE66481	GSM1623160	GPL16085	26258987	WT pH5.5 1	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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> . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR1824558	GSE66481	GSM1623161	GPL16085	26258987	WT pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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> . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR1824559	GSE66481	GSM1623162	GPL16085	26258987	ΔgadE pH5.5 1	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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> . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR1824560	GSE66481	GSM1623163	GPL16085	26258987	ΔgadE pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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> . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR1824561	GSE66481	GSM1623164	GPL16085	26258987	ΔgadW pH5.5 1	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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> . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR1824562	GSE66481	GSM1623165	GPL16085	26258987	ΔgadW pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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> . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR1824563	GSE66481	GSM1623166	GPL16085	26258987	ΔgadX pH5.5 1	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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> . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR1824564	GSE66481	GSM1623167	GPL16085	26258987	ΔgadX pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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> . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR3194453	GSE78756	GSM2075722	GPL14548-GPL15010-GPL21530-GPL21531-GPL21532-GPL21533-GPL21534	27667363	Crooks_aero	Quantifying variation within the bacterial species E. coli	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])	growth_protocol	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	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> . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE78756/GSE78756.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR3194455SRR3194456	GSE78756	GSM2075723	GPL14548-GPL15010-GPL21530-GPL21531-GPL21532-GPL21533-GPL21534	27667363	Crooks_anaero	Quantifying variation within the bacterial species E. coli	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])	growth_protocol	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	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> . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE78756/GSE78756.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR4435464	GSE88980	GSM2356687	GPL17439	28526842	WT NaCl 1	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]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88980/GSE88980.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR4435465	GSE88980	GSM2356688	GPL17439	28526842	WT NaCl 2	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]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88980/GSE88980.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR4435466	GSE88980	GSM2356689	GPL17439	28526842	ΔompR NaCl 1	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]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88980/GSE88980.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR4435467	GSE88980	GSM2356690	GPL17439	28526842	ΔompR NaCl 2	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]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	M9 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88980/GSE88980.soft.gz	M9 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002526
SRR6781997	GSE111094	GSM3022135	GPL24659	33149261	WT rep1	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	phase: mid-log phase PGCGROWTHCONDITIONS	phase : <Phase> mid-log phase </Phase> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR6781998	GSE111094	GSM3022136	GPL24659	33149261	WT rep2	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	phase: mid-log phase PGCGROWTHCONDITIONS	phase : <Phase> mid-log phase </Phase> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR6781999	GSE111094	GSM3022137	GPL24659	33149261	yafC-KO rep1	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	phase: mid-log phase PGCGROWTHCONDITIONS	phase : <Phase> mid-log phase </Phase> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR6782000	GSE111094	GSM3022138	GPL24659	33149261	yafC-KO rep2	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	phase: mid-log phase PGCGROWTHCONDITIONS	phase : <Phase> mid-log phase </Phase> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR6782001	GSE111094	GSM3022139	GPL24659	33149261	yeiE-KO rep1	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	phase: mid-log phase PGCGROWTHCONDITIONS	phase : <Phase> mid-log phase </Phase> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR6782002	GSE111094	GSM3022140	GPL24659	33149261	yeiE-KO rep2	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	phase: mid-log phase PGCGROWTHCONDITIONS	phase : <Phase> mid-log phase </Phase> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR6782003	GSE111094	GSM3022141	GPL24659	33149261	yiaJ-KO rep1	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	phase: mid-log phase PGCGROWTHCONDITIONS	phase : <Phase> mid-log phase </Phase> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR6782004	GSE111094	GSM3022142	GPL24659	33149261	yiaJ-KO rep2	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	phase: mid-log phase PGCGROWTHCONDITIONS	phase : <Phase> mid-log phase </Phase> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR6782005	GSE111094	GSM3022143	GPL24659	33149261	yieP-KO rep1	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	phase: mid-log phase PGCGROWTHCONDITIONS	phase : <Phase> mid-log phase </Phase> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR6782006	GSE111094	GSM3022144	GPL24659	33149261	yieP-KO rep2	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	phase: mid-log phase PGCGROWTHCONDITIONS	phase : <Phase> mid-log phase </Phase> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR7057985	GSE111094	GSM3108934	GPL24659	33149261	WT-low-ph rep1	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	phase: mid-log phase PGCGROWTHCONDITIONS	phase : <Phase> mid-log phase </Phase> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR7057986	GSE111094	GSM3108935	GPL24659	33149261	WT-low-ph rep2	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	phase: mid-log phase PGCGROWTHCONDITIONS	phase : <Phase> mid-log phase </Phase> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR7057987	GSE111094	GSM3108936	GPL24659	33149261	WT-high-ph rep1	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	phase: mid-log phase PGCGROWTHCONDITIONS	phase : <Phase> mid-log phase </Phase> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR7057988	GSE111094	GSM3108937	GPL24659	33149261	WT-high-ph rep2	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	phase: mid-log phase PGCGROWTHCONDITIONS	phase : <Phase> mid-log phase </Phase> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR7057989	GSE111094	GSM3108938	GPL24659	33149261	ybaO-KO rep1	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	phase: mid-log phase PGCGROWTHCONDITIONS	phase : <Phase> mid-log phase </Phase> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR7057990	GSE111094	GSM3108939	GPL24659	33149261	ybaO-KO rep2	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	phase: mid-log phase PGCGROWTHCONDITIONS	phase : <Phase> mid-log phase </Phase> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR7057991	GSE111094	GSM3108940	GPL24659	33149261	ybaQ-KO rep1	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	phase: mid-log phase PGCGROWTHCONDITIONS	phase : <Phase> mid-log phase </Phase> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR7057992	GSE111094	GSM3108941	GPL24659	33149261	ybaQ-KO rep2	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	phase: mid-log phase PGCGROWTHCONDITIONS	phase : <Phase> mid-log phase </Phase> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR7057993	GSE111094	GSM3108942	GPL24659	33149261	ybiH-KO rep1	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	phase: mid-log phase PGCGROWTHCONDITIONS	phase : <Phase> mid-log phase </Phase> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR7057994	GSE111094	GSM3108943	GPL24659	33149261	ybiH-KO rep2	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	phase: mid-log phase PGCGROWTHCONDITIONS	phase : <Phase> mid-log phase </Phase> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR7057995	GSE111094	GSM3108944	GPL24659	33149261	ydcI-KO-low-ph rep1	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	phase: mid-log phase PGCGROWTHCONDITIONS	phase : <Phase> mid-log phase </Phase> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR7057996	GSE111094	GSM3108945	GPL24659	33149261	ydcI-KO-low-ph rep2	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	phase: mid-log phase PGCGROWTHCONDITIONS	phase : <Phase> mid-log phase </Phase> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR7057997	GSE111094	GSM3108946	GPL24659	33149261	ydcI-KO-high-ph rep1	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	phase: mid-log phase PGCGROWTHCONDITIONS	phase : <Phase> mid-log phase </Phase> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR7057998	GSE111094	GSM3108947	GPL24659	33149261	ydcI-KO-high-ph rep2	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	phase: mid-log phase PGCGROWTHCONDITIONS	phase : <Phase> mid-log phase </Phase> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR7057999	GSE111094	GSM3108948	GPL24659	33149261	yddM-KO rep1	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	phase: mid-log phase PGCGROWTHCONDITIONS	phase : <Phase> mid-log phase </Phase> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR7058000	GSE111094	GSM3108949	GPL24659	33149261	yddM-KO rep2	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	phase: mid-log phase PGCGROWTHCONDITIONS	phase : <Phase> mid-log phase </Phase> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR7058001	GSE111094	GSM3108950	GPL24659	33149261	yheO-KO rep1	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	phase: mid-log phase PGCGROWTHCONDITIONS	phase : <Phase> mid-log phase </Phase> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR7058002	GSE111094	GSM3108951	GPL24659	33149261	yheO-KO rep2	Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655 (RNA-seq data set)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	phase: mid-log phase PGCGROWTHCONDITIONS	phase : <Phase> mid-log phase </Phase> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE111094/GSE111094.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR8173221	GSE122296	GSM3463601	GPL16085	31797920	MG1655_1	Expression profiling of multiple Escherichia coli strains on glucose minimal media	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 ) . 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122296/GSE122296.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR8173222	GSE122296	GSM3463602	GPL16085	31797920	MG1655_2	Expression profiling of multiple Escherichia coli strains on glucose minimal media	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	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	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 ) . 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122296/GSE122296.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR364363	GSE33671	GSM832606	GPL10328	22153074	DSP1_AP	Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	characteristics	growth stage: mid-log phase PGCGROWTHCONDITIONS	growth stage : <Phase> mid-log phase </Phase> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE33671/GSE33671.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR364364	GSE33671	GSM832607	GPL10328	22153074	DSP1_Total	Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	characteristics	growth stage: mid-log phase PGCGROWTHCONDITIONS	growth stage : <Phase> mid-log phase </Phase> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE33671/GSE33671.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR364365	GSE33671	GSM832608	GPL10328	22153074	DSP2_AP	Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	characteristics	growth stage: mid-log phase PGCGROWTHCONDITIONS	growth stage : <Phase> mid-log phase </Phase> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE33671/GSE33671.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR364366	GSE33671	GSM832609	GPL10328	22153074	DSP2_Total	Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	characteristics	growth stage: mid-log phase PGCGROWTHCONDITIONS	growth stage : <Phase> mid-log phase </Phase> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE33671/GSE33671.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR364367	GSE33671	GSM832610	GPL10328	22153074	DSP3_AP	Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	characteristics	growth stage: mid-log phase PGCGROWTHCONDITIONS	growth stage : <Phase> mid-log phase </Phase> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE33671/GSE33671.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR364368	GSE33671	GSM832611	GPL10328	22153074	DSP3_Total	Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	characteristics	growth stage: mid-log phase PGCGROWTHCONDITIONS	growth stage : <Phase> mid-log phase </Phase> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE33671/GSE33671.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR364369	GSE33671	GSM832612	GPL10328	22153074	EDC1_AP	Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	characteristics	growth stage: mid-log phase PGCGROWTHCONDITIONS	growth stage : <Phase> mid-log phase </Phase> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE33671/GSE33671.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR364370	GSE33671	GSM832613	GPL10328	22153074	EDC1_Total	Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	characteristics	growth stage: mid-log phase PGCGROWTHCONDITIONS	growth stage : <Phase> mid-log phase </Phase> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE33671/GSE33671.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR1692165	GSE63817	GSM1558078	GPL14548-GPL18945	26495981	LB mRNA	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	growth_protocol	E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media PGCGROWTHCONDITIONS	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> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE63817/GSE63817.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR1692166	GSE63817	GSM1558079	GPL14548-GPL18945	26495981	LB RPF	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	growth_protocol	E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media PGCGROWTHCONDITIONS	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> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE63817/GSE63817.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR1692167	GSE63817	GSM1558080	GPL14548-GPL18945	26495981	LB mRNA technical replicate	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	growth_protocol	E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media PGCGROWTHCONDITIONS	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> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE63817/GSE63817.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR1692168	GSE63817	GSM1558081	GPL14548-GPL18945	26495981	LB RPF biological replicate	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	growth_protocol	E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media PGCGROWTHCONDITIONS	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> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE63817/GSE63817.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR1692169	GSE63817	GSM1558082	GPL14548-GPL18945	26495981	LB mRNA biological replicate	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	growth_protocol	E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media PGCGROWTHCONDITIONS	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> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE63817/GSE63817.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR1692173	GSE63817	GSM1558086	GPL14548-GPL18945	26495981	AT1 biological replicate	Secondary structure across the bacterial transcriptome reveals versatile roles in mRNA regulation and function	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL18945: Illumina Genome Analyzer IIx (Escherichia coli)	growth_protocol	E. coli MC4100 strain was cultured at 37°C to mid-log phase (OD600 ~ 0.4) in LB media PGCGROWTHCONDITIONS	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> 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE63817/GSE63817.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR1824557	GSE66481	GSM1623160	GPL16085	26258987	WT pH5.5 1	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	growth phase: mid-log phase (OD600 = 0.3) PGCGROWTHCONDITIONS	growth phase : <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR1824558	GSE66481	GSM1623161	GPL16085	26258987	WT pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	growth phase: mid-log phase (OD600 = 0.3) PGCGROWTHCONDITIONS	growth phase : <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR1824559	GSE66481	GSM1623162	GPL16085	26258987	ΔgadE pH5.5 1	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	growth phase: mid-log phase (OD600 = 0.3) PGCGROWTHCONDITIONS	growth phase : <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR1824560	GSE66481	GSM1623163	GPL16085	26258987	ΔgadE pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	growth phase: mid-log phase (OD600 = 0.3) PGCGROWTHCONDITIONS	growth phase : <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR1824561	GSE66481	GSM1623164	GPL16085	26258987	ΔgadW pH5.5 1	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	growth phase: mid-log phase (OD600 = 0.3) PGCGROWTHCONDITIONS	growth phase : <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR1824562	GSE66481	GSM1623165	GPL16085	26258987	ΔgadW pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	growth phase: mid-log phase (OD600 = 0.3) PGCGROWTHCONDITIONS	growth phase : <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR1824563	GSE66481	GSM1623166	GPL16085	26258987	ΔgadX pH5.5 1	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	growth phase: mid-log phase (OD600 = 0.3) PGCGROWTHCONDITIONS	growth phase : <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR1824564	GSE66481	GSM1623167	GPL16085	26258987	ΔgadX pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	growth phase: mid-log phase (OD600 = 0.3) PGCGROWTHCONDITIONS	growth phase : <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) 	mid-log phase	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	mid log phase	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002872
SRR7140738	GSE114262	GSM3138597	GPL18133	30948634	dnaB-Ts ΔahpC_30°C	RNA-seq Analyzes Transcriptomes of dnaB-Ts and dnaB-Ts ΔahpC at Both Permissive and Non-permissive Temperature	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	Genome_build: E.coli K12 BW25113 PGCGROWTHCONDITIONS	Genome _ build : <Gtype> E.coli K12 BW25113 </Gtype> 	E.coli K12 BW25113	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE114262/GSE114262.soft.gz	Escherichia coli BW25113	80	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002505
SRR7140739	GSE114262	GSM3138598	GPL18133	30948634	dnaB-Ts_42°C	RNA-seq Analyzes Transcriptomes of dnaB-Ts and dnaB-Ts ΔahpC at Both Permissive and Non-permissive Temperature	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	Genome_build: E.coli K12 BW25113 PGCGROWTHCONDITIONS	Genome _ build : <Gtype> E.coli K12 BW25113 </Gtype> 	E.coli K12 BW25113	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE114262/GSE114262.soft.gz	Escherichia coli BW25113	80	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002505
SRR7140740	GSE114262	GSM3138599	GPL18133	30948634	dnaB-Ts ΔahpC_42°C	RNA-seq Analyzes Transcriptomes of dnaB-Ts and dnaB-Ts ΔahpC at Both Permissive and Non-permissive Temperature	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	Genome_build: E.coli K12 BW25113 PGCGROWTHCONDITIONS	Genome _ build : <Gtype> E.coli K12 BW25113 </Gtype> 	E.coli K12 BW25113	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE114262/GSE114262.soft.gz	Escherichia coli BW25113	80	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002505
SRR7140738	GSE114262	GSM3138597	GPL18133	30948634	dnaB-Ts ΔahpC_30°C	RNA-seq Analyzes Transcriptomes of dnaB-Ts and dnaB-Ts ΔahpC at Both Permissive and Non-permissive Temperature	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	SB medium	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE114262/GSE114262.soft.gz	synH medium	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003163
SRR7140739	GSE114262	GSM3138598	GPL18133	30948634	dnaB-Ts_42°C	RNA-seq Analyzes Transcriptomes of dnaB-Ts and dnaB-Ts ΔahpC at Both Permissive and Non-permissive Temperature	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	SB medium	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE114262/GSE114262.soft.gz	synH medium	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003163
SRR7140740	GSE114262	GSM3138599	GPL18133	30948634	dnaB-Ts ΔahpC_42°C	RNA-seq Analyzes Transcriptomes of dnaB-Ts and dnaB-Ts ΔahpC at Both Permissive and Non-permissive Temperature	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	SB medium	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE114262/GSE114262.soft.gz	synH medium	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003163
SRR7537397	GSE117326	GSM3291044	GPL25346		envz600	Gene expression profiles in E. coli under different frequency signals	GPL25346: HiSeq X Ten (Escherichia coli)	characteristics	plasmid: pLCenvZ, pPCB (wild type) PGCGROWTHCONDITIONS	plasmid : <Gtype> pLCenvZ , pPCB ( wild type ) </Gtype> 	pLCenvZ , pPCB ( wild type )	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117326/GSE117326.soft.gz	wild type	100	58	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002470
SRR7537398	GSE117326	GSM3291045	GPL25346		envz900	Gene expression profiles in E. coli under different frequency signals	GPL25346: HiSeq X Ten (Escherichia coli)	characteristics	plasmid: pLCenvZ, pPCB (wild type) PGCGROWTHCONDITIONS	plasmid : <Gtype> pLCenvZ , pPCB ( wild type ) </Gtype> 	pLCenvZ , pPCB ( wild type )	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117326/GSE117326.soft.gz	wild type	100	58	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002470
SRR7537402	GSE117326	GSM3291049	GPL25346		envz3600	Gene expression profiles in E. coli under different frequency signals	GPL25346: HiSeq X Ten (Escherichia coli)	characteristics	plasmid: pLCenvZ, pPCB (wild type) PGCGROWTHCONDITIONS	plasmid : <Gtype> pLCenvZ , pPCB ( wild type ) </Gtype> 	pLCenvZ , pPCB ( wild type )	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117326/GSE117326.soft.gz	wild type	100	58	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002470
SRR8449235	GSE117737	GSM3566393	GPL16085-GPL21222	31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 4	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	growth_protocol	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	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 . 	LB media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	LB medium	82	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002533
SRR8449235	GSE117737	GSM3566393	GPL16085-GPL21222	31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 4	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	treatment_protocol	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	<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 . 	LB media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	LB medium	82	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002533
SRR8449236	GSE117737	GSM3566394	GPL16085-GPL21222	31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 5	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	growth_protocol	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	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 . 	LB media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	LB medium	82	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002533
SRR8449236	GSE117737	GSM3566394	GPL16085-GPL21222	31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 5	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	treatment_protocol	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	<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 . 	LB media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	LB medium	82	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002533
SRR8449237	GSE117737	GSM3566395	GPL16085-GPL21222	31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 6	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	growth_protocol	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	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 . 	LB media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	LB medium	82	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002533
SRR8449237	GSE117737	GSM3566395	GPL16085-GPL21222	31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 6	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	treatment_protocol	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	<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 . 	LB media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	LB medium	82	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002533
SRR8449238	GSE117737	GSM3566396	GPL16085-GPL21222	31308523	RNA-seq WT log phase related to total SEnd-seq WT stationary phase rep4	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	growth_protocol	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	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 . 	LB media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	LB medium	82	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002533
SRR8449238	GSE117737	GSM3566396	GPL16085-GPL21222	31308523	RNA-seq WT log phase related to total SEnd-seq WT stationary phase rep4	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	treatment_protocol	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	<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 . 	LB media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	LB medium	82	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002533
SRR1927169	GSE67218	GSM1642593	GPL17439		RNA-seq 37C LB rep1	Transcriptional expression level of E. coli at 37 ℃ in LB media	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	extract_protocol	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	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 ) . 	LB media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE67218/GSE67218.soft.gz	LB medium	82	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002533
SRR1927170	GSE67218	GSM1642594	GPL17439		RNA-seq 37C LB rep2	Transcriptional expression level of E. coli at 37 ℃ in LB media	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	extract_protocol	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	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 ) . 	LB media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE67218/GSE67218.soft.gz	LB medium	82	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002533
SRR8449235	GSE117737	GSM3566393	GPL16085-GPL21222	31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 4	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	treatment_protocol	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	<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 . 	Wild type	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	wild type	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002470
SRR8449236	GSE117737	GSM3566394	GPL16085-GPL21222	31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 5	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	treatment_protocol	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	<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 . 	Wild type	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	wild type	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002470
SRR8449237	GSE117737	GSM3566395	GPL16085-GPL21222	31308523	RNA-seq WT log phase related to total SEnd-seq WT log phase rep 6	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	treatment_protocol	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	<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 . 	Wild type	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	wild type	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002470
SRR8449238	GSE117737	GSM3566396	GPL16085-GPL21222	31308523	RNA-seq WT log phase related to total SEnd-seq WT stationary phase rep4	Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria	GPL16085: Illumina MiSeq (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	treatment_protocol	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	<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 . 	Wild type	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE117737/GSE117737.soft.gz	wild type	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002470
SRR1411272	GSE58556	GSM1413874	GPL18814	25483350	WT_glucose_log	RNA sequencing based analysis of the bacterial transcriptome	GPL18814: Illumina HiSeq 2000 (Escherichia coli BW38028)	growth_protocol	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	<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 . 	Wild type	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE58556/GSE58556.soft.gz	wild type	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002470
SRR8164476	GSE122211	GSM3461156	GPL17024-GPL17439-GPL18995-GPL25769	31797920	MG_no_te_1	Expression profiling of E. coli K-12 MG1655	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)	growth_protocol	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	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 . 	37 ℃	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	37.0 C	100	50	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002697
SRR8164477	GSE122211	GSM3461157	GPL17024-GPL17439-GPL18995-GPL25769	31797920	MG_no_te_2	Expression profiling of E. coli K-12 MG1655	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)	growth_protocol	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	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 . 	37 ℃	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	37.0 C	100	50	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002697
SRR8164484	GSE122211	GSM3461164	GPL17024-GPL17439-GPL18995-GPL25769	31797920	MG_glu_1	Expression profiling of E. coli K-12 MG1655	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)	growth_protocol	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	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 . 	37 ℃	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	37.0 C	100	50	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002697
SRR8164485	GSE122211	GSM3461165	GPL17024-GPL17439-GPL18995-GPL25769	31797920	MG_glu_2	Expression profiling of E. coli K-12 MG1655	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)	growth_protocol	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	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 . 	37 ℃	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	37.0 C	100	50	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002697
SRR8164486	GSE122211	GSM3461166	GPL17024-GPL17439-GPL18995-GPL25769	31797920	MG_glc	Expression profiling of E. coli K-12 MG1655	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)	growth_protocol	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	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 . 	37 ℃	Temperature	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122211/GSE122211.soft.gz	37.0 C	100	50	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002697
SRR8173227	GSE122295	GSM3463565	GPL21433	31797920	wt_glc__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	2g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	glucose 2 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003239
SRR8173228	GSE122295	GSM3463566	GPL21433	31797920	wt_glc__2	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	2g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	glucose 2 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003239
SRR8173229	GSE122295	GSM3463567	GPL21433	31797920	wt_glc__3	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	2g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	glucose 2 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003239
SRR8173230	GSE122295	GSM3463568	GPL21433	31797920	wt_glc__4	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	2g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	glucose 2 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003239
SRR8173235	GSE122295	GSM3463573	GPL21433	31797920	gth__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	2g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	glucose 2 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003239
SRR8173236	GSE122295	GSM3463574	GPL21433	31797920	gth__2	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	2g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	glucose 2 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003239
SRR8173239	GSE122295	GSM3463577	GPL21433	31797920	met_glc__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	2g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	glucose 2 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003239
SRR8173240	GSE122295	GSM3463578	GPL21433	31797920	met_glc__2	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	2g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	glucose 2 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003239
SRR8173241	GSE122295	GSM3463579	GPL21433	31797920	no3_anaero__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: anaerobic M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	media : <Air> anaerobic </Air> <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	2g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	glucose 2 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003239
SRR8173242	GSE122295	GSM3463580	GPL21433	31797920	no3_anaero__2	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: anaerobic M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	media : <Air> anaerobic </Air> <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	2g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	glucose 2 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003239
SRR9204648	GSE122295	GSM3854833	GPL21433	31797920	wt_glc_5__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	2g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	glucose 2 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003239
SRR9204649	GSE122295	GSM3854834	GPL21433	31797920	wt_glc_6__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	2g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	glucose 2 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003239
SRR9204652	GSE122295	GSM3854837	GPL21433	31797920	ade_glc__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 2g/L glucose and 100 mg/L adenine PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> and 100 mg/L adenine 	2g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	glucose 2 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003239
SRR9204653	GSE122295	GSM3854838	GPL21433	31797920	ade_glc__2	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 2g/L glucose and 100 mg/L adenine PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> and 100 mg/L adenine 	2g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	glucose 2 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003239
SRR8173221	GSE122296	GSM3463601	GPL16085	31797920	MG1655_1	Expression profiling of multiple Escherichia coli strains on glucose minimal media	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	2g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122296/GSE122296.soft.gz	glucose 2 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003239
SRR8173222	GSE122296	GSM3463602	GPL16085	31797920	MG1655_2	Expression profiling of multiple Escherichia coli strains on glucose minimal media	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	media: M9 minimal media w/ 2g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose </Supp> 	2g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122296/GSE122296.soft.gz	glucose 2 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003239
SRR8173233	GSE122295	GSM3463571	GPL21433	31797920	cytd_rib__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	supplement: Cytidine (1 mM) PGCGROWTHCONDITIONS	supplement : <Anti> Cytidine </Anti> <Supp> ( 1 mM ) </Supp> 	( 1 mM )	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	mm	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000011586
SRR8173234	GSE122295	GSM3463572	GPL21433	31797920	cytd_rib__2	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	supplement: Cytidine (1 mM) PGCGROWTHCONDITIONS	supplement : <Anti> Cytidine </Anti> <Supp> ( 1 mM ) </Supp> 	( 1 mM )	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	mm	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000011586
SRR9204650	GSE122295	GSM3854835	GPL21433	31797920	bw_delpurR_cytd__1	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 2g/L glucose and 1 mM cytidine PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose and 1 mM cytidine </Supp> 	2g/L glucose and 1 mM cytidine	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	glucose 120 mM	83	59	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002775
SRR9204651	GSE122295	GSM3854836	GPL21433	31797920	bw_delpurR_cytd__2	Expression profiling to identify independent regulatory signals in Escherichia coli	GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	media: M9 minimal media w/ 2g/L glucose and 1 mM cytidine PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 2g/L glucose and 1 mM cytidine </Supp> 	2g/L glucose and 1 mM cytidine	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE122295/GSE122295.soft.gz	glucose 120 mM	83	59	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002775
SRR8309841	GSE123554	GSM3507068	GPL18133		delta-fis rep1	Reconstruction of transcriptional regulatory networks of Fis and H-NS in Escherichia coli from genome wide data analysis	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	characteristics	material type: whole organism PGCGROWTHCONDITIONS	<Gtype> material type </Gtype> : <Gtype> whole organism </Gtype> 	whole organism	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE123554/GSE123554.soft.gz	Organism	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002467
SRR8309842	GSE123554	GSM3507069	GPL18133		delta-fis rep2	Reconstruction of transcriptional regulatory networks of Fis and H-NS in Escherichia coli from genome wide data analysis	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	characteristics	material type: whole organism PGCGROWTHCONDITIONS	<Gtype> material type </Gtype> : <Gtype> whole organism </Gtype> 	whole organism	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE123554/GSE123554.soft.gz	Organism	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002467
SRR8309843	GSE123554	GSM3507070	GPL18133		delta-hns rep1	Reconstruction of transcriptional regulatory networks of Fis and H-NS in Escherichia coli from genome wide data analysis	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	characteristics	material type: whole organism PGCGROWTHCONDITIONS	<Gtype> material type </Gtype> : <Gtype> whole organism </Gtype> 	whole organism	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE123554/GSE123554.soft.gz	Organism	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002467
SRR8309844	GSE123554	GSM3507071	GPL18133		delta-hns rep2	Reconstruction of transcriptional regulatory networks of Fis and H-NS in Escherichia coli from genome wide data analysis	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	characteristics	material type: whole organism PGCGROWTHCONDITIONS	<Gtype> material type </Gtype> : <Gtype> whole organism </Gtype> 	whole organism	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE123554/GSE123554.soft.gz	Organism	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002467
SRR8587784	GSE126710	GSM3611666	GPL26204	31208335	E. coli K-12 MG1655_R1 [MG_1]	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GPL26204: NextSeq 550 (Escherichia coli K-12)	characteristics	genotype/variation: naive (wild type) PGCGROWTHCONDITIONS	genotype/variation : <Gtype> naive ( wild type ) </Gtype> 	naive ( wild type )	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE126710/GSE126710.soft.gz	wild type	100	75	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002470
SRR8587785	GSE126710	GSM3611667	GPL26204	31208335	E. coli K-12 MG1655_R2 [MG_2]	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GPL26204: NextSeq 550 (Escherichia coli K-12)	characteristics	genotype/variation: naive (wild type) PGCGROWTHCONDITIONS	genotype/variation : <Gtype> naive ( wild type ) </Gtype> 	naive ( wild type )	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE126710/GSE126710.soft.gz	wild type	100	75	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002470
SRR8587786	GSE126710	GSM3611668	GPL26204	31208335	E. coli K-12 MG1655_R3 [MG_3]	RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens	GPL26204: NextSeq 550 (Escherichia coli K-12)	characteristics	genotype/variation: naive (wild type) PGCGROWTHCONDITIONS	genotype/variation : <Gtype> naive ( wild type ) </Gtype> 	naive ( wild type )	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE126710/GSE126710.soft.gz	wild type	100	75	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002470
SRR9919224	GSE135516	GSM4013462	GPL24377	31651953	WT_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	source_name	WT_mid-log phase bacteria culture PGCGROWTHCONDITIONS	<Gtype> WT </Gtype> _ <Phase> mid-log phase </Phase> bacteria culture 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR9919225	GSE135516	GSM4013463	GPL24377	31651953	WT_2	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	source_name	WT_mid-log phase bacteria culture PGCGROWTHCONDITIONS	<Gtype> WT </Gtype> _ <Phase> mid-log phase </Phase> bacteria culture 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR9919226	GSE135516	GSM4013464	GPL24377	31651953	WT_H2O2_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	source_name	WT_H2O2_mid-log phase bacteria culture PGCGROWTHCONDITIONS	<Gtype> WT </Gtype> _ H2O2 _ <Phase> mid-log phase </Phase> bacteria culture 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR9919227	GSE135516	GSM4013465	GPL24377	31651953	WT_H2O2_2	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	source_name	WT_H2O2_mid-log phase bacteria culture PGCGROWTHCONDITIONS	<Gtype> WT </Gtype> _ H2O2 _ <Phase> mid-log phase </Phase> bacteria culture 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR10907640	GSE143855	GSM4275442	GPL24659	33172971	WT_LB_R1	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	genotype: WT PGCGROWTHCONDITIONS	genotype : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR10907641	GSE143855	GSM4275443	GPL24659	33172971	WT_LB_R2	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	genotype: WT PGCGROWTHCONDITIONS	genotype : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR10907642	GSE143855	GSM4275444	GPL24659	33172971	WT_EtOH_R1	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	genotype: WT PGCGROWTHCONDITIONS	genotype : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR10907656	GSE143855	GSM4275458	GPL24659	33172971	WT_01-KCl_R1	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	genotype: WT PGCGROWTHCONDITIONS	genotype : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR10907657	GSE143855	GSM4275459	GPL24659	33172971	WT_01-KCl_R2	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	genotype: WT PGCGROWTHCONDITIONS	genotype : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR10907658	GSE143855	GSM4275460	GPL24659	33172971	WT_115-KCl_R1	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	genotype: WT PGCGROWTHCONDITIONS	genotype : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR10907659	GSE143855	GSM4275461	GPL24659	33172971	WT_115-KCl_R2	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	genotype: WT PGCGROWTHCONDITIONS	genotype : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR10907664	GSE143855	GSM4275466	GPL24659	33172971	WT_M9-P_R1	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	genotype: WT PGCGROWTHCONDITIONS	genotype : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR10907665	GSE143855	GSM4275467	GPL24659	33172971	WT_M9-P_R2	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	genotype: WT PGCGROWTHCONDITIONS	genotype : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR10907670	GSE143855	GSM4275472	GPL24659	33172971	WT_ZnCl2_R1	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	genotype: WT PGCGROWTHCONDITIONS	genotype : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR10907671	GSE143855	GSM4275473	GPL24659	33172971	WT_ZnCl2_R2	Validated transcriptional regulatory roles for five two-component systems in E. coli (RNA-seq dataset)	GPL24659: Illumina HiSeq 4000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	genotype: WT PGCGROWTHCONDITIONS	genotype : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE143855/GSE143855.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR794848	GSE45443	GSM1104402	GPL15010	23716638	WT_1	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	genotype: WT PGCGROWTHCONDITIONS	genotype : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR794849	GSE45443	GSM1104403	GPL15010	23716638	WT_2	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	genotype: WT PGCGROWTHCONDITIONS	genotype : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR794850	GSE45443	GSM1104404	GPL15010	23716638	WT_3	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	genotype: WT PGCGROWTHCONDITIONS	genotype : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR794851	GSE45443	GSM1104405	GPL15010	23716638	wt_T_1	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	genotype: WT PGCGROWTHCONDITIONS	genotype : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR794852	GSE45443	GSM1104406	GPL15010	23716638	wt_T_2	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	genotype: WT PGCGROWTHCONDITIONS	genotype : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR794853	GSE45443	GSM1104407	GPL15010	23716638	wt_T_3	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	genotype: WT PGCGROWTHCONDITIONS	genotype : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR794854	GSE45443	GSM1104408	GPL15010	23716638	wt_un_1	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	genotype: WT PGCGROWTHCONDITIONS	genotype : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR794856	GSE45443	GSM1104410	GPL15010	23716638	wt_un_3	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	genotype: WT PGCGROWTHCONDITIONS	genotype : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR794869	GSE45443	GSM1104423	GPL15010	23716638	WT_minus_2DG_1	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	genotype: WT PGCGROWTHCONDITIONS	genotype : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR794870	GSE45443	GSM1104424	GPL15010	23716638	WT_minus_2DG_2	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	genotype: WT PGCGROWTHCONDITIONS	genotype : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR794871	GSE45443	GSM1104425	GPL15010	23716638	WT_minus_2DG_3	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	genotype: WT PGCGROWTHCONDITIONS	genotype : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR794872	GSE45443	GSM1104426	GPL15010	23716638	WT_plus_2DG_1	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	genotype: WT PGCGROWTHCONDITIONS	genotype : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR794873	GSE45443	GSM1104427	GPL15010	23716638	WT_plus_2DG_2	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	genotype: WT PGCGROWTHCONDITIONS	genotype : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR794874	GSE45443	GSM1104428	GPL15010	23716638	WT_plus_2DG_3	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	genotype: WT PGCGROWTHCONDITIONS	genotype : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR1168133	GSE54900	GSM1326347	GPL17439	25222563	WT with Fe 1 (RNA-seq)	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	characteristics	genotype/variation: WT PGCGROWTHCONDITIONS	genotype/variation : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR1168134	GSE54900	GSM1326348	GPL17439	25222563	WT with Fe 2 (RNA-seq)	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	characteristics	genotype/variation: WT PGCGROWTHCONDITIONS	genotype/variation : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR1168135	GSE54900	GSM1326349	GPL17439	25222563	WT with DPD 1 (RNA-seq)	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	characteristics	genotype/variation: WT PGCGROWTHCONDITIONS	genotype/variation : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR1168136	GSE54900	GSM1326350	GPL17439	25222563	WT with DPD 2 (RNA-seq)	Deciphering the Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli [RNA-seq]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	characteristics	genotype/variation: WT PGCGROWTHCONDITIONS	genotype/variation : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE54900/GSE54900.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR1787590	GSE65642	GSM1602347	GPL16085	29394395	WT glucose 1	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	source_name	WT_glucose PGCGROWTHCONDITIONS	<Gtype> WT </Gtype> _ <Supp> glucose </Supp> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR1787590	GSE65642	GSM1602347	GPL16085	29394395	WT glucose 1	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	genotype/variation: WT PGCGROWTHCONDITIONS	genotype/variation : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR1787591	GSE65642	GSM1602348	GPL16085	29394395	WT glucose 2	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	source_name	WT_glucose PGCGROWTHCONDITIONS	<Gtype> WT </Gtype> _ <Supp> glucose </Supp> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR1787591	GSE65642	GSM1602348	GPL16085	29394395	WT glucose 2	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	genotype/variation: WT PGCGROWTHCONDITIONS	genotype/variation : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR1787592	GSE65642	GSM1602349	GPL16085	29394395	WT fructose 1	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	source_name	WT_fructose PGCGROWTHCONDITIONS	<Gtype> WT </Gtype> _ <Supp> fructose </Supp> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR1787592	GSE65642	GSM1602349	GPL16085	29394395	WT fructose 1	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	genotype/variation: WT PGCGROWTHCONDITIONS	genotype/variation : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR1787593	GSE65642	GSM1602350	GPL16085	29394395	WT fructose 2	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	source_name	WT_fructose PGCGROWTHCONDITIONS	<Gtype> WT </Gtype> _ <Supp> fructose </Supp> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR1787593	GSE65642	GSM1602350	GPL16085	29394395	WT fructose 2	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	genotype/variation: WT PGCGROWTHCONDITIONS	genotype/variation : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR1787594	GSE65642	GSM1602351	GPL16085	29394395	WT acetate 1	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	source_name	WT_acetate PGCGROWTHCONDITIONS	<Gtype> WT </Gtype> _ <Supp> acetate </Supp> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR1787594	GSE65642	GSM1602351	GPL16085	29394395	WT acetate 1	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	genotype/variation: WT PGCGROWTHCONDITIONS	genotype/variation : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR1787595	GSE65642	GSM1602352	GPL16085	29394395	WT acetate 2	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	source_name	WT_acetate PGCGROWTHCONDITIONS	<Gtype> WT </Gtype> _ <Supp> acetate </Supp> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR1787595	GSE65642	GSM1602352	GPL16085	29394395	WT acetate 2	Systems approach elucidates convoluted transcriptional regulation on carbon metabolism [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	genotype/variation: WT PGCGROWTHCONDITIONS	genotype/variation : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65642/GSE65642.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR1796598	GSE65711	GSM1603386	GPL16085	26279566	WT PQ 1	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	source_name	WT PQ PGCGROWTHCONDITIONS	<Gtype> WT </Gtype> <Supp> PQ </Supp> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR1796598	GSE65711	GSM1603386	GPL16085	26279566	WT PQ 1	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	genotype/variation: WT PGCGROWTHCONDITIONS	genotype/variation : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR1796599	GSE65711	GSM1603387	GPL16085	26279566	WT PQ 2	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	source_name	WT PQ PGCGROWTHCONDITIONS	<Gtype> WT </Gtype> <Supp> PQ </Supp> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR1796599	GSE65711	GSM1603387	GPL16085	26279566	WT PQ 2	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	genotype/variation: WT PGCGROWTHCONDITIONS	genotype/variation : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR1824557	GSE66481	GSM1623160	GPL16085	26258987	WT pH5.5 1	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	source_name	WT pH5.5 PGCGROWTHCONDITIONS	<Gtype> WT </Gtype> <pH> pH5 .5 </pH> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR1824557	GSE66481	GSM1623160	GPL16085	26258987	WT pH5.5 1	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	genotype/variation: WT PGCGROWTHCONDITIONS	genotype/variation : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR1824558	GSE66481	GSM1623161	GPL16085	26258987	WT pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	source_name	WT pH5.5 PGCGROWTHCONDITIONS	<Gtype> WT </Gtype> <pH> pH5 .5 </pH> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR1824558	GSE66481	GSM1623161	GPL16085	26258987	WT pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	genotype/variation: WT PGCGROWTHCONDITIONS	genotype/variation : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547467	GSE73672	GSM1900470	GPL20227	27713404	Parent LB rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547467	GSE73672	GSM1900470	GPL20227	27713404	Parent LB rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	genotype/variation: WT PGCGROWTHCONDITIONS	genotype/variation : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547469	GSE73672	GSM1900472	GPL20227	27713404	cysG KO LB rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547471	GSE73672	GSM1900474	GPL20227	27713404	cysH KO LB rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547472	GSE73672	GSM1900475	GPL20227	27713404	cysH KO LB rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547473	GSE73672	GSM1900476	GPL20227	27713404	dcd KO LB rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547474	GSE73672	GSM1900477	GPL20227	27713404	dcd KO LB rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547475	GSE73672	GSM1900478	GPL20227	27713404	fadr KO LB rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547476	GSE73672	GSM1900479	GPL20227	27713404	fadr KO LB rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547477	GSE73672	GSM1900480	GPL20227	27713404	ppk KO LB rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547479	GSE73672	GSM1900482	GPL20227	27713404	wzc KO LB rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547480	GSE73672	GSM1900483	GPL20227	27713404	wzc KO LB rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547482	GSE73672	GSM1900485	GPL20227	27713404	yghD KO LB rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547483	GSE73672	GSM1900486	GPL20227	27713404	fepA KO LB rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547485	GSE73672	GSM1900488	GPL20227	27713404	lacA KO LB rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547487	GSE73672	GSM1900490	GPL20227	27713404	Parent M9 rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547487	GSE73672	GSM1900490	GPL20227	27713404	Parent M9 rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	genotype/variation: WT PGCGROWTHCONDITIONS	genotype/variation : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547488	GSE73672	GSM1900491	GPL20227	27713404	Parent M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547488	GSE73672	GSM1900491	GPL20227	27713404	Parent M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	genotype/variation: WT PGCGROWTHCONDITIONS	genotype/variation : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547489	GSE73672	GSM1900492	GPL20227	27713404	dcd KO M9 rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547490	GSE73672	GSM1900493	GPL20227	27713404	dcd KO M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547491	GSE73672	GSM1900494	GPL20227	27713404	fadr KO M9 rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547492	GSE73672	GSM1900495	GPL20227	27713404	fadr KO M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547493	GSE73672	GSM1900496	GPL20227	27713404	ppk KO M9 rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547494	GSE73672	GSM1900497	GPL20227	27713404	ppk KO M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547495	GSE73672	GSM1900498	GPL20227	27713404	wzc KO M9 rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547496	GSE73672	GSM1900499	GPL20227	27713404	wzc KO M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547497	GSE73672	GSM1900500	GPL20227	27713404	yghD KO M9 rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547498	GSE73672	GSM1900501	GPL20227	27713404	yghD KO M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547499	GSE73672	GSM1900502	GPL20227	27713404	fepA KO M9 rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547504	GSE73672	GSM1900507	GPL20227	27713404	WT rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547504	GSE73672	GSM1900507	GPL20227	27713404	WT rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	genotype/variation: WT PGCGROWTHCONDITIONS	genotype/variation : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547506	GSE73672	GSM1900509	GPL20227	27713404	mgtA KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547507	GSE73672	GSM1900510	GPL20227	27713404	mgtA KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547510	GSE73672	GSM1900513	GPL20227	27713404	gabT KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547511	GSE73672	GSM1900514	GPL20227	27713404	gabT KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547512	GSE73672	GSM1900515	GPL20227	27713404	sdhC KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547513	GSE73672	GSM1900516	GPL20227	27713404	sdhC KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547515	GSE73672	GSM1900518	GPL20227	27713404	putP KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547517	GSE73672	GSM1900520	GPL20227	27713404	putP KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547518	GSE73672	GSM1900521	GPL20227	27713404	rfbA KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547519	GSE73672	GSM1900522	GPL20227	27713404	rfbA KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547521	GSE73672	GSM1900524	GPL20227	27713404	entF KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547522	GSE73672	GSM1900525	GPL20227	27713404	entF KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547523	GSE73672	GSM1900526	GPL20227	27713404	entF KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547524	GSE73672	GSM1900527	GPL20227	27713404	kefB KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547526	GSE73672	GSM1900529	GPL20227	27713404	kefB KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547527	GSE73672	GSM1900530	GPL20227	27713404	cysA KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547528	GSE73672	GSM1900531	GPL20227	27713404	cysA KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547529	GSE73672	GSM1900532	GPL20227	27713404	cysA KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547531	GSE73672	GSM1900534	GPL20227	27713404	galE KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547533	GSE73672	GSM1900536	GPL20227	27713404	mhpD KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547534	GSE73672	GSM1900537	GPL20227	27713404	mhpD KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547535	GSE73672	GSM1900538	GPL20227	27713404	mhpD KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547536	GSE73672	GSM1900539	GPL20227	27713404	fliY KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547537	GSE73672	GSM1900540	GPL20227	27713404	fliY KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547538	GSE73672	GSM1900541	GPL20227	27713404	fliY KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547539	GSE73672	GSM1900542	GPL20227	27713404	lplA KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547540	GSE73672	GSM1900543	GPL20227	27713404	lplA KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547541	GSE73672	GSM1900544	GPL20227	27713404	lplA KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547542	GSE73672	GSM1900545	GPL20227	27713404	khc KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547543	GSE73672	GSM1900546	GPL20227	27713404	khc KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547544	GSE73672	GSM1900547	GPL20227	27713404	khc KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547545	GSE73672	GSM1900548	GPL20227	27713404	ugpC KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547546	GSE73672	GSM1900549	GPL20227	27713404	ugpC KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547547	GSE73672	GSM1900550	GPL20227	27713404	ugpC KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547548	GSE73672	GSM1900551	GPL20227	27713404	trpD KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547549	GSE73672	GSM1900552	GPL20227	27713404	trpD KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547550	GSE73672	GSM1900553	GPL20227	27713404	trpD KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547551	GSE73672	GSM1900554	GPL20227	27713404	aspC KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547552	GSE73672	GSM1900555	GPL20227	27713404	aspC KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2547553	GSE73672	GSM1900556	GPL20227	27713404	aspC KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	growth_protocol	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	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 . 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2982421	GSE75818	GSM1968346	GPL14548-GPL21222	27198188	WTRep1_0min	Spatial organization shapes the turnover of a bacterial transcriptome	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	characteristics	genotype/variaion: WT PGCGROWTHCONDITIONS	genotype/variaion : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2982422	GSE75818	GSM1968347	GPL14548-GPL21222	27198188	WTRep1_2min	Spatial organization shapes the turnover of a bacterial transcriptome	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	characteristics	genotype/variaion: WT PGCGROWTHCONDITIONS	genotype/variaion : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2982423	GSE75818	GSM1968348	GPL14548-GPL21222	27198188	WTRep1_4min	Spatial organization shapes the turnover of a bacterial transcriptome	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	characteristics	genotype/variaion: WT PGCGROWTHCONDITIONS	genotype/variaion : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2982424	GSE75818	GSM1968349	GPL14548-GPL21222	27198188	WTRep1_6min	Spatial organization shapes the turnover of a bacterial transcriptome	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	characteristics	genotype/variaion: WT PGCGROWTHCONDITIONS	genotype/variaion : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2982425	GSE75818	GSM1968350	GPL14548-GPL21222	27198188	WTRep1_8min	Spatial organization shapes the turnover of a bacterial transcriptome	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	characteristics	genotype/variaion: WT PGCGROWTHCONDITIONS	genotype/variaion : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2982426	GSE75818	GSM1968351	GPL14548-GPL21222	27198188	WTRep1_10min	Spatial organization shapes the turnover of a bacterial transcriptome	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	characteristics	genotype/variaion: WT PGCGROWTHCONDITIONS	genotype/variaion : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2982427	GSE75818	GSM1968352	GPL14548-GPL21222	27198188	WTRep1_15min	Spatial organization shapes the turnover of a bacterial transcriptome	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	characteristics	genotype/variaion: WT PGCGROWTHCONDITIONS	genotype/variaion : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2982428	GSE75818	GSM1968353	GPL14548-GPL21222	27198188	WTRep1_20min	Spatial organization shapes the turnover of a bacterial transcriptome	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	characteristics	genotype/variaion: WT PGCGROWTHCONDITIONS	genotype/variaion : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2982429	GSE75818	GSM1968354	GPL14548-GPL21222	27198188	WTRep2_0min	Spatial organization shapes the turnover of a bacterial transcriptome	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	characteristics	genotype/variaion: WT PGCGROWTHCONDITIONS	genotype/variaion : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2982430	GSE75818	GSM1968355	GPL14548-GPL21222	27198188	WTRep2_2min	Spatial organization shapes the turnover of a bacterial transcriptome	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	characteristics	genotype/variaion: WT PGCGROWTHCONDITIONS	genotype/variaion : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2982431	GSE75818	GSM1968356	GPL14548-GPL21222	27198188	WTRep2_4min	Spatial organization shapes the turnover of a bacterial transcriptome	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	characteristics	genotype/variaion: WT PGCGROWTHCONDITIONS	genotype/variaion : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2982432	GSE75818	GSM1968357	GPL14548-GPL21222	27198188	WTRep2_6min	Spatial organization shapes the turnover of a bacterial transcriptome	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	characteristics	genotype/variaion: WT PGCGROWTHCONDITIONS	genotype/variaion : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2982433	GSE75818	GSM1968358	GPL14548-GPL21222	27198188	WTRep2_8min	Spatial organization shapes the turnover of a bacterial transcriptome	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	characteristics	genotype/variaion: WT PGCGROWTHCONDITIONS	genotype/variaion : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2982434	GSE75818	GSM1968359	GPL14548-GPL21222	27198188	WTRep2_10min	Spatial organization shapes the turnover of a bacterial transcriptome	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	characteristics	genotype/variaion: WT PGCGROWTHCONDITIONS	genotype/variaion : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2982435	GSE75818	GSM1968360	GPL14548-GPL21222	27198188	WTRep2_15min	Spatial organization shapes the turnover of a bacterial transcriptome	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	characteristics	genotype/variaion: WT PGCGROWTHCONDITIONS	genotype/variaion : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR2982436	GSE75818	GSM1968361	GPL14548-GPL21222	27198188	WTRep2_20min	Spatial organization shapes the turnover of a bacterial transcriptome	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21222: Illumina NextSeq 500 (Escherichia coli)	characteristics	genotype/variaion: WT PGCGROWTHCONDITIONS	genotype/variaion : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE75818/GSE75818.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR4435464	GSE88980	GSM2356687	GPL17439	28526842	WT NaCl 1	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]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	characteristics	genotype: WT PGCGROWTHCONDITIONS	genotype : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88980/GSE88980.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR4435465	GSE88980	GSM2356688	GPL17439	28526842	WT NaCl 2	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]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	characteristics	genotype: WT PGCGROWTHCONDITIONS	genotype : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88980/GSE88980.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR5085370	GSE91001	GSM2418921	GPL14548-GPL20262	28224117	ATCACG-D1	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	characteristics	genotype/variation: {delta}perC::kanR, coisogenic to WT PGCGROWTHCONDITIONS	genotype/variation : <Gtype> -LCB- delta -RCB- perC : : kanR </Gtype> , coisogenic to <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE91001/GSE91001.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR5085371	GSE91001	GSM2418922	GPL14548-GPL20262	28224117	CGATGT-D2	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	characteristics	genotype/variation: {delta}perC::kanR, coisogenic to WT PGCGROWTHCONDITIONS	genotype/variation : <Gtype> -LCB- delta -RCB- perC : : kanR </Gtype> , coisogenic to <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE91001/GSE91001.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR5085373	GSE91001	GSM2418923	GPL14548-GPL20262	28224117	TTAGGC-D3	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	characteristics	genotype/variation: {delta}perC::kanR, coisogenic to WT PGCGROWTHCONDITIONS	genotype/variation : <Gtype> -LCB- delta -RCB- perC : : kanR </Gtype> , coisogenic to <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE91001/GSE91001.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR5121117	GSE92601	GSM2433298	GPL18956	29807996	WT1_IPTG	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	characteristics	replicates: WT replicate 1 / induced PGCGROWTHCONDITIONS	replicates : <Gtype> WT </Gtype> replicate 1 / induced 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR5121118	GSE92601	GSM2433299	GPL18956	29807996	WT2_IPTG	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	characteristics	replicates: WT replicate 2 / induced PGCGROWTHCONDITIONS	replicates : <Gtype> WT </Gtype> replicate 2 / induced 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR5416993	GSE97406	GSM2564001	GPL16085		WT rep 1	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	genotype/variation: WT PGCGROWTHCONDITIONS	genotype/variation : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR5416994	GSE97406	GSM2564002	GPL16085		WT rep 2	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	genotype/variation: WT PGCGROWTHCONDITIONS	genotype/variation : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR5416995	GSE97406	GSM2564003	GPL16085		WT rep 3	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	genotype/variation: WT PGCGROWTHCONDITIONS	genotype/variation : <Gtype> WT </Gtype> 	WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR9919224	GSE135516	GSM4013462	GPL24377	31651953	WT_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	4g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	glucose 4 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002778
SRR9919225	GSE135516	GSM4013463	GPL24377	31651953	WT_2	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	4g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	glucose 4 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002778
SRR9919226	GSE135516	GSM4013464	GPL24377	31651953	WT_H2O2_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	4g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	glucose 4 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002778
SRR9919227	GSE135516	GSM4013465	GPL24377	31651953	WT_H2O2_2	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	4g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	glucose 4 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002778
SRR9919228	GSE135516	GSM4013466	GPL24377	31651953	GMOS_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	4g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	glucose 4 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002778
SRR9919229	GSE135516	GSM4013467	GPL24377	31651953	GMOS_2	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	4g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	glucose 4 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002778
SRR9919230	GSE135516	GSM4013468	GPL24377	31651953	GMOS_H2O2_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	4g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	glucose 4 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002778
SRR9919232	GSE135516	GSM4013470	GPL24377	31651953	EC ALE-1_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	4g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	glucose 4 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002778
SRR9919233	GSE135516	GSM4013471	GPL24377	31651953	EC ALE-1_2	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	4g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	glucose 4 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002778
SRR9919234	GSE135516	GSM4013472	GPL24377	31651953	EC ALE-1_H2O2_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	4g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	glucose 4 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002778
SRR9919235	GSE135516	GSM4013473	GPL24377	31651953	EC ALE-1_H2O2_2	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	4g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	glucose 4 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002778
SRR9919236	GSE135516	GSM4013474	GPL24377	31651953	EC ALE-2_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	4g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	glucose 4 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002778
SRR9919237	GSE135516	GSM4013475	GPL24377	31651953	EC ALE-2_2	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	4g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	glucose 4 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002778
SRR9919238	GSE135516	GSM4013476	GPL24377	31651953	EC ALE-2_H2O2_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	4g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	glucose 4 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002778
SRR9919239	GSE135516	GSM4013477	GPL24377	31651953	EC ALE-2_H2O2_2	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	4g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	glucose 4 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002778
SRR9919240	GSE135516	GSM4013478	GPL24377	31651953	EC ALE-3_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	4g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	glucose 4 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002778
SRR9919241	GSE135516	GSM4013479	GPL24377	31651953	EC ALE-3_2	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	4g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	glucose 4 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002778
SRR9919242	GSE135516	GSM4013480	GPL24377	31651953	EC ALE-3_H2O2_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	4g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	glucose 4 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002778
SRR9919243	GSE135516	GSM4013481	GPL24377	31651953	EC ALE-3_H2O2_2	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	4g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	glucose 4 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002778
SRR9919244	GSE135516	GSM4013482	GPL24377	31651953	EC ALE-4_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	4g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	glucose 4 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002778
SRR9919245	GSE135516	GSM4013483	GPL24377	31651953	EC ALE-4_2	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	4g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	glucose 4 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002778
SRR9919246	GSE135516	GSM4013484	GPL24377	31651953	EC ALE-4_H2O2_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	4g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	glucose 4 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002778
SRR9919247	GSE135516	GSM4013485	GPL24377	31651953	EC ALE-4_H2O2_2	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	media: M9 minimal media w/ 4g/L glucose PGCGROWTHCONDITIONS	media : <Med> M9 minimal media </Med> w / <Supp> 4g/L glucose </Supp> 	4g/L glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	glucose 4 g/L	96	96	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002778
SRR9919226	GSE135516	GSM4013464	GPL24377	31651953	WT_H2O2_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	treatment: 2 mM Hydrogen peroxide PGCGROWTHCONDITIONS	treatment : <Supp> 2 mM Hydrogen peroxide </Supp> 	2 mM Hydrogen peroxide	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	hydrogen peroxide 1 mM	95	95	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003162
SRR9919227	GSE135516	GSM4013465	GPL24377	31651953	WT_H2O2_2	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	treatment: 2 mM Hydrogen peroxide PGCGROWTHCONDITIONS	treatment : <Supp> 2 mM Hydrogen peroxide </Supp> 	2 mM Hydrogen peroxide	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	hydrogen peroxide 1 mM	95	95	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003162
SRR9919230	GSE135516	GSM4013468	GPL24377	31651953	GMOS_H2O2_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	treatment: 2 mM Hydrogen peroxide PGCGROWTHCONDITIONS	treatment : <Supp> 2 mM Hydrogen peroxide </Supp> 	2 mM Hydrogen peroxide	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	hydrogen peroxide 1 mM	95	95	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003162
SRR9919234	GSE135516	GSM4013472	GPL24377	31651953	EC ALE-1_H2O2_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	treatment: 2 mM Hydrogen peroxide PGCGROWTHCONDITIONS	treatment : <Supp> 2 mM Hydrogen peroxide </Supp> 	2 mM Hydrogen peroxide	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	hydrogen peroxide 1 mM	95	95	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003162
SRR9919235	GSE135516	GSM4013473	GPL24377	31651953	EC ALE-1_H2O2_2	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	treatment: 2 mM Hydrogen peroxide PGCGROWTHCONDITIONS	treatment : <Supp> 2 mM Hydrogen peroxide </Supp> 	2 mM Hydrogen peroxide	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	hydrogen peroxide 1 mM	95	95	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003162
SRR9919238	GSE135516	GSM4013476	GPL24377	31651953	EC ALE-2_H2O2_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	treatment: 2 mM Hydrogen peroxide PGCGROWTHCONDITIONS	treatment : <Supp> 2 mM Hydrogen peroxide </Supp> 	2 mM Hydrogen peroxide	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	hydrogen peroxide 1 mM	95	95	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003162
SRR9919239	GSE135516	GSM4013477	GPL24377	31651953	EC ALE-2_H2O2_2	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	treatment: 2 mM Hydrogen peroxide PGCGROWTHCONDITIONS	treatment : <Supp> 2 mM Hydrogen peroxide </Supp> 	2 mM Hydrogen peroxide	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	hydrogen peroxide 1 mM	95	95	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003162
SRR9919242	GSE135516	GSM4013480	GPL24377	31651953	EC ALE-3_H2O2_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	treatment: 2 mM Hydrogen peroxide PGCGROWTHCONDITIONS	treatment : <Supp> 2 mM Hydrogen peroxide </Supp> 	2 mM Hydrogen peroxide	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	hydrogen peroxide 1 mM	95	95	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003162
SRR9919243	GSE135516	GSM4013481	GPL24377	31651953	EC ALE-3_H2O2_2	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	treatment: 2 mM Hydrogen peroxide PGCGROWTHCONDITIONS	treatment : <Supp> 2 mM Hydrogen peroxide </Supp> 	2 mM Hydrogen peroxide	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	hydrogen peroxide 1 mM	95	95	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003162
SRR9919246	GSE135516	GSM4013484	GPL24377	31651953	EC ALE-4_H2O2_1	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	treatment: 2 mM Hydrogen peroxide PGCGROWTHCONDITIONS	treatment : <Supp> 2 mM Hydrogen peroxide </Supp> 	2 mM Hydrogen peroxide	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	hydrogen peroxide 1 mM	95	95	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003162
SRR9919247	GSE135516	GSM4013485	GPL24377	31651953	EC ALE-4_H2O2_2	OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states	GPL24377: Illumina HiSeq 4000 (Escherichia coli K-12)	characteristics	treatment: 2 mM Hydrogen peroxide PGCGROWTHCONDITIONS	treatment : <Supp> 2 mM Hydrogen peroxide </Supp> 	2 mM Hydrogen peroxide	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE135516/GSE135516.soft.gz	hydrogen peroxide 1 mM	95	95	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003162
SRR11431046	GSE147611	GSM4435425	GPL23030-GPL28314	33568644	sigma70WT_RNA-seq_rep1	Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria	GPL23030: Illumina MiSeq (Escherichia coli str. K-12 substr. W3110). GPL28314: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. W3110)	data_processing	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	<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 . 	In	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE147611/GSE147611.soft.gz	ion	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000580
SRR11431047	GSE147611	GSM4435426	GPL23030-GPL28314	33568644	sigma70WT_RNA-seq_rep2	Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria	GPL23030: Illumina MiSeq (Escherichia coli str. K-12 substr. W3110). GPL28314: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. W3110)	data_processing	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	<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 . 	In	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE147611/GSE147611.soft.gz	ion	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000580
SRR11431048	GSE147611	GSM4435427	GPL23030-GPL28314	33568644	sigma70WT_RNA-seq_rep3	Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria	GPL23030: Illumina MiSeq (Escherichia coli str. K-12 substr. W3110). GPL28314: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. W3110)	data_processing	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	<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 . 	In	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE147611/GSE147611.soft.gz	ion	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000580
SRR11431049	GSE147611	GSM4435428	GPL23030-GPL28314	33568644	sigma70greAB-_RNA-seq_rep1	Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria	GPL23030: Illumina MiSeq (Escherichia coli str. K-12 substr. W3110). GPL28314: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. W3110)	data_processing	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	<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 . 	In	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE147611/GSE147611.soft.gz	ion	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000580
SRR11431050	GSE147611	GSM4435429	GPL23030-GPL28314	33568644	sigma70greAB-_RNA-seq_rep2	Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria	GPL23030: Illumina MiSeq (Escherichia coli str. K-12 substr. W3110). GPL28314: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. W3110)	data_processing	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	<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 . 	In	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE147611/GSE147611.soft.gz	ion	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000580
SRR11431051	GSE147611	GSM4435430	GPL23030-GPL28314	33568644	sigma70greAB-_RNA-seq_rep3	Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria	GPL23030: Illumina MiSeq (Escherichia coli str. K-12 substr. W3110). GPL28314: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. W3110)	data_processing	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	<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 . 	In	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE147611/GSE147611.soft.gz	ion	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000580
SRR5282299	GSE95318	GSM2507165	GPL18133	28351917	WTA_time0	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	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	<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 	In	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	ion	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000580
SRR5282300	GSE95318	GSM2507166	GPL18133	28351917	WTA_time2.5	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	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	<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 	In	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	ion	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000580
SRR5282301	GSE95318	GSM2507167	GPL18133	28351917	WTA_time5	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	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	<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 	In	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	ion	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000580
SRR5282302	GSE95318	GSM2507168	GPL18133	28351917	WTA_time7.5	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	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	<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 	In	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	ion	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000580
SRR5282303	GSE95318	GSM2507169	GPL18133	28351917	WTA_time10	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	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	<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 	In	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	ion	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000580
SRR5282304	GSE95318	GSM2507170	GPL18133	28351917	WTA_time20	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	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	<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 	In	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	ion	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000580
SRR5282305	GSE95318	GSM2507171	GPL18133	28351917	WTB_time0	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	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	<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 	In	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	ion	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000580
SRR5282306	GSE95318	GSM2507172	GPL18133	28351917	WTB_time2.5	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	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	<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 	In	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	ion	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000580
SRR5282307	GSE95318	GSM2507173	GPL18133	28351917	WTB_time7.5	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	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	<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 	In	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	ion	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000580
SRR5282308	GSE95318	GSM2507174	GPL18133	28351917	rnc-_time0	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	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	<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 	In	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	ion	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000580
SRR5282309	GSE95318	GSM2507175	GPL18133	28351917	rnc-_time2.5	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	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	<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 	In	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	ion	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000580
SRR5282310	GSE95318	GSM2507176	GPL18133	28351917	rnc-_time5	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	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	<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 	In	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	ion	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000580
SRR5282311	GSE95318	GSM2507177	GPL18133	28351917	rnc-_time7.5	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	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	<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 	In	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	ion	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000580
SRR5282312	GSE95318	GSM2507178	GPL18133	28351917	rnc-_time10	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	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	<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 	In	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	ion	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000580
SRR5282313	GSE95318	GSM2507179	GPL18133	28351917	rnc-_time20	RNA-sequencing identifies new RNase III cleavage sites in E. coli and reveals increased regulation of mRNA	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	data_processing	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	<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 	In	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95318/GSE95318.soft.gz	ion	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000580
SRR057747	GSE21341	GSM533304	GPL10328	20671182	time point 0	genome-wide measurement of mRNA lifetime in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	characteristics	treatment group: rifampicin time point 0 PGCGROWTHCONDITIONS	treatment group : <Supp> rifampicin time point 0 </Supp> 	rifampicin time point 0	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE21341/GSE21341.soft.gz	rifampicin 50 µM	80	68	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011583
SRR057748	GSE21341	GSM533305	GPL10328	20671182	time point 2	genome-wide measurement of mRNA lifetime in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	characteristics	treatment group: rifampicin time point 2 PGCGROWTHCONDITIONS	treatment group : <Supp> rifampicin time point </Supp> 2 	rifampicin time point	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE21341/GSE21341.soft.gz	rifampicin	100	65	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000828
SRR057749	GSE21341	GSM533306	GPL10328	20671182	time point 4	genome-wide measurement of mRNA lifetime in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	characteristics	treatment group: rifampicin time point 4 PGCGROWTHCONDITIONS	treatment group : <Supp> rifampicin time point 4 </Supp> 	rifampicin time point 4	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE21341/GSE21341.soft.gz	rifampicin 50 µM	80	63	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011583
SRR057750	GSE21341	GSM533307	GPL10328	20671182	time point 6	genome-wide measurement of mRNA lifetime in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	characteristics	treatment group: rifampicin time point 6 PGCGROWTHCONDITIONS	treatment group : <Supp> rifampicin time point 6 </Supp> 	rifampicin time point 6	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE21341/GSE21341.soft.gz	rifampicin 50 µM	80	63	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011583
SRR057751	GSE21341	GSM533308	GPL10328	20671182	time point 8	genome-wide measurement of mRNA lifetime in Escherichia coli	GPL10328: Illumina Genome Analyzer II (Escherichia coli)	characteristics	treatment group: rifampicin time point 8 PGCGROWTHCONDITIONS	treatment group : <Supp> rifampicin time point 8 </Supp> 	rifampicin time point 8	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE21341/GSE21341.soft.gz	rifampicin 50 µM	80	63	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011583
SRR771533	GSE44928	GSM1094082	GPL16760		BL21_2	Physiology study of Escherichia coli harboring high intracellular ATP driven by artificial Pck expression	GPL16760: Illumina Genome Analyzer II (Escherichia coli BL21(DE3))	characteristics	genotype: wild-type PGCGROWTHCONDITIONS	genotype : <Gtype> wild-type </Gtype> 	wild-type	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE44928/GSE44928.soft.gz	wild type	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002470
SRR836184	GSE46507	GSM1131348	GPL15206-GPL17096		E. coli - TAP	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	GPL15206: Illumina HiSeq 2000 (Escherichia coli BW25113). GPL17096: Illumina HiSeq 2000 (Streptomyces coelicolor A3(2))	characteristics	genotype: wild-type PGCGROWTHCONDITIONS	genotype : <Gtype> wild-type </Gtype> 	wild-type	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE46507/GSE46507.soft.gz	wild type	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002470
SRR836185	GSE46507	GSM1131349	GPL15206-GPL17096		E. coli + TAP	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	GPL15206: Illumina HiSeq 2000 (Escherichia coli BW25113). GPL17096: Illumina HiSeq 2000 (Streptomyces coelicolor A3(2))	characteristics	genotype: wild-type PGCGROWTHCONDITIONS	genotype : <Gtype> wild-type </Gtype> 	wild-type	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE46507/GSE46507.soft.gz	wild type	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002470
SRR771533	GSE44928	GSM1094082	GPL16760		BL21_2	Physiology study of Escherichia coli harboring high intracellular ATP driven by artificial Pck expression	GPL16760: Illumina Genome Analyzer II (Escherichia coli BL21(DE3))	characteristics	condition: LB+3g/L Glc +0.1mM IPTG PGCGROWTHCONDITIONS	condition : <Gtype> LB </Gtype> +3 g/L Glc +0.1 <Supp> mM IPTG </Supp> 	mM IPTG	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE44928/GSE44928.soft.gz	iptg	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002105
SRR794827	GSE45443	GSM1104381	GPL15010	23716638	pHDB3_1	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794832	GSE45443	GSM1104386	GPL15010	23716638	pLCV1_3	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794833	GSE45443	GSM1104387	GPL15010	23716638	MG1655-aMG_1	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794834	GSE45443	GSM1104388	GPL15010	23716638	MG1655-aMG_2	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794835	GSE45443	GSM1104389	GPL15010	23716638	MG1655-aMG_3	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794836	GSE45443	GSM1104390	GPL15010	23716638	MG1655+aMG_1	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794837	GSE45443	GSM1104391	GPL15010	23716638	MG1655+aMG_2	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794838	GSE45443	GSM1104392	GPL15010	23716638	MG1655+aMG_3	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794839	GSE45443	GSM1104393	GPL15010	23716638	SgrR_1	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794840	GSE45443	GSM1104394	GPL15010	23716638	SgrR_2	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794841	GSE45443	GSM1104395	GPL15010	23716638	SgrR_3	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794842	GSE45443	GSM1104396	GPL15010	23716638	sgrS_T_1	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794843	GSE45443	GSM1104397	GPL15010	23716638	sgrS_T_2	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794844	GSE45443	GSM1104398	GPL15010	23716638	sgrS_T_3	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794845	GSE45443	GSM1104399	GPL15010	23716638	sgrS_un_1	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794846	GSE45443	GSM1104400	GPL15010	23716638	sgrS_un_2	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794847	GSE45443	GSM1104401	GPL15010	23716638	sgrS_un_3	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794848	GSE45443	GSM1104402	GPL15010	23716638	WT_1	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794849	GSE45443	GSM1104403	GPL15010	23716638	WT_2	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794850	GSE45443	GSM1104404	GPL15010	23716638	WT_3	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794851	GSE45443	GSM1104405	GPL15010	23716638	wt_T_1	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794852	GSE45443	GSM1104406	GPL15010	23716638	wt_T_2	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794853	GSE45443	GSM1104407	GPL15010	23716638	wt_T_3	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794854	GSE45443	GSM1104408	GPL15010	23716638	wt_un_1	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794856	GSE45443	GSM1104410	GPL15010	23716638	wt_un_3	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794857	GSE45443	GSM1104411	GPL15010	23716638	CV108_minus_aMG_1	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794858	GSE45443	GSM1104412	GPL15010	23716638	CV108_minus_aMG_2	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794859	GSE45443	GSM1104413	GPL15010	23716638	CV108_minus_aMG_3	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794860	GSE45443	GSM1104414	GPL15010	23716638	CV108_plus_aMG_1	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794861	GSE45443	GSM1104415	GPL15010	23716638	CV108_plus_aMG_2	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794862	GSE45443	GSM1104416	GPL15010	23716638	CV108_plus_aMG_3	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794863	GSE45443	GSM1104417	GPL15010	23716638	MG1655_minus_aMG_1	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794864	GSE45443	GSM1104418	GPL15010	23716638	MG1655_minus_aMG_2	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794865	GSE45443	GSM1104419	GPL15010	23716638	MG1655_minus_aMG_3	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794866	GSE45443	GSM1104420	GPL15010	23716638	MG1655_plus_aMG_1	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794867	GSE45443	GSM1104421	GPL15010	23716638	MG1655_plus_aMG_2	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794868	GSE45443	GSM1104422	GPL15010	23716638	MG1655_plus_aMG_3	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794869	GSE45443	GSM1104423	GPL15010	23716638	WT_minus_2DG_1	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794870	GSE45443	GSM1104424	GPL15010	23716638	WT_minus_2DG_2	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794871	GSE45443	GSM1104425	GPL15010	23716638	WT_minus_2DG_3	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794872	GSE45443	GSM1104426	GPL15010	23716638	WT_plus_2DG_1	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794873	GSE45443	GSM1104427	GPL15010	23716638	WT_plus_2DG_2	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR794874	GSE45443	GSM1104428	GPL15010	23716638	WT_plus_2DG_3	RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	Aerobic growth at 37°C  in specified media PGCGROWTHCONDITIONS	<Air> Aerobic </Air> growth at <Temp> 37 °C </Temp> in specified media 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE45443/GSE45443.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR922260	GSE48324	GSM1174823	GPL16227	24987116	Mid log_wildtype_glc minimal media_aerobic rep1	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR922261	GSE48324	GSM1174824	GPL16227	24987116	Mid log_wildtype_glc minimal media_aerobic rep2	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR922262	GSE48324	GSM1174825	GPL16227	24987116	Mid log_wildtype_glc minimal media_aerobic rep3	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR922263	GSE48324	GSM1174826	GPL16227	24987116	Mid log_wildtype_glc minimal media + adenine_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR922264	GSE48324	GSM1174827	GPL16227	24987116	Mid log_wildtype_glc minimal media + L-tryptophan_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR922265	GSE48324	GSM1174828	GPL16227	24987116	Mid log_wildtype_glc minimal media_anaerobic rep1	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR922266	GSE48324	GSM1174829	GPL16227	24987116	Mid log_wildtype_glc minimal media_anaerobic rep2	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR922267	GSE48324	GSM1174830	GPL16227	24987116	Mid log_wildtype_glc minimal media_anaerobic rep3	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR922268	GSE48324	GSM1174831	GPL16227	24987116	Mid log_nac KO_glc minimal media_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR922269	GSE48324	GSM1174832	GPL16227	24987116	Mid log_nac KO_glc minimal media + adenine_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR922270	GSE48324	GSM1174833	GPL16227	24987116	Mid log_cra KO_glc minimal media_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR922271	GSE48324	GSM1174834	GPL16227	24987116	Mid log_cra KO_glc minimal media + L-tryptophan_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR922272	GSE48324	GSM1174835	GPL16227	24987116	Mid log_mntR KO_glc minimal media_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR922273	GSE48324	GSM1174836	GPL16227	24987116	Mid log_mntR KO_glc minimal media_anaerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	growth_protocol	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	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 . 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR1211036	GSE56372	GSM1360031	GPL14548	24927582	Wild-type (MG1655) T0 RNA rep 2	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	Aerobic culture PGCGROWTHCONDITIONS	<Air> Aerobic </Air> culture 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR1211037	GSE56372	GSM1360032	GPL14548	24927582	Wild-type (MG1655) T1 RNA rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	Aerobic culture PGCGROWTHCONDITIONS	<Air> Aerobic </Air> culture 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR1211038	GSE56372	GSM1360033	GPL14548	24927582	Wild-type (MG1655) T1 RNA rep 2	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	Aerobic culture PGCGROWTHCONDITIONS	<Air> Aerobic </Air> culture 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR1211039	GSE56372	GSM1360034	GPL14548	24927582	Wild-type (MG1655) T2 RNA rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	Aerobic culture PGCGROWTHCONDITIONS	<Air> Aerobic </Air> culture 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR1211040	GSE56372	GSM1360035	GPL14548	24927582	Wild-type (MG1655) T2 RNA rep 2	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	Aerobic culture PGCGROWTHCONDITIONS	<Air> Aerobic </Air> culture 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR1211041	GSE56372	GSM1360036	GPL14548	24927582	Mutant (EP61) T0 RNA rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	Aerobic culture PGCGROWTHCONDITIONS	<Air> Aerobic </Air> culture 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR1211042	GSE56372	GSM1360037	GPL14548	24927582	Mutant (EP61) T0 RNA rep 2	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	Aerobic culture PGCGROWTHCONDITIONS	<Air> Aerobic </Air> culture 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR1211043	GSE56372	GSM1360038	GPL14548	24927582	Mutant (EP61) T1 RNA rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	Aerobic culture PGCGROWTHCONDITIONS	<Air> Aerobic </Air> culture 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR1211044	GSE56372	GSM1360039	GPL14548	24927582	Mutant (EP61) T1 RNA rep 2	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	Aerobic culture PGCGROWTHCONDITIONS	<Air> Aerobic </Air> culture 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR1211045	GSE56372	GSM1360040	GPL14548	24927582	Mutant (EP61) T2 RNA rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	Aerobic culture PGCGROWTHCONDITIONS	<Air> Aerobic </Air> culture 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR1211046	GSE56372	GSM1360041	GPL14548	24927582	Mutant (EP61) T2 RNA rep 2	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	Aerobic culture PGCGROWTHCONDITIONS	<Air> Aerobic </Air> culture 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR1211047	GSE56372	GSM1360042	GPL14548	24927582	Wild-type (MG1655) T0 RP rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	Aerobic culture PGCGROWTHCONDITIONS	<Air> Aerobic </Air> culture 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR1211048	GSE56372	GSM1360043	GPL14548	24927582	Wild-type (MG1655) T0 RP rep 2	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	Aerobic culture PGCGROWTHCONDITIONS	<Air> Aerobic </Air> culture 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR1211049	GSE56372	GSM1360044	GPL14548	24927582	Wild-type (MG1655) T1 RP rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	Aerobic culture PGCGROWTHCONDITIONS	<Air> Aerobic </Air> culture 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR1211050	GSE56372	GSM1360045	GPL14548	24927582	Wild-type (MG1655) T1 RP rep 2	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	Aerobic culture PGCGROWTHCONDITIONS	<Air> Aerobic </Air> culture 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR1211051	GSE56372	GSM1360046	GPL14548	24927582	Wild-type (MG1655) T2 RP rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	Aerobic culture PGCGROWTHCONDITIONS	<Air> Aerobic </Air> culture 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR1211052	GSE56372	GSM1360047	GPL14548	24927582	Wild-type (MG1655) T2 RP rep 2	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	Aerobic culture PGCGROWTHCONDITIONS	<Air> Aerobic </Air> culture 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR1211053	GSE56372	GSM1360048	GPL14548	24927582	Mutant (EP61) T0 RP rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	Aerobic culture PGCGROWTHCONDITIONS	<Air> Aerobic </Air> culture 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR1211054	GSE56372	GSM1360049	GPL14548	24927582	Mutant (EP61) T0 RP rep 2	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	Aerobic culture PGCGROWTHCONDITIONS	<Air> Aerobic </Air> culture 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR1211055	GSE56372	GSM1360050	GPL14548	24927582	Mutant (EP61) T1 RP rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	Aerobic culture PGCGROWTHCONDITIONS	<Air> Aerobic </Air> culture 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR1211056	GSE56372	GSM1360051	GPL14548	24927582	Mutant (EP61) T1 RP rep 2	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	Aerobic culture PGCGROWTHCONDITIONS	<Air> Aerobic </Air> culture 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR1211057	GSE56372	GSM1360052	GPL14548	24927582	Mutant (EP61) T2 RP rep 1	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	Aerobic culture PGCGROWTHCONDITIONS	<Air> Aerobic </Air> culture 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR1211058	GSE56372	GSM1360053	GPL14548	24927582	Mutant (EP61) T2 RP rep 2	Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	source_name	Aerobic culture PGCGROWTHCONDITIONS	<Air> Aerobic </Air> culture 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE56372/GSE56372.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR3403686	GSE80451	GSM2127617	GPL14548	28103245	Aerobic 1	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	<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. 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80451/GSE80451.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR3403686	GSE80451	GSM2127617	GPL14548	28103245	Aerobic 1	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	growth environment: Aerobic PGCGROWTHCONDITIONS	growth environment : <Air> Aerobic </Air> 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80451/GSE80451.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR3403687	GSE80451	GSM2127618	GPL14548	28103245	Aerobic 2	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	<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. 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80451/GSE80451.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR3403687	GSE80451	GSM2127618	GPL14548	28103245	Aerobic 2	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	growth environment: Aerobic PGCGROWTHCONDITIONS	growth environment : <Air> Aerobic </Air> 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80451/GSE80451.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR3403688	GSE80451	GSM2127619	GPL14548	28103245	Aerobic 3	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	<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. 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80451/GSE80451.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR3403688	GSE80451	GSM2127619	GPL14548	28103245	Aerobic 3	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	growth environment: Aerobic PGCGROWTHCONDITIONS	growth environment : <Air> Aerobic </Air> 	Aerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80451/GSE80451.soft.gz	aerobic	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011679
SRR847728	GSE46737	GSM1137316	GPL17137	24461193	E. coli stationary 1	Genome-scale reconstruction of the sigma factor network in E. coli	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	W2 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE46737/GSE46737.soft.gz	W2 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003317
SRR847730	GSE46737	GSM1137318	GPL17137	24461193	E. coli glutamine 1	Genome-scale reconstruction of the sigma factor network in E. coli	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	W2 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE46737/GSE46737.soft.gz	W2 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003317
SRR847731	GSE46737	GSM1137319	GPL17137	24461193	E. coli glutamine 2	Genome-scale reconstruction of the sigma factor network in E. coli	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	W2 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE46737/GSE46737.soft.gz	W2 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003317
SRR847732	GSE46737	GSM1137320	GPL17137	24461193	E. coli heatshock 1	Genome-scale reconstruction of the sigma factor network in E. coli	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	W2 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE46737/GSE46737.soft.gz	W2 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003317
SRR847733	GSE46737	GSM1137321	GPL17137	24461193	E. coli heatshock 2	Genome-scale reconstruction of the sigma factor network in E. coli	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	W2 minimal media	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE46737/GSE46737.soft.gz	W2 minimal medium	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003317
SRR847730	GSE46737	GSM1137318	GPL17137	24461193	E. coli glutamine 1	Genome-scale reconstruction of the sigma factor network in E. coli	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	source_name	Cells at mid-log phase (OD600nm 0.5) in W2 media supplemented with 0.2% glucose and 0.2% glutamine PGCGROWTHCONDITIONS	Cells at mid-log phase ( OD600nm 0.5 ) in W2 media supplemented with <Supp> 0.2 % glucose </Supp> and <Supp> 0.2 % glutamine </Supp> 	0.2 % glutamine	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE46737/GSE46737.soft.gz	L-glutamine 0.2%	100	93	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002720
SRR847731	GSE46737	GSM1137319	GPL17137	24461193	E. coli glutamine 2	Genome-scale reconstruction of the sigma factor network in E. coli	GPL17137: Illumina Genome Analyzer (Escherichia coli str. K-12 substr. MG1655)	source_name	Cells at mid-log phase (OD600nm 0.5) in W2 media supplemented with 0.2% glucose and 0.2% glutamine PGCGROWTHCONDITIONS	Cells at mid-log phase ( OD600nm 0.5 ) in W2 media supplemented with <Supp> 0.2 % glucose </Supp> and <Supp> 0.2 % glutamine </Supp> 	0.2 % glutamine	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE46737/GSE46737.soft.gz	L-glutamine 0.2%	100	93	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002720
SRR915696	GSE48151	GSM1170035	GPL10328-GPL14548	23899370	M-P2h_r1_HiSeq	Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coliK12 through accurate full-length transcripts assembling	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	culture/growth condition: MOPS-P 2h PGCGROWTHCONDITIONS	culture/growth condition : <Supp> MOPS-P 2h </Supp> 	MOPS-P 2h	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48151/GSE48151.soft.gz	MOPS	100	62	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000001665
SRR915697	GSE48151	GSM1170036	GPL10328-GPL14548	23899370	M-P2h_r2_HiSeq	Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coliK12 through accurate full-length transcripts assembling	GPL10328: Illumina Genome Analyzer II (Escherichia coli). GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	culture/growth condition: MOPS-P 2h PGCGROWTHCONDITIONS	culture/growth condition : <Supp> MOPS-P 2h </Supp> 	MOPS-P 2h	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48151/GSE48151.soft.gz	MOPS	100	62	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000001665
SRR922260	GSE48324	GSM1174823	GPL16227	24987116	Mid log_wildtype_glc minimal media_aerobic rep1	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	source_name	WT PGCGROWTHCONDITIONS	<Gtype> WT WT </Gtype> 	WT WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	wt	100	57	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR922261	GSE48324	GSM1174824	GPL16227	24987116	Mid log_wildtype_glc minimal media_aerobic rep2	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	source_name	WT PGCGROWTHCONDITIONS	<Gtype> WT WT </Gtype> 	WT WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	wt	100	57	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR922262	GSE48324	GSM1174825	GPL16227	24987116	Mid log_wildtype_glc minimal media_aerobic rep3	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	source_name	WT PGCGROWTHCONDITIONS	<Gtype> WT WT </Gtype> 	WT WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	wt	100	57	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR5416993	GSE97406	GSM2564001	GPL16085		WT rep 1	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	source_name	WT PGCGROWTHCONDITIONS	<Gtype> WT WT </Gtype> 	WT WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	wt	100	57	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR5416994	GSE97406	GSM2564002	GPL16085		WT rep 2	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	source_name	WT PGCGROWTHCONDITIONS	<Gtype> WT WT </Gtype> 	WT WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	wt	100	57	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR5416995	GSE97406	GSM2564003	GPL16085		WT rep 3	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	source_name	WT PGCGROWTHCONDITIONS	<Gtype> WT WT </Gtype> 	WT WT	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	wt	100	57	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR922260	GSE48324	GSM1174823	GPL16227	24987116	Mid log_wildtype_glc minimal media_aerobic rep1	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	characteristics	genotype/variation: wild type; MG1655 PGCGROWTHCONDITIONS	genotype/variation : <Gtype> wild type ; MG1655 </Gtype> 	wild type ; MG1655	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	wild type	100	72	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002470
SRR922261	GSE48324	GSM1174824	GPL16227	24987116	Mid log_wildtype_glc minimal media_aerobic rep2	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	characteristics	genotype/variation: wild type; MG1655 PGCGROWTHCONDITIONS	genotype/variation : <Gtype> wild type ; MG1655 </Gtype> 	wild type ; MG1655	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	wild type	100	72	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002470
SRR922262	GSE48324	GSM1174825	GPL16227	24987116	Mid log_wildtype_glc minimal media_aerobic rep3	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	characteristics	genotype/variation: wild type; MG1655 PGCGROWTHCONDITIONS	genotype/variation : <Gtype> wild type ; MG1655 </Gtype> 	wild type ; MG1655	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	wild type	100	72	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002470
SRR922263	GSE48324	GSM1174826	GPL16227	24987116	Mid log_wildtype_glc minimal media + adenine_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	characteristics	genotype/variation: wild type; MG1655 PGCGROWTHCONDITIONS	genotype/variation : <Gtype> wild type ; MG1655 </Gtype> 	wild type ; MG1655	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	wild type	100	72	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002470
SRR922264	GSE48324	GSM1174827	GPL16227	24987116	Mid log_wildtype_glc minimal media + L-tryptophan_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	characteristics	genotype/variation: wild type; MG1655 PGCGROWTHCONDITIONS	genotype/variation : <Gtype> wild type ; MG1655 </Gtype> 	wild type ; MG1655	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	wild type	100	72	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002470
SRR922265	GSE48324	GSM1174828	GPL16227	24987116	Mid log_wildtype_glc minimal media_anaerobic rep1	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	characteristics	genotype/variation: wild type; MG1655 PGCGROWTHCONDITIONS	genotype/variation : <Gtype> wild type ; MG1655 </Gtype> 	wild type ; MG1655	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	wild type	100	72	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002470
SRR922266	GSE48324	GSM1174829	GPL16227	24987116	Mid log_wildtype_glc minimal media_anaerobic rep2	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	characteristics	genotype/variation: wild type; MG1655 PGCGROWTHCONDITIONS	genotype/variation : <Gtype> wild type ; MG1655 </Gtype> 	wild type ; MG1655	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	wild type	100	72	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002470
SRR922267	GSE48324	GSM1174830	GPL16227	24987116	Mid log_wildtype_glc minimal media_anaerobic rep3	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	characteristics	genotype/variation: wild type; MG1655 PGCGROWTHCONDITIONS	genotype/variation : <Gtype> wild type ; MG1655 </Gtype> 	wild type ; MG1655	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	wild type	100	72	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002470
SRR922260	GSE48324	GSM1174823	GPL16227	24987116	Mid log_wildtype_glc minimal media_aerobic rep1	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	characteristics	basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS	basal media : <Med> M9 + 4 g/L glc ( glucose minimal media ) </Med> 	M9 + 4 g/L glc ( glucose minimal media )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	glucose 2 g/l	92	51	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002776
SRR922261	GSE48324	GSM1174824	GPL16227	24987116	Mid log_wildtype_glc minimal media_aerobic rep2	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	characteristics	basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS	basal media : <Med> M9 + 4 g/L glc ( glucose minimal media ) </Med> 	M9 + 4 g/L glc ( glucose minimal media )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	glucose 2 g/l	92	51	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002776
SRR922262	GSE48324	GSM1174825	GPL16227	24987116	Mid log_wildtype_glc minimal media_aerobic rep3	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	characteristics	basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS	basal media : <Med> M9 + 4 g/L glc ( glucose minimal media ) </Med> 	M9 + 4 g/L glc ( glucose minimal media )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	glucose 2 g/l	92	51	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002776
SRR922263	GSE48324	GSM1174826	GPL16227	24987116	Mid log_wildtype_glc minimal media + adenine_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	characteristics	basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS	basal media : <Med> M9 + 4 g/L glc ( glucose minimal media ) </Med> 	M9 + 4 g/L glc ( glucose minimal media )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	glucose 2 g/l	92	51	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002776
SRR922264	GSE48324	GSM1174827	GPL16227	24987116	Mid log_wildtype_glc minimal media + L-tryptophan_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	characteristics	basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS	basal media : <Med> M9 + 4 g/L glc ( glucose minimal media ) </Med> 	M9 + 4 g/L glc ( glucose minimal media )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	glucose 2 g/l	92	51	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002776
SRR922265	GSE48324	GSM1174828	GPL16227	24987116	Mid log_wildtype_glc minimal media_anaerobic rep1	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	characteristics	basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS	basal media : <Med> M9 + 4 g/L glc ( glucose minimal media ) </Med> 	M9 + 4 g/L glc ( glucose minimal media )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	glucose 2 g/l	92	51	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002776
SRR922266	GSE48324	GSM1174829	GPL16227	24987116	Mid log_wildtype_glc minimal media_anaerobic rep2	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	characteristics	basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS	basal media : <Med> M9 + 4 g/L glc ( glucose minimal media ) </Med> 	M9 + 4 g/L glc ( glucose minimal media )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	glucose 2 g/l	92	51	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002776
SRR922267	GSE48324	GSM1174830	GPL16227	24987116	Mid log_wildtype_glc minimal media_anaerobic rep3	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	characteristics	basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS	basal media : <Med> M9 + 4 g/L glc ( glucose minimal media ) </Med> 	M9 + 4 g/L glc ( glucose minimal media )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	glucose 2 g/l	92	51	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002776
SRR922268	GSE48324	GSM1174831	GPL16227	24987116	Mid log_nac KO_glc minimal media_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	characteristics	basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS	basal media : <Med> M9 + 4 g/L glc ( glucose minimal media ) </Med> 	M9 + 4 g/L glc ( glucose minimal media )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	glucose 2 g/l	92	51	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002776
SRR922269	GSE48324	GSM1174832	GPL16227	24987116	Mid log_nac KO_glc minimal media + adenine_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	characteristics	basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS	basal media : <Med> M9 + 4 g/L glc ( glucose minimal media ) </Med> 	M9 + 4 g/L glc ( glucose minimal media )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	glucose 2 g/l	92	51	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002776
SRR922270	GSE48324	GSM1174833	GPL16227	24987116	Mid log_cra KO_glc minimal media_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	characteristics	basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS	basal media : <Med> M9 + 4 g/L glc ( glucose minimal media ) </Med> 	M9 + 4 g/L glc ( glucose minimal media )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	glucose 2 g/l	92	51	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002776
SRR922271	GSE48324	GSM1174834	GPL16227	24987116	Mid log_cra KO_glc minimal media + L-tryptophan_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	characteristics	basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS	basal media : <Med> M9 + 4 g/L glc ( glucose minimal media ) </Med> 	M9 + 4 g/L glc ( glucose minimal media )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	glucose 2 g/l	92	51	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002776
SRR922272	GSE48324	GSM1174835	GPL16227	24987116	Mid log_mntR KO_glc minimal media_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	characteristics	basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS	basal media : <Med> M9 + 4 g/L glc ( glucose minimal media ) </Med> 	M9 + 4 g/L glc ( glucose minimal media )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	glucose 2 g/l	92	51	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002776
SRR922273	GSE48324	GSM1174836	GPL16227	24987116	Mid log_mntR KO_glc minimal media_anaerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	characteristics	basal media: M9 + 4 g/L glc (glucose minimal media) PGCGROWTHCONDITIONS	basal media : <Med> M9 + 4 g/L glc ( glucose minimal media ) </Med> 	M9 + 4 g/L glc ( glucose minimal media )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	glucose 2 g/l	92	51	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002776
SRR922263	GSE48324	GSM1174826	GPL16227	24987116	Mid log_wildtype_glc minimal media + adenine_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	source_name	WT + ade PGCGROWTHCONDITIONS	<Gtype> WT + </Gtype> <Supp> ade </Supp> 	WT +	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR922264	GSE48324	GSM1174827	GPL16227	24987116	Mid log_wildtype_glc minimal media + L-tryptophan_aerobic	Minimal metabolic pathway structure is consistent with associated macromolecular interactions.	GPL16227: Illumina Genome Analyzer IIx (Escherichia coli K-12)	source_name	WT + L-trp PGCGROWTHCONDITIONS	<Gtype> WT + </Gtype> <Supp> L-trp </Supp> 	WT +	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE48324/GSE48324.soft.gz	wt	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR1173971	GSE55199	GSM1331415	GPL15010-GPL17024	25266388	LB 2.0 B1 TEX neg L1 GA	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	characteristics	growth phase: stationary PGCGROWTHCONDITIONS	growth phase : <Phase> stationary </Phase> 	stationary	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	stationary phase	100	77	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002866
SRR1173972	GSE55199	GSM1331416	GPL15010-GPL17024	25266388	LB 2.0 B1 TEX neg L2 HS2	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	characteristics	growth phase: stationary PGCGROWTHCONDITIONS	growth phase : <Phase> stationary </Phase> 	stationary	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	stationary phase	100	77	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002866
SRR1173973	GSE55199	GSM1331417	GPL15010-GPL17024	25266388	LB 2.0 B1 TEX pos L1 GA	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	characteristics	growth phase: stationary PGCGROWTHCONDITIONS	growth phase : <Phase> stationary </Phase> 	stationary	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	stationary phase	100	77	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002866
SRR1173974	GSE55199	GSM1331418	GPL15010-GPL17024	25266388	LB 2.0 B1 TEX pos L2 HS2	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	characteristics	growth phase: stationary PGCGROWTHCONDITIONS	growth phase : <Phase> stationary </Phase> 	stationary	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	stationary phase	100	77	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002866
SRR1173975	GSE55199	GSM1331419	GPL15010-GPL17024	25266388	LB 2.0 B2 TEX neg L1 HS1	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	characteristics	growth phase: stationary PGCGROWTHCONDITIONS	growth phase : <Phase> stationary </Phase> 	stationary	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	stationary phase	100	77	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002866
SRR1173976	GSE55199	GSM1331420	GPL15010-GPL17024	25266388	LB 2.0 B2 TEX neg L1 HS2	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	characteristics	growth phase: stationary PGCGROWTHCONDITIONS	growth phase : <Phase> stationary </Phase> 	stationary	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	stationary phase	100	77	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002866
SRR1173977	GSE55199	GSM1331421	GPL15010-GPL17024	25266388	LB 2.0 B2 TEX neg L2 HS2	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	characteristics	growth phase: stationary PGCGROWTHCONDITIONS	growth phase : <Phase> stationary </Phase> 	stationary	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	stationary phase	100	77	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002866
SRR1173978	GSE55199	GSM1331422	GPL15010-GPL17024	25266388	LB 2.0 B2 TEX pos L1 HS1	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	characteristics	growth phase: stationary PGCGROWTHCONDITIONS	growth phase : <Phase> stationary </Phase> 	stationary	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	stationary phase	100	77	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002866
SRR1173979	GSE55199	GSM1331423	GPL15010-GPL17024	25266388	LB 2.0 B2 TEX pos L1 HS2	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	characteristics	growth phase: stationary PGCGROWTHCONDITIONS	growth phase : <Phase> stationary </Phase> 	stationary	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	stationary phase	100	77	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002866
SRR1173980	GSE55199	GSM1331424	GPL15010-GPL17024	25266388	LB 2.0 B2 TEX pos L2 HS2	Identification and validation of antisense RNAs in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655). GPL17024: Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)	characteristics	growth phase: stationary PGCGROWTHCONDITIONS	growth phase : <Phase> stationary </Phase> 	stationary	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE55199/GSE55199.soft.gz	stationary phase	100	77	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002866
SRR1363864	GSE58285	GSM1405877	GPL14548	25237058	rne wild-type	Direct entry by RNase E is a major pathway for the degradation and processing of RNA in Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	genotype: rne wild-type PGCGROWTHCONDITIONS	genotype : <Gtype> rne wild-type </Gtype> 	rne wild-type	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE58285/GSE58285.soft.gz	wild type	100	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002470
SRR1411272	GSE58556	GSM1413874	GPL18814	25483350	WT_glucose_log	RNA sequencing based analysis of the bacterial transcriptome	GPL18814: Illumina HiSeq 2000 (Escherichia coli BW38028)	growth_protocol	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	<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 . 	MOPS glucose minimal medium	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE58556/GSE58556.soft.gz	MOPS minimal medium	100	83	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002528
SRR1411272	GSE58556	GSM1413874	GPL18814	25483350	WT_glucose_log	RNA sequencing based analysis of the bacterial transcriptome	GPL18814: Illumina HiSeq 2000 (Escherichia coli BW38028)	characteristics	treatment: log phase sample PGCGROWTHCONDITIONS	treatment : <Phase> log phase sample </Phase> 	log phase sample	Growth phase	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE58556/GSE58556.soft.gz	log phase	100	72	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002864
SRR1425203	GSE58637	GSM1415871	GPL14548	25030700	ribosome profiling MicL t0	MicL, a new σE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	treatment_protocol	At OD ~0.3, cultures were induced with 1mM IPTG for the appropriate length of time. PGCGROWTHCONDITIONS	At OD ~ 0.3 , cultures were induced with <Supp> 1mM IPTG </Supp> for the appropriate length of time . 	1mM IPTG	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE58637/GSE58637.soft.gz	iptg	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002105
SRR1425204	GSE58637	GSM1415872	GPL14548	25030700	ribosome profiling MicL t20	MicL, a new σE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	treatment_protocol	At OD ~0.3, cultures were induced with 1mM IPTG for the appropriate length of time. PGCGROWTHCONDITIONS	At OD ~ 0.3 , cultures were induced with <Supp> 1mM IPTG </Supp> for the appropriate length of time . 	1mM IPTG	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE58637/GSE58637.soft.gz	iptg	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002105
SRR5186139	GSE77617	GSM2462936	GPL14548-GPL21433	28139975	mRNA-seq 37°C in WT with control plasmid	Operon mRNAs are organized into ORF-centric structures that predict translation efficiency	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	treatment: 1mM IPTG PGCGROWTHCONDITIONS	treatment : <Supp> 1mM IPTG </Supp> 	1mM IPTG	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE77617/GSE77617.soft.gz	iptg	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002105
SRR5186140	GSE77617	GSM2462937	GPL14548-GPL21433	28139975	mRNA-seq 37°C in WT with plasmid expressing mini-ORF CUA	Operon mRNAs are organized into ORF-centric structures that predict translation efficiency	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	treatment: 1mM IPTG PGCGROWTHCONDITIONS	treatment : <Supp> 1mM IPTG </Supp> 	1mM IPTG	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE77617/GSE77617.soft.gz	iptg	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002105
SRR5186141	GSE77617	GSM2462938	GPL14548-GPL21433	28139975	mRNA-seq 37°C in WT with plasmid expressing mini-ORF CUG	Operon mRNAs are organized into ORF-centric structures that predict translation efficiency	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL21433: Illumina HiSeq 4000 (Escherichia coli)	characteristics	treatment: 1mM IPTG PGCGROWTHCONDITIONS	treatment : <Supp> 1mM IPTG </Supp> 	1mM IPTG	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE77617/GSE77617.soft.gz	iptg	100	67	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002105
SRR1536586	GSE60107	GSM1465035	GPL14548	2575788830486791	WT_RNA-Seq	Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	genotype: Wild-type PGCGROWTHCONDITIONS	genotype : <Gtype> Wild-type </Gtype> 	Wild-type	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE60107/GSE60107.soft.gz	wild type	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002470
SRR1536587	GSE60107	GSM1465036	GPL14548	2575788830486791	∆rnb_RNA-Seq	Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	genotype: RNase II mutant PGCGROWTHCONDITIONS	genotype : <Gtype> RNase II mutant </Gtype> 	RNase II mutant	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE60107/GSE60107.soft.gz	mutant	100	57	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002469
SRR1536588	GSE60107	GSM1465037	GPL14548	2575788830486791	∆rnr_RNA-Seq	Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	genotype: RNase R mutant PGCGROWTHCONDITIONS	genotype : <Gtype> RNase R mutant </Gtype> 	RNase R mutant	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE60107/GSE60107.soft.gz	mutant	100	60	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002469
SRR1536589	GSE60107	GSM1465038	GPL14548	2575788830486791	∆pnp_RNA-Seq	Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	genotype: PNPase mutant PGCGROWTHCONDITIONS	genotype : <Gtype> PNPase mutant </Gtype> 	PNPase mutant	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE60107/GSE60107.soft.gz	mutant	100	63	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002469
SRR1771414	GSE65244	GSM1590712	GPL14548		Wt – 60 min	Temporal gene expression in Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS	<Med> LB medium , </Med> <Temp> 37 °C </Temp> , airated , constant pH 7.5 	LB medium ,	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65244/GSE65244.soft.gz	LB medium	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002533
SRR1771419	GSE65244	GSM1590717	GPL14548		Fis – 60 min	Temporal gene expression in Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS	<Med> LB medium , </Med> <Temp> 37 °C </Temp> , airated , constant pH 7.5 	LB medium ,	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65244/GSE65244.soft.gz	LB medium	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002533
SRR1771420	GSE65244	GSM1590718	GPL14548		Fis – 120 min	Temporal gene expression in Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS	<Med> LB medium , </Med> <Temp> 37 °C </Temp> , airated , constant pH 7.5 	LB medium ,	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65244/GSE65244.soft.gz	LB medium	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002533
SRR1771421	GSE65244	GSM1590719	GPL14548		Fis – 180 min	Temporal gene expression in Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS	<Med> LB medium , </Med> <Temp> 37 °C </Temp> , airated , constant pH 7.5 	LB medium ,	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65244/GSE65244.soft.gz	LB medium	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002533
SRR1771422	GSE65244	GSM1590720	GPL14548		Fis – 420 min	Temporal gene expression in Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS	<Med> LB medium , </Med> <Temp> 37 °C </Temp> , airated , constant pH 7.5 	LB medium ,	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65244/GSE65244.soft.gz	LB medium	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002533
SRR1771423	GSE65244	GSM1590721	GPL14548		Hns – 60 min	Temporal gene expression in Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS	<Med> LB medium , </Med> <Temp> 37 °C </Temp> , airated , constant pH 7.5 	LB medium ,	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65244/GSE65244.soft.gz	LB medium	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002533
SRR1771424	GSE65244	GSM1590722	GPL14548		Hns – 120 min	Temporal gene expression in Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	LB medium, 37°C, airated, constant pH 7.5 PGCGROWTHCONDITIONS	<Med> LB medium , </Med> <Temp> 37 °C </Temp> , airated , constant pH 7.5 	LB medium ,	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65244/GSE65244.soft.gz	LB medium	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002533
SRR1796598	GSE65711	GSM1603386	GPL16085	26279566	WT PQ 1	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	treated with: 250 uM of paraquat at mid-log pahse for 20 min PGCGROWTHCONDITIONS	treated with : <Supp> 250 uM of paraquat </Supp> at mid-log pahse for <Supp> 20 min </Supp> 	250 uM of paraquat	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	paraquat 250 µM	92	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011582
SRR1796599	GSE65711	GSM1603387	GPL16085	26279566	WT PQ 2	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	treated with: 250 uM of paraquat at mid-log pahse for 20 min PGCGROWTHCONDITIONS	treated with : <Supp> 250 uM of paraquat </Supp> at mid-log pahse for <Supp> 20 min </Supp> 	250 uM of paraquat	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	paraquat 250 µM	92	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011582
SRR1796600	GSE65711	GSM1603388	GPL16085	26279566	ΔoxyR PQ 1	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	treated with: 250 uM of paraquat at mid-log pahse for 20 min PGCGROWTHCONDITIONS	treated with : <Supp> 250 uM of paraquat </Supp> at mid-log pahse for <Supp> 20 min </Supp> 	250 uM of paraquat	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	paraquat 250 µM	92	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011582
SRR1796601	GSE65711	GSM1603389	GPL16085	26279566	ΔoxyR PQ 2	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	treated with: 250 uM of paraquat at mid-log pahse for 20 min PGCGROWTHCONDITIONS	treated with : <Supp> 250 uM of paraquat </Supp> at mid-log pahse for <Supp> 20 min </Supp> 	250 uM of paraquat	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	paraquat 250 µM	92	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011582
SRR1796603	GSE65711	GSM1603391	GPL16085	26279566	ΔsoxR PQ 2	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	treated with: 250 uM of paraquat at mid-log pahse for 20 min PGCGROWTHCONDITIONS	treated with : <Supp> 250 uM of paraquat </Supp> at mid-log pahse for <Supp> 20 min </Supp> 	250 uM of paraquat	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	paraquat 250 µM	92	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011582
SRR1796604	GSE65711	GSM1603392	GPL16085	26279566	ΔsoxS PQ 1	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	treated with: 250 uM of paraquat at mid-log pahse for 20 min PGCGROWTHCONDITIONS	treated with : <Supp> 250 uM of paraquat </Supp> at mid-log pahse for <Supp> 20 min </Supp> 	250 uM of paraquat	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	paraquat 250 µM	92	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011582
SRR1796605	GSE65711	GSM1603393	GPL16085	26279566	ΔsoxS PQ 2	Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	treated with: 250 uM of paraquat at mid-log pahse for 20 min PGCGROWTHCONDITIONS	treated with : <Supp> 250 uM of paraquat </Supp> at mid-log pahse for <Supp> 20 min </Supp> 	250 uM of paraquat	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE65711/GSE65711.soft.gz	paraquat 250 µM	92	81	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011582
SRR1824557	GSE66481	GSM1623160	GPL16085	26258987	WT pH5.5 1	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	growth phase: mid-log phase (OD600 = 0.3) PGCGROWTHCONDITIONS	growth phase : <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) 	OD600 = 0.3	Optical Density (OD)	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	OD600 of 0.3	100	86	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002564
SRR1824558	GSE66481	GSM1623161	GPL16085	26258987	WT pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	growth phase: mid-log phase (OD600 = 0.3) PGCGROWTHCONDITIONS	growth phase : <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) 	OD600 = 0.3	Optical Density (OD)	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	OD600 of 0.3	100	86	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002564
SRR1824559	GSE66481	GSM1623162	GPL16085	26258987	ΔgadE pH5.5 1	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	growth phase: mid-log phase (OD600 = 0.3) PGCGROWTHCONDITIONS	growth phase : <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) 	OD600 = 0.3	Optical Density (OD)	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	OD600 of 0.3	100	86	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002564
SRR1824560	GSE66481	GSM1623163	GPL16085	26258987	ΔgadE pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	growth phase: mid-log phase (OD600 = 0.3) PGCGROWTHCONDITIONS	growth phase : <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) 	OD600 = 0.3	Optical Density (OD)	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	OD600 of 0.3	100	86	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002564
SRR1824561	GSE66481	GSM1623164	GPL16085	26258987	ΔgadW pH5.5 1	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	growth phase: mid-log phase (OD600 = 0.3) PGCGROWTHCONDITIONS	growth phase : <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) 	OD600 = 0.3	Optical Density (OD)	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	OD600 of 0.3	100	86	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002564
SRR1824562	GSE66481	GSM1623165	GPL16085	26258987	ΔgadW pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	growth phase: mid-log phase (OD600 = 0.3) PGCGROWTHCONDITIONS	growth phase : <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) 	OD600 = 0.3	Optical Density (OD)	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	OD600 of 0.3	100	86	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002564
SRR1824563	GSE66481	GSM1623166	GPL16085	26258987	ΔgadX pH5.5 1	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	growth phase: mid-log phase (OD600 = 0.3) PGCGROWTHCONDITIONS	growth phase : <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) 	OD600 = 0.3	Optical Density (OD)	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	OD600 of 0.3	100	86	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002564
SRR1824564	GSE66481	GSM1623167	GPL16085	26258987	ΔgadX pH5.5 2	Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	growth phase: mid-log phase (OD600 = 0.3) PGCGROWTHCONDITIONS	growth phase : <Phase> mid-log phase </Phase> ( <OD> OD600 = 0.3 </OD> ) 	OD600 = 0.3	Optical Density (OD)	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE66481/GSE66481.soft.gz	OD600 of 0.3	100	86	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002564
SRR1927169	GSE67218	GSM1642593	GPL17439		RNA-seq 37C LB rep1	Transcriptional expression level of E. coli at 37 ℃ in LB media	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	characteristics	cell type: Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS	<Gtype> cell type </Gtype> : Escherichia coli str . <Strain> K-12 </Strain> substr . <Substrain> MG1655 </Substrain> 	cell type	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE67218/GSE67218.soft.gz	T cell	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011472
SRR1927170	GSE67218	GSM1642594	GPL17439		RNA-seq 37C LB rep2	Transcriptional expression level of E. coli at 37 ℃ in LB media	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	characteristics	cell type: Escherichia coli str. K-12 substr. MG1655 PGCGROWTHCONDITIONS	<Gtype> cell type </Gtype> : Escherichia coli str . <Strain> K-12 </Strain> substr . <Substrain> MG1655 </Substrain> 	cell type	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE67218/GSE67218.soft.gz	T cell	80	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011472
SRR2547467	GSE73672	GSM1900470	GPL20227	27713404	Parent LB rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.3% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.3 % glucose </Supp> 	0.3 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.5%	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002772
SRR2547469	GSE73672	GSM1900472	GPL20227	27713404	cysG KO LB rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.3% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.3 % glucose </Supp> 	0.3 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.5%	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002772
SRR2547471	GSE73672	GSM1900474	GPL20227	27713404	cysH KO LB rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.3% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.3 % glucose </Supp> 	0.3 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.5%	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002772
SRR2547472	GSE73672	GSM1900475	GPL20227	27713404	cysH KO LB rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.3% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.3 % glucose </Supp> 	0.3 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.5%	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002772
SRR2547473	GSE73672	GSM1900476	GPL20227	27713404	dcd KO LB rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.3% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.3 % glucose </Supp> 	0.3 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.5%	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002772
SRR2547474	GSE73672	GSM1900477	GPL20227	27713404	dcd KO LB rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.3% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.3 % glucose </Supp> 	0.3 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.5%	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002772
SRR2547475	GSE73672	GSM1900478	GPL20227	27713404	fadr KO LB rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.3% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.3 % glucose </Supp> 	0.3 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.5%	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002772
SRR2547476	GSE73672	GSM1900479	GPL20227	27713404	fadr KO LB rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.3% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.3 % glucose </Supp> 	0.3 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.5%	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002772
SRR2547477	GSE73672	GSM1900480	GPL20227	27713404	ppk KO LB rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.3% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.3 % glucose </Supp> 	0.3 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.5%	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002772
SRR2547479	GSE73672	GSM1900482	GPL20227	27713404	wzc KO LB rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.3% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.3 % glucose </Supp> 	0.3 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.5%	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002772
SRR2547480	GSE73672	GSM1900483	GPL20227	27713404	wzc KO LB rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.3% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.3 % glucose </Supp> 	0.3 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.5%	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002772
SRR2547482	GSE73672	GSM1900485	GPL20227	27713404	yghD KO LB rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.3% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.3 % glucose </Supp> 	0.3 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.5%	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002772
SRR2547483	GSE73672	GSM1900486	GPL20227	27713404	fepA KO LB rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.3% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.3 % glucose </Supp> 	0.3 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.5%	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002772
SRR2547485	GSE73672	GSM1900488	GPL20227	27713404	lacA KO LB rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.3% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.3 % glucose </Supp> 	0.3 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.5%	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002772
SRR2547487	GSE73672	GSM1900490	GPL20227	27713404	Parent M9 rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.3% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.3 % glucose </Supp> 	0.3 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.5%	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002772
SRR2547488	GSE73672	GSM1900491	GPL20227	27713404	Parent M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.3% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.3 % glucose </Supp> 	0.3 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.5%	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002772
SRR2547489	GSE73672	GSM1900492	GPL20227	27713404	dcd KO M9 rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.3% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.3 % glucose </Supp> 	0.3 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.5%	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002772
SRR2547490	GSE73672	GSM1900493	GPL20227	27713404	dcd KO M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.3% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.3 % glucose </Supp> 	0.3 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.5%	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002772
SRR2547491	GSE73672	GSM1900494	GPL20227	27713404	fadr KO M9 rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.3% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.3 % glucose </Supp> 	0.3 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.5%	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002772
SRR2547492	GSE73672	GSM1900495	GPL20227	27713404	fadr KO M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.3% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.3 % glucose </Supp> 	0.3 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.5%	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002772
SRR2547493	GSE73672	GSM1900496	GPL20227	27713404	ppk KO M9 rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.3% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.3 % glucose </Supp> 	0.3 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.5%	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002772
SRR2547494	GSE73672	GSM1900497	GPL20227	27713404	ppk KO M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.3% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.3 % glucose </Supp> 	0.3 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.5%	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002772
SRR2547495	GSE73672	GSM1900498	GPL20227	27713404	wzc KO M9 rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.3% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.3 % glucose </Supp> 	0.3 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.5%	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002772
SRR2547496	GSE73672	GSM1900499	GPL20227	27713404	wzc KO M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.3% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.3 % glucose </Supp> 	0.3 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.5%	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002772
SRR2547497	GSE73672	GSM1900500	GPL20227	27713404	yghD KO M9 rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.3% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.3 % glucose </Supp> 	0.3 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.5%	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002772
SRR2547498	GSE73672	GSM1900501	GPL20227	27713404	yghD KO M9 rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.3% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.3 % glucose </Supp> 	0.3 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.5%	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002772
SRR2547499	GSE73672	GSM1900502	GPL20227	27713404	fepA KO M9 rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.3% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.3 % glucose </Supp> 	0.3 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.5%	91	91	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002772
SRR2547504	GSE73672	GSM1900507	GPL20227	27713404	WT rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, WT, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , WT , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547506	GSE73672	GSM1900509	GPL20227	27713404	mgtA KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, mgtA KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , mgtA KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547507	GSE73672	GSM1900510	GPL20227	27713404	mgtA KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, mgtA KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , mgtA KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547510	GSE73672	GSM1900513	GPL20227	27713404	gabT KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, gabT KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , gabT KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547511	GSE73672	GSM1900514	GPL20227	27713404	gabT KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, gabT KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , gabT KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547512	GSE73672	GSM1900515	GPL20227	27713404	sdhC KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, sdhC KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , sdhC KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547513	GSE73672	GSM1900516	GPL20227	27713404	sdhC KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, sdhC KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , sdhC KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547515	GSE73672	GSM1900518	GPL20227	27713404	putP KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, putP KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , putP KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547517	GSE73672	GSM1900520	GPL20227	27713404	putP KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, putP KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , putP KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547518	GSE73672	GSM1900521	GPL20227	27713404	rfbA KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, rfbA KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , rfbA KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547519	GSE73672	GSM1900522	GPL20227	27713404	rfbA KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, rfbA KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , rfbA KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547521	GSE73672	GSM1900524	GPL20227	27713404	entF KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, entF KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , entF KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547522	GSE73672	GSM1900525	GPL20227	27713404	entF KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, entF KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , entF KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547523	GSE73672	GSM1900526	GPL20227	27713404	entF KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, entF KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , entF KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547524	GSE73672	GSM1900527	GPL20227	27713404	kefB KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, kefB KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , kefB KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547526	GSE73672	GSM1900529	GPL20227	27713404	kefB KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, kefB KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , kefB KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547527	GSE73672	GSM1900530	GPL20227	27713404	cysA KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, cysA KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , cysA KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547528	GSE73672	GSM1900531	GPL20227	27713404	cysA KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, cysA KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , cysA KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547529	GSE73672	GSM1900532	GPL20227	27713404	cysA KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, cysA KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , cysA KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547531	GSE73672	GSM1900534	GPL20227	27713404	galE KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, galE KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , galE KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547533	GSE73672	GSM1900536	GPL20227	27713404	mhpD KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, mhpD KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , mhpD KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547534	GSE73672	GSM1900537	GPL20227	27713404	mhpD KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, mhpD KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , mhpD KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547535	GSE73672	GSM1900538	GPL20227	27713404	mhpD KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, mhpD KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , mhpD KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547536	GSE73672	GSM1900539	GPL20227	27713404	fliY KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, fliY KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , fliY KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547537	GSE73672	GSM1900540	GPL20227	27713404	fliY KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, fliY KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , fliY KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547538	GSE73672	GSM1900541	GPL20227	27713404	fliY KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, fliY KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , fliY KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547539	GSE73672	GSM1900542	GPL20227	27713404	lplA KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, lplA KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , lplA KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547540	GSE73672	GSM1900543	GPL20227	27713404	lplA KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, lplA KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , lplA KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547541	GSE73672	GSM1900544	GPL20227	27713404	lplA KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, lplA KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , lplA KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547542	GSE73672	GSM1900545	GPL20227	27713404	khc KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, khc KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , khc KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547543	GSE73672	GSM1900546	GPL20227	27713404	khc KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, khc KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , khc KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547544	GSE73672	GSM1900547	GPL20227	27713404	khc KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, khc KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , khc KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547545	GSE73672	GSM1900548	GPL20227	27713404	ugpC KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, ugpC KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , ugpC KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547546	GSE73672	GSM1900549	GPL20227	27713404	ugpC KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, ugpC KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , ugpC KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547547	GSE73672	GSM1900550	GPL20227	27713404	ugpC KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, ugpC KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , ugpC KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547548	GSE73672	GSM1900551	GPL20227	27713404	trpD KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, trpD KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , trpD KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547549	GSE73672	GSM1900552	GPL20227	27713404	trpD KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, trpD KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , trpD KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547550	GSE73672	GSM1900553	GPL20227	27713404	trpD KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, trpD KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , trpD KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547551	GSE73672	GSM1900554	GPL20227	27713404	aspC KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, aspC KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , aspC KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547552	GSE73672	GSM1900555	GPL20227	27713404	aspC KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, aspC KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , aspC KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547553	GSE73672	GSM1900556	GPL20227	27713404	aspC KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	source_name	Whole cell, aspC KO, M9 and 0.4% glucose PGCGROWTHCONDITIONS	Whole cell , aspC KO , M9 and 0.4 <Supp> % glucose </Supp> 	% glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000245
SRR2547504	GSE73672	GSM1900507	GPL20227	27713404	WT rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547506	GSE73672	GSM1900509	GPL20227	27713404	mgtA KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547507	GSE73672	GSM1900510	GPL20227	27713404	mgtA KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547510	GSE73672	GSM1900513	GPL20227	27713404	gabT KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547511	GSE73672	GSM1900514	GPL20227	27713404	gabT KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547512	GSE73672	GSM1900515	GPL20227	27713404	sdhC KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547513	GSE73672	GSM1900516	GPL20227	27713404	sdhC KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547515	GSE73672	GSM1900518	GPL20227	27713404	putP KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547517	GSE73672	GSM1900520	GPL20227	27713404	putP KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547518	GSE73672	GSM1900521	GPL20227	27713404	rfbA KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547519	GSE73672	GSM1900522	GPL20227	27713404	rfbA KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547521	GSE73672	GSM1900524	GPL20227	27713404	entF KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547522	GSE73672	GSM1900525	GPL20227	27713404	entF KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547523	GSE73672	GSM1900526	GPL20227	27713404	entF KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547524	GSE73672	GSM1900527	GPL20227	27713404	kefB KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547526	GSE73672	GSM1900529	GPL20227	27713404	kefB KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547527	GSE73672	GSM1900530	GPL20227	27713404	cysA KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547528	GSE73672	GSM1900531	GPL20227	27713404	cysA KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547529	GSE73672	GSM1900532	GPL20227	27713404	cysA KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547531	GSE73672	GSM1900534	GPL20227	27713404	galE KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547533	GSE73672	GSM1900536	GPL20227	27713404	mhpD KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547534	GSE73672	GSM1900537	GPL20227	27713404	mhpD KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547535	GSE73672	GSM1900538	GPL20227	27713404	mhpD KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547536	GSE73672	GSM1900539	GPL20227	27713404	fliY KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547537	GSE73672	GSM1900540	GPL20227	27713404	fliY KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547538	GSE73672	GSM1900541	GPL20227	27713404	fliY KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547539	GSE73672	GSM1900542	GPL20227	27713404	lplA KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547540	GSE73672	GSM1900543	GPL20227	27713404	lplA KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547541	GSE73672	GSM1900544	GPL20227	27713404	lplA KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547542	GSE73672	GSM1900545	GPL20227	27713404	khc KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547543	GSE73672	GSM1900546	GPL20227	27713404	khc KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547544	GSE73672	GSM1900547	GPL20227	27713404	khc KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547545	GSE73672	GSM1900548	GPL20227	27713404	ugpC KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547546	GSE73672	GSM1900549	GPL20227	27713404	ugpC KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547547	GSE73672	GSM1900550	GPL20227	27713404	ugpC KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547548	GSE73672	GSM1900551	GPL20227	27713404	trpD KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547549	GSE73672	GSM1900552	GPL20227	27713404	trpD KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547550	GSE73672	GSM1900553	GPL20227	27713404	trpD KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547551	GSE73672	GSM1900554	GPL20227	27713404	aspC KO rep1	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547552	GSE73672	GSM1900555	GPL20227	27713404	aspC KO rep2	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2547553	GSE73672	GSM1900556	GPL20227	27713404	aspC KO rep3	Targeted experimentation to increase functional coverage in omics dataset	GPL20227: Illumina HiSeq 2500 (Escherichia coli BW25113)	characteristics	treatment: 0.4% glucose PGCGROWTHCONDITIONS	treatment : <Supp> 0.4 % glucose </Supp> 	0.4 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73672/GSE73672.soft.gz	glucose 0.4%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002771
SRR2637695	GSE73969	GSM1906887	GPL21021	2717363528288207	wt_1	RNA-seq to profile the H-NS transcriptome in EHEC O157:H7 strain EDL933	GPL21021: Illumina HiSeq 2500 (Escherichia coli O157:H7 str. EDL933)	growth_protocol	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	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> . 	OD600 of about 0.8	Optical Density (OD)	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73969/GSE73969.soft.gz	OD600 of 0.8	100	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003177
SRR2637696	GSE73969	GSM1906888	GPL21021	2717363528288207	wt_2	RNA-seq to profile the H-NS transcriptome in EHEC O157:H7 strain EDL933	GPL21021: Illumina HiSeq 2500 (Escherichia coli O157:H7 str. EDL933)	growth_protocol	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	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> . 	OD600 of about 0.8	Optical Density (OD)	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73969/GSE73969.soft.gz	OD600 of 0.8	100	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003177
SRR2637697	GSE73969	GSM1906889	GPL21021	2717363528288207	hns_1	RNA-seq to profile the H-NS transcriptome in EHEC O157:H7 strain EDL933	GPL21021: Illumina HiSeq 2500 (Escherichia coli O157:H7 str. EDL933)	growth_protocol	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	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> . 	OD600 of about 0.8	Optical Density (OD)	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73969/GSE73969.soft.gz	OD600 of 0.8	100	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003177
SRR2637698	GSE73969	GSM1906890	GPL21021	2717363528288207	hns_2	RNA-seq to profile the H-NS transcriptome in EHEC O157:H7 strain EDL933	GPL21021: Illumina HiSeq 2500 (Escherichia coli O157:H7 str. EDL933)	growth_protocol	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	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> . 	OD600 of about 0.8	Optical Density (OD)	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE73969/GSE73969.soft.gz	OD600 of 0.8	100	80	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003177
SRR2932665	GSE74809	GSM1933982	GPL15982	29686109	rpoS_TS_1	Growth-phase dependent regulation of transcription by Rsd and 6S RNA	GPL15982: Illumina HiSeq 1000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	0.5 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE74809/GSE74809.soft.gz	glucose 0.5%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002772
SRR2932682	GSE74809	GSM1933999	GPL15982	29686109	ssrS_LS_2	Growth-phase dependent regulation of transcription by Rsd and 6S RNA	GPL15982: Illumina HiSeq 1000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	0.5 % glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE74809/GSE74809.soft.gz	glucose 0.5%	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002772
SRR2932682	GSE74809	GSM1933999	GPL15982	29686109	ssrS_LS_2	Growth-phase dependent regulation of transcription by Rsd and 6S RNA	GPL15982: Illumina HiSeq 1000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	growth phase: Late Stationary PGCGROWTHCONDITIONS	growth phase : <Gtype> Late Stationary </Gtype> 	Late Stationary	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE74809/GSE74809.soft.gz	stationary phase	84	84	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002866
SRR3033275SRR3033276SRR3033277SRR3033278SRR3033279	GSE76167	GSM1975603	GPL18133	2737513027668277	Rodrigue_1-WT-phiNi-1	Mechanisms of nickel toxicity in bacteria	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	50 µM NiCl2	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE76167/GSE76167.soft.gz	nicl2 5 µm	95	95	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002790
SRR3033280SRR3033281SRR3033282SRR3033283	GSE76167	GSM1975604	GPL18133	2737513027668277	Rodrigue_6-WT-phiNi-2	Mechanisms of nickel toxicity in bacteria	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	50 µM NiCl2	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE76167/GSE76167.soft.gz	nicl2 5 µm	95	95	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002790
SRR3033284SRR3033285SRR3033286SRR3033287	GSE76167	GSM1975605	GPL18133	2737513027668277	Rodrigue_9-WT-phiNi-3	Mechanisms of nickel toxicity in bacteria	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	50 µM NiCl2	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE76167/GSE76167.soft.gz	nicl2 5 µm	95	95	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002790
SRR3033288SRR3033289SRR3033290SRR3033291SRR3033292	GSE76167	GSM1975606	GPL18133	2737513027668277	Rodrigue_2-WT-Ni-1	Mechanisms of nickel toxicity in bacteria	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	50 µM NiCl2	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE76167/GSE76167.soft.gz	nicl2 5 µm	95	95	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002790
SRR3033293SRR3033294SRR3033295SRR3033296	GSE76167	GSM1975607	GPL18133	2737513027668277	Rodrigue_5-WT-Ni-2	Mechanisms of nickel toxicity in bacteria	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	50 µM NiCl2	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE76167/GSE76167.soft.gz	nicl2 5 µm	95	95	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002790
SRR3033297SRR3033298SRR3033299SRR3033300SRR3033301	GSE76167	GSM1975608	GPL18133	2737513027668277	Rodrigue_10-WT-Ni-3	Mechanisms of nickel toxicity in bacteria	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	growth_protocol	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	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 . 	50 µM NiCl2	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE76167/GSE76167.soft.gz	nicl2 5 µm	95	95	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002790
SRR3379590	GSE80251	GSM2122743	GPL21726	27645242	Untreated_replicate_1	Genome-wide transcriptome analyses of E. coli treated with ribosome-targeting antibiotics	GPL21726: Ion Torrent Proton (Escherichia coli)	growth_protocol	E. coli strain NM580 (genotype MG1655 ermBL-ermB’::LacZ) cells were grown in LB broth (37°C) until OD600 of ~0.3. PGCGROWTHCONDITIONS	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> . 	OD600 of ~ 0.3	Optical Density (OD)	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80251/GSE80251.soft.gz	OD600 of 0.3	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002564
SRR3379591	GSE80251	GSM2122744	GPL21726	27645242	Untreated_replicate_2	Genome-wide transcriptome analyses of E. coli treated with ribosome-targeting antibiotics	GPL21726: Ion Torrent Proton (Escherichia coli)	growth_protocol	E. coli strain NM580 (genotype MG1655 ermBL-ermB’::LacZ) cells were grown in LB broth (37°C) until OD600 of ~0.3. PGCGROWTHCONDITIONS	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> . 	OD600 of ~ 0.3	Optical Density (OD)	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80251/GSE80251.soft.gz	OD600 of 0.3	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002564
SRR3379592	GSE80251	GSM2122745	GPL21726	27645242	Untreated_replicate_3	Genome-wide transcriptome analyses of E. coli treated with ribosome-targeting antibiotics	GPL21726: Ion Torrent Proton (Escherichia coli)	growth_protocol	E. coli strain NM580 (genotype MG1655 ermBL-ermB’::LacZ) cells were grown in LB broth (37°C) until OD600 of ~0.3. PGCGROWTHCONDITIONS	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> . 	OD600 of ~ 0.3	Optical Density (OD)	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80251/GSE80251.soft.gz	OD600 of 0.3	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002564
SRR3379593	GSE80251	GSM2122746	GPL21726	27645242	Erythromycin_replicate_1	Genome-wide transcriptome analyses of E. coli treated with ribosome-targeting antibiotics	GPL21726: Ion Torrent Proton (Escherichia coli)	growth_protocol	E. coli strain NM580 (genotype MG1655 ermBL-ermB’::LacZ) cells were grown in LB broth (37°C) until OD600 of ~0.3. PGCGROWTHCONDITIONS	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> . 	OD600 of ~ 0.3	Optical Density (OD)	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80251/GSE80251.soft.gz	OD600 of 0.3	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002564
SRR3379594	GSE80251	GSM2122747	GPL21726	27645242	Erythromycin_replicate_2	Genome-wide transcriptome analyses of E. coli treated with ribosome-targeting antibiotics	GPL21726: Ion Torrent Proton (Escherichia coli)	growth_protocol	E. coli strain NM580 (genotype MG1655 ermBL-ermB’::LacZ) cells were grown in LB broth (37°C) until OD600 of ~0.3. PGCGROWTHCONDITIONS	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> . 	OD600 of ~ 0.3	Optical Density (OD)	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80251/GSE80251.soft.gz	OD600 of 0.3	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002564
SRR3379595	GSE80251	GSM2122748	GPL21726	27645242	Erythromycin_replicate_3	Genome-wide transcriptome analyses of E. coli treated with ribosome-targeting antibiotics	GPL21726: Ion Torrent Proton (Escherichia coli)	growth_protocol	E. coli strain NM580 (genotype MG1655 ermBL-ermB’::LacZ) cells were grown in LB broth (37°C) until OD600 of ~0.3. PGCGROWTHCONDITIONS	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> . 	OD600 of ~ 0.3	Optical Density (OD)	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80251/GSE80251.soft.gz	OD600 of 0.3	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002564
SRR3379596	GSE80251	GSM2122749	GPL21726	27645242	Clindamycin_replicate_1	Genome-wide transcriptome analyses of E. coli treated with ribosome-targeting antibiotics	GPL21726: Ion Torrent Proton (Escherichia coli)	growth_protocol	E. coli strain NM580 (genotype MG1655 ermBL-ermB’::LacZ) cells were grown in LB broth (37°C) until OD600 of ~0.3. PGCGROWTHCONDITIONS	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> . 	OD600 of ~ 0.3	Optical Density (OD)	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80251/GSE80251.soft.gz	OD600 of 0.3	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002564
SRR3379597	GSE80251	GSM2122750	GPL21726	27645242	Clindamycin_replicate_2	Genome-wide transcriptome analyses of E. coli treated with ribosome-targeting antibiotics	GPL21726: Ion Torrent Proton (Escherichia coli)	growth_protocol	E. coli strain NM580 (genotype MG1655 ermBL-ermB’::LacZ) cells were grown in LB broth (37°C) until OD600 of ~0.3. PGCGROWTHCONDITIONS	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> . 	OD600 of ~ 0.3	Optical Density (OD)	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80251/GSE80251.soft.gz	OD600 of 0.3	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002564
SRR3379598	GSE80251	GSM2122751	GPL21726	27645242	Clindamycin_replicate_3	Genome-wide transcriptome analyses of E. coli treated with ribosome-targeting antibiotics	GPL21726: Ion Torrent Proton (Escherichia coli)	growth_protocol	E. coli strain NM580 (genotype MG1655 ermBL-ermB’::LacZ) cells were grown in LB broth (37°C) until OD600 of ~0.3. PGCGROWTHCONDITIONS	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> . 	OD600 of ~ 0.3	Optical Density (OD)	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80251/GSE80251.soft.gz	OD600 of 0.3	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002564
SRR3403686	GSE80451	GSM2127617	GPL14548	28103245	Aerobic 1	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	<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. 	Aerobic and anaerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80451/GSE80451.soft.gz	anaerobic	100	60	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011680
SRR3403687	GSE80451	GSM2127618	GPL14548	28103245	Aerobic 2	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	<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. 	Aerobic and anaerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80451/GSE80451.soft.gz	anaerobic	100	60	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011680
SRR3403688	GSE80451	GSM2127619	GPL14548	28103245	Aerobic 3	Transcriptome analysis of E. coli REL4536 grown aerobically and anaerobically	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	growth_protocol	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	<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. 	Aerobic and anaerobic	Aeration	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE80451/GSE80451.soft.gz	anaerobic	100	60	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011680
SRR3584193SRR3584194SRR3584195	GSE81584	GSM2157648	GPL14548		MG1655_1	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	genotype: Wildtype PGCGROWTHCONDITIONS	genotype : <Gtype> Wildtype </Gtype> 	Wildtype	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE81584/GSE81584.soft.gz	wildtype	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR3584196SRR3584197SRR3584198	GSE81584	GSM2157649	GPL14548		MG1655_2	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	genotype: Wildtype PGCGROWTHCONDITIONS	genotype : <Gtype> Wildtype </Gtype> 	Wildtype	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE81584/GSE81584.soft.gz	wildtype	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR3584199SRR3584200	GSE81584	GSM2157650	GPL14548		MG1655_3	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	genotype: Wildtype PGCGROWTHCONDITIONS	genotype : <Gtype> Wildtype </Gtype> 	Wildtype	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE81584/GSE81584.soft.gz	wildtype	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR3584208SRR3584209	GSE81584	GSM2157654	GPL14548		MG1655_vector_1	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	genotype: Wildtype with vector PGCGROWTHCONDITIONS	genotype : <Gtype> Wildtype </Gtype> with <Supp> vector </Supp> 	Wildtype	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE81584/GSE81584.soft.gz	wildtype	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR3584210SRR3584211	GSE81584	GSM2157655	GPL14548		MG1655_vector_2	Mfd alters global transcription patterns in undamaged Escherichia coli cells	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	genotype: Wildtype with vector PGCGROWTHCONDITIONS	genotype : <Gtype> Wildtype </Gtype> with <Supp> vector </Supp> 	Wildtype	Genetic background	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE81584/GSE81584.soft.gz	wildtype	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002470
SRR4416202	GSE87856	GSM2341961	GPL14548	28115545	100% rep1	The genome-wide transcriptional response to varying RpoS levels in Escherichia coli.	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	rpos level: 100% PGCGROWTHCONDITIONS	rpos level : <Supp> 100 % </Supp> 	100 %	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE87856/GSE87856.soft.gz	100.003	100	60	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002063
SRR4416205	GSE87856	GSM2341964	GPL14548	28115545	100% rep2	The genome-wide transcriptional response to varying RpoS levels in Escherichia coli.	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	rpos level: 100% PGCGROWTHCONDITIONS	rpos level : <Supp> 100 % </Supp> 	100 %	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE87856/GSE87856.soft.gz	100.003	100	60	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002063
SRR4416203	GSE87856	GSM2341962	GPL14548	28115545	0% rep1	The genome-wide transcriptional response to varying RpoS levels in Escherichia coli.	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	rpos level: 0% PGCGROWTHCONDITIONS	rpos level : <Supp> 0 % </Supp> 	0 %	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE87856/GSE87856.soft.gz	0	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000000748
SRR4416206	GSE87856	GSM2341965	GPL14548	28115545	0% rep2	The genome-wide transcriptional response to varying RpoS levels in Escherichia coli.	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	rpos level: 0% PGCGROWTHCONDITIONS	rpos level : <Supp> 0 % </Supp> 	0 %	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE87856/GSE87856.soft.gz	0	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000000748
SRR4416204	GSE87856	GSM2341963	GPL14548	28115545	26% rep1	The genome-wide transcriptional response to varying RpoS levels in Escherichia coli.	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	rpos level: 26% PGCGROWTHCONDITIONS	rpos level : <Supp> 26 % </Supp> 	26 %	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE87856/GSE87856.soft.gz	26.0 C	100	50	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003196
SRR4416207	GSE87856	GSM2341966	GPL14548	28115545	26% rep2	The genome-wide transcriptional response to varying RpoS levels in Escherichia coli.	GPL14548: Illumina HiSeq 2000 (Escherichia coli)	characteristics	rpos level: 26% PGCGROWTHCONDITIONS	rpos level : <Supp> 26 % </Supp> 	26 %	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE87856/GSE87856.soft.gz	26.0 C	100	50	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003196
SRR4435464	GSE88980	GSM2356687	GPL17439	28526842	WT NaCl 1	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]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	0.3 M of NaCl	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88980/GSE88980.soft.gz	nacl 0.35 m	84	83	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002726
SRR4435465	GSE88980	GSM2356688	GPL17439	28526842	WT NaCl 2	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]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	0.3 M of NaCl	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88980/GSE88980.soft.gz	nacl 0.35 m	84	83	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002726
SRR4435466	GSE88980	GSM2356689	GPL17439	28526842	ΔompR NaCl 1	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]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	0.3 M of NaCl	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88980/GSE88980.soft.gz	nacl 0.35 m	84	83	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002726
SRR4435467	GSE88980	GSM2356690	GPL17439	28526842	ΔompR NaCl 2	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]	GPL17439: Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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 . 	0.3 M of NaCl	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE88980/GSE88980.soft.gz	nacl 0.35 m	84	83	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002726
SRR5036057	GSE90056	GSM2396709	GPL15010	29183994	ecoli_k12_pBAD_30C_m_1	Translation efficiency is maintained during heat shock in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	induction: 0.2% arabinose PGCGROWTHCONDITIONS	induction : <Supp> 0.2 % arabinose </Supp> 	0.2 % arabinose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90056/GSE90056.soft.gz	arabinose	100	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000402
SRR5036059	GSE90056	GSM2396711	GPL15010	29183994	ecoli_k12_pBADsigma32wt_30C_m_1	Translation efficiency is maintained during heat shock in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	induction: 0.2% arabinose PGCGROWTHCONDITIONS	induction : <Supp> 0.2 % arabinose </Supp> 	0.2 % arabinose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90056/GSE90056.soft.gz	arabinose	100	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000402
SRR5036061	GSE90056	GSM2396713	GPL15010	29183994	ecoli_k12_pBAD_30C_m_2	Translation efficiency is maintained during heat shock in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	induction: 0.2% arabinose PGCGROWTHCONDITIONS	induction : <Supp> 0.2 % arabinose </Supp> 	0.2 % arabinose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90056/GSE90056.soft.gz	arabinose	100	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000402
SRR5036063	GSE90056	GSM2396715	GPL15010	29183994	ecoli_k12_pBADsigma32wt_30C_m_2	Translation efficiency is maintained during heat shock in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	induction: 0.2% arabinose PGCGROWTHCONDITIONS	induction : <Supp> 0.2 % arabinose </Supp> 	0.2 % arabinose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90056/GSE90056.soft.gz	arabinose	100	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000402
SRR5036065	GSE90056	GSM2396717	GPL15010	29183994	ecoli_k12_pBAD_30C_m_3	Translation efficiency is maintained during heat shock in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	induction: 0.2% arabinose PGCGROWTHCONDITIONS	induction : <Supp> 0.2 % arabinose </Supp> 	0.2 % arabinose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90056/GSE90056.soft.gz	arabinose	100	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000402
SRR5036067	GSE90056	GSM2396719	GPL15010	29183994	ecoli_k12_pBADsigma32wt_30C_m_3	Translation efficiency is maintained during heat shock in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	induction: 0.2% arabinose PGCGROWTHCONDITIONS	induction : <Supp> 0.2 % arabinose </Supp> 	0.2 % arabinose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90056/GSE90056.soft.gz	arabinose	100	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000402
SRR5036087	GSE90056	GSM2396739	GPL15010	29183994	ecoli_k12_pBAD_30C_m_4	Translation efficiency is maintained during heat shock in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	induction: 0.2% arabinose PGCGROWTHCONDITIONS	induction : <Supp> 0.2 % arabinose </Supp> 	0.2 % arabinose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90056/GSE90056.soft.gz	arabinose	100	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000402
SRR5036089	GSE90056	GSM2396741	GPL15010	29183994	ecoli_k12_pBADsigma32I54N_30C_m_1	Translation efficiency is maintained during heat shock in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	induction: 0.2% arabinose PGCGROWTHCONDITIONS	induction : <Supp> 0.2 % arabinose </Supp> 	0.2 % arabinose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90056/GSE90056.soft.gz	arabinose	100	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000402
SRR5036091	GSE90056	GSM2396743	GPL15010	29183994	ecoli_k12_pBADsigma32I54N_30C_m_2	Translation efficiency is maintained during heat shock in Escherichia coli	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	characteristics	induction: 0.2% arabinose PGCGROWTHCONDITIONS	induction : <Supp> 0.2 % arabinose </Supp> 	0.2 % arabinose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE90056/GSE90056.soft.gz	arabinose	100	82	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000402
SRR5085370	GSE91001	GSM2418921	GPL14548-GPL20262	28224117	ATCACG-D1	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	growth_protocol	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	<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 ) . 	LB	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE91001/GSE91001.soft.gz	LB agar	100	44	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011703
SRR5085371	GSE91001	GSM2418922	GPL14548-GPL20262	28224117	CGATGT-D2	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	growth_protocol	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	<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 ) . 	LB	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE91001/GSE91001.soft.gz	LB agar	100	44	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011703
SRR5085373	GSE91001	GSM2418923	GPL14548-GPL20262	28224117	TTAGGC-D3	PerC manipulates metabolism and surface antigens in enteropathogenic Escherichia coli	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL20262: Illumina HiSeq 2000 (Escherichia coli O127:H6 str. E2348/69)	growth_protocol	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	<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 ) . 	LB	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE91001/GSE91001.soft.gz	LB agar	100	44	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000011703
SRR5121109	GSE92601	GSM2433290	GPL18956	29807996	ORF1_1_IPTG	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	data_processing	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	<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 	IPTG	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	iptg	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002105
SRR5121110	GSE92601	GSM2433291	GPL18956	29807996	ORF1_1	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	data_processing	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	<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 	IPTG	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	iptg	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002105
SRR5121111	GSE92601	GSM2433292	GPL18956	29807996	ORF1_2_IPTG	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	data_processing	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	<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 	IPTG	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	iptg	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002105
SRR5121112	GSE92601	GSM2433293	GPL18956	29807996	ORF1_2	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	data_processing	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	<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 	IPTG	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	iptg	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002105
SRR5121113	GSE92601	GSM2433294	GPL18956	29807996	Svi3_3_1_IPTG	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	data_processing	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	<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 	IPTG	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	iptg	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002105
SRR5121114	GSE92601	GSM2433295	GPL18956	29807996	Svi3_3_1	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	data_processing	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	<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 	IPTG	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	iptg	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002105
SRR5121115	GSE92601	GSM2433296	GPL18956	29807996	Svi3_3_2_IPTG	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	data_processing	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	<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 	IPTG	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	iptg	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002105
SRR5121116	GSE92601	GSM2433297	GPL18956	29807996	Svi3_3_2	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	data_processing	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	<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 	IPTG	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	iptg	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002105
SRR5121117	GSE92601	GSM2433298	GPL18956	29807996	WT1_IPTG	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	data_processing	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	<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 	IPTG	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	iptg	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002105
SRR5121118	GSE92601	GSM2433299	GPL18956	29807996	WT2_IPTG	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	data_processing	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	<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 	IPTG	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	iptg	100	100	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/mco_terms_v0.2.json	MCO000002105
SRR5121109	GSE92601	GSM2433290	GPL18956	29807996	ORF1_1_IPTG	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	characteristics	induction: induced 50 µM IPTG PGCGROWTHCONDITIONS	induction : <Supp> induced 50 µM IPTG </Supp> 	induced 50 µM IPTG	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	plasmid PK8263 (4 µM IPTG-induced fnr)	90	58	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003316
SRR5121111	GSE92601	GSM2433292	GPL18956	29807996	ORF1_2_IPTG	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	characteristics	induction: induced 50 µM IPTG PGCGROWTHCONDITIONS	induction : <Supp> induced 50 µM IPTG </Supp> 	induced 50 µM IPTG	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	plasmid PK8263 (4 µM IPTG-induced fnr)	90	58	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003316
SRR5121113	GSE92601	GSM2433294	GPL18956	29807996	Svi3_3_1_IPTG	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	characteristics	induction: induced 50 µM IPTG PGCGROWTHCONDITIONS	induction : <Supp> induced 50 µM IPTG </Supp> 	induced 50 µM IPTG	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	plasmid PK8263 (4 µM IPTG-induced fnr)	90	58	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003316
SRR5121115	GSE92601	GSM2433296	GPL18956	29807996	Svi3_3_2_IPTG	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	characteristics	induction: induced 50 µM IPTG PGCGROWTHCONDITIONS	induction : <Supp> induced 50 µM IPTG </Supp> 	induced 50 µM IPTG	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	plasmid PK8263 (4 µM IPTG-induced fnr)	90	58	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003316
SRR5121117	GSE92601	GSM2433298	GPL18956	29807996	WT1_IPTG	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	characteristics	induction: induced 50 µM IPTG PGCGROWTHCONDITIONS	induction : <Supp> induced 50 µM IPTG </Supp> 	induced 50 µM IPTG	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	plasmid PK8263 (4 µM IPTG-induced fnr)	90	58	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003316
SRR5121118	GSE92601	GSM2433299	GPL18956	29807996	WT2_IPTG	A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.	GPL18956: Illumina HiSeq 2500 (Escherichia coli str. K-12 substr. MG1655)	characteristics	induction: induced 50 µM IPTG PGCGROWTHCONDITIONS	induction : <Supp> induced 50 µM IPTG </Supp> 	induced 50 µM IPTG	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE92601/GSE92601.soft.gz	plasmid PK8263 (4 µM IPTG-induced fnr)	90	58	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000003316
SRR5143868	GSE93125	GSM2445155	GPL18133	28959742	Eco_TolC_30min_control_A	Transcriptomal changes of Escherichia coli TolC grown with the biofilm inhibitor Carolacton	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	characteristics	time point (minutes): 30 PGCGROWTHCONDITIONS	time point ( minutes ) : <Supp> 30 </Supp> 	30	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE93125/GSE93125.soft.gz	30.0 C	100	50	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002695
SRR5143869	GSE93125	GSM2445157	GPL18133	28959742	Eco_TolC_30min_control_B	Transcriptomal changes of Escherichia coli TolC grown with the biofilm inhibitor Carolacton	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	characteristics	time point (minutes): 30 PGCGROWTHCONDITIONS	time point ( minutes ) : <Supp> 30 </Supp> 	30	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE93125/GSE93125.soft.gz	30.0 C	100	50	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002695
SRR5143870	GSE93125	GSM2445159	GPL18133	28959742	Eco_TolC_30min_Carolacton_A	Transcriptomal changes of Escherichia coli TolC grown with the biofilm inhibitor Carolacton	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	characteristics	time point (minutes): 30 PGCGROWTHCONDITIONS	time point ( minutes ) : <Supp> 30 </Supp> 	30	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE93125/GSE93125.soft.gz	30.0 C	100	50	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002695
SRR5143871	GSE93125	GSM2445161	GPL18133	28959742	Eco_TolC_30min_Carolacton_B	Transcriptomal changes of Escherichia coli TolC grown with the biofilm inhibitor Carolacton	GPL18133: Illumina HiSeq 2500 (Escherichia coli)	characteristics	time point (minutes): 30 PGCGROWTHCONDITIONS	time point ( minutes ) : <Supp> 30 </Supp> 	30	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE93125/GSE93125.soft.gz	30.0 C	100	50	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002695
SRR5282168	GSE95310	GSM2501621	GPL14548-GPL19659-GPL23101		MG1655_LB1	Cross-talk between species that do not share often the same environment	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL19659: Illumina HiSeq 2000 (Pseudomonas putida). GPL23101: Illumina HiSeq 2000 (Escherichia coli; Pseudomonas putida)	extract_protocol	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	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 ) . 	rifampicin and	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95310/GSE95310.soft.gz	rifampicin	100	83	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000828
SRR5282169	GSE95310	GSM2501622	GPL14548-GPL19659-GPL23101		MG1655_LB2	Cross-talk between species that do not share often the same environment	GPL14548: Illumina HiSeq 2000 (Escherichia coli). GPL19659: Illumina HiSeq 2000 (Pseudomonas putida). GPL23101: Illumina HiSeq 2000 (Escherichia coli; Pseudomonas putida)	extract_protocol	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	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 ) . 	rifampicin and	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95310/GSE95310.soft.gz	rifampicin	100	83	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000000828
SRR5304286	GSE95575	GSM2516609	GPL15010	29338696	1A_MG_t0	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	MOPS minimal medium	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002528
SRR5304287	GSE95575	GSM2516610	GPL15010	29338696	2A_MG_t10	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	MOPS minimal medium	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002528
SRR5304288	GSE95575	GSM2516611	GPL15010	29338696	3A_MG_t30	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	MOPS minimal medium	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002528
SRR5304289	GSE95575	GSM2516612	GPL15010	29338696	4A_MG_t60	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	MOPS minimal medium	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002528
SRR5304290	GSE95575	GSM2516613	GPL15010	29338696	5A_MG+Hg_t10	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	MOPS minimal medium	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002528
SRR5304291	GSE95575	GSM2516614	GPL15010	29338696	6A_MG+Hg_t30	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	MOPS minimal medium	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002528
SRR5304292	GSE95575	GSM2516615	GPL15010	29338696	7A_MG+Hg_t60	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	MOPS minimal medium	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002528
SRR5304293	GSE95575	GSM2516616	GPL15010	29338696	8A_MG+PMA_t10	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	MOPS minimal medium	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002528
SRR5304294	GSE95575	GSM2516617	GPL15010	29338696	9A_MG+PMA_t30	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	MOPS minimal medium	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002528
SRR5304295	GSE95575	GSM2516618	GPL15010	29338696	10A_MG+PMA_t60	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	MOPS minimal medium	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002528
SRR5304296	GSE95575	GSM2516619	GPL15010	29338696	1B_MG_t0	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	MOPS minimal medium	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002528
SRR5304297	GSE95575	GSM2516620	GPL15010	29338696	2B_MG_t10	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	MOPS minimal medium	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002528
SRR5304298	GSE95575	GSM2516621	GPL15010	29338696	3B_MG_t30	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	MOPS minimal medium	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002528
SRR5304299	GSE95575	GSM2516622	GPL15010	29338696	4B_MG_t60	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	MOPS minimal medium	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002528
SRR5304300	GSE95575	GSM2516623	GPL15010	29338696	5B_MG+Hg_t10	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	MOPS minimal medium	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002528
SRR5304301	GSE95575	GSM2516624	GPL15010	29338696	6B_MG+Hg_t30	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	MOPS minimal medium	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002528
SRR5304302	GSE95575	GSM2516625	GPL15010	29338696	7B_MG+Hg_t60	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	MOPS minimal medium	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002528
SRR5304303	GSE95575	GSM2516626	GPL15010	29338696	8B_MG+PMA_t10	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	MOPS minimal medium	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002528
SRR5304304	GSE95575	GSM2516627	GPL15010	29338696	9B_MG+PMA_t30	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	MOPS minimal medium	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002528
SRR5304305	GSE95575	GSM2516628	GPL15010	29338696	10B_MG+PMA_t60	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	MOPS minimal medium	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002528
SRR5304306	GSE95575	GSM2516629	GPL15010	29338696	1C_MG_t0	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	MOPS minimal medium	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002528
SRR5304307	GSE95575	GSM2516630	GPL15010	29338696	2C_MG_t10	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	MOPS minimal medium	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002528
SRR5304308	GSE95575	GSM2516631	GPL15010	29338696	3C_MG_t30	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	MOPS minimal medium	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002528
SRR5304309	GSE95575	GSM2516632	GPL15010	29338696	4C_MG_t60	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	MOPS minimal medium	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002528
SRR5304310	GSE95575	GSM2516633	GPL15010	29338696	5C_MG+Hg_t10	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	MOPS minimal medium	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002528
SRR5304311	GSE95575	GSM2516634	GPL15010	29338696	6C_MG+Hg_t30	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	MOPS minimal medium	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002528
SRR5304312	GSE95575	GSM2516635	GPL15010	29338696	7C_MG+Hg_t60	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	MOPS minimal medium	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002528
SRR5304313	GSE95575	GSM2516636	GPL15010	29338696	8C_MG+PMA_t10	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	MOPS minimal medium	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002528
SRR5304314	GSE95575	GSM2516637	GPL15010	29338696	9C_MG+PMA_t30	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	MOPS minimal medium	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002528
SRR5304315	GSE95575	GSM2516638	GPL15010	29338696	10C_MG+PMA_t60	Transcriptional responses of Escherichia coli during recovery from inorganic or organic mercury exposure	GPL15010: Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)	growth_protocol	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	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> . 	Neidhardt MOPS Minimal Medium ( NM3 )	Medium	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE95575/GSE95575.soft.gz	MOPS minimal medium	100	73	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002528
SRR5416991	GSE97406	GSM2563999	GPL16085		AR1-/AR2- rep 2	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8. PGCGROWTHCONDITIONS	Cells were grown in TB7 supplemented with <Supp> 22 mM glucose </Supp> until OD600 ~ 1.8 . 	22 mM glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	glucose 120 mM	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002775
SRR5416991	GSE97406	GSM2563999	GPL16085		AR1-/AR2- rep 2	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	media: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose PGCGROWTHCONDITIONS	media : <Gtype> Tryptone </Gtype> broth buffered to pH 7 supplemented with <Supp> 22 mM glucose </Supp> 	22 mM glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	glucose 120 mM	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002775
SRR5416992	GSE97406	GSM2564000	GPL16085		AR1-/AR2- rep 3	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8. PGCGROWTHCONDITIONS	Cells were grown in TB7 supplemented with <Supp> 22 mM glucose </Supp> until OD600 ~ 1.8 . 	22 mM glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	glucose 120 mM	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002775
SRR5416992	GSE97406	GSM2564000	GPL16085		AR1-/AR2- rep 3	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	media: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose PGCGROWTHCONDITIONS	media : <Gtype> Tryptone </Gtype> broth buffered to pH 7 supplemented with <Supp> 22 mM glucose </Supp> 	22 mM glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	glucose 120 mM	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002775
SRR5416993	GSE97406	GSM2564001	GPL16085		WT rep 1	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8. PGCGROWTHCONDITIONS	Cells were grown in TB7 supplemented with <Supp> 22 mM glucose </Supp> until OD600 ~ 1.8 . 	22 mM glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	glucose 120 mM	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002775
SRR5416993	GSE97406	GSM2564001	GPL16085		WT rep 1	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	media: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose PGCGROWTHCONDITIONS	media : <Gtype> Tryptone </Gtype> broth buffered to pH 7 supplemented with <Supp> 22 mM glucose </Supp> 	22 mM glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	glucose 120 mM	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002775
SRR5416994	GSE97406	GSM2564002	GPL16085		WT rep 2	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8. PGCGROWTHCONDITIONS	Cells were grown in TB7 supplemented with <Supp> 22 mM glucose </Supp> until OD600 ~ 1.8 . 	22 mM glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	glucose 120 mM	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002775
SRR5416994	GSE97406	GSM2564002	GPL16085		WT rep 2	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	media: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose PGCGROWTHCONDITIONS	media : <Gtype> Tryptone </Gtype> broth buffered to pH 7 supplemented with <Supp> 22 mM glucose </Supp> 	22 mM glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	glucose 120 mM	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002775
SRR5416995	GSE97406	GSM2564003	GPL16085		WT rep 3	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8. PGCGROWTHCONDITIONS	Cells were grown in TB7 supplemented with <Supp> 22 mM glucose </Supp> until OD600 ~ 1.8 . 	22 mM glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	glucose 120 mM	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002775
SRR5416995	GSE97406	GSM2564003	GPL16085		WT rep 3	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	media: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose PGCGROWTHCONDITIONS	media : <Gtype> Tryptone </Gtype> broth buffered to pH 7 supplemented with <Supp> 22 mM glucose </Supp> 	22 mM glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	glucose 120 mM	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002775
SRR5416996	GSE97406	GSM2564004	GPL16085		K100Q rep 1	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8. PGCGROWTHCONDITIONS	Cells were grown in TB7 supplemented with <Supp> 22 mM glucose </Supp> until OD600 ~ 1.8 . 	22 mM glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	glucose 120 mM	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002775
SRR5416996	GSE97406	GSM2564004	GPL16085		K100Q rep 1	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	media: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose PGCGROWTHCONDITIONS	media : <Gtype> Tryptone </Gtype> broth buffered to pH 7 supplemented with <Supp> 22 mM glucose </Supp> 	22 mM glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	glucose 120 mM	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002775
SRR5416997	GSE97406	GSM2564005	GPL16085		K100Q rep 2	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8. PGCGROWTHCONDITIONS	Cells were grown in TB7 supplemented with <Supp> 22 mM glucose </Supp> until OD600 ~ 1.8 . 	22 mM glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	glucose 120 mM	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002775
SRR5416997	GSE97406	GSM2564005	GPL16085		K100Q rep 2	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	media: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose PGCGROWTHCONDITIONS	media : <Gtype> Tryptone </Gtype> broth buffered to pH 7 supplemented with <Supp> 22 mM glucose </Supp> 	22 mM glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	glucose 120 mM	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002775
SRR5416998	GSE97406	GSM2564006	GPL16085		K100Q rep 3	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8. PGCGROWTHCONDITIONS	Cells were grown in TB7 supplemented with <Supp> 22 mM glucose </Supp> until OD600 ~ 1.8 . 	22 mM glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	glucose 120 mM	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002775
SRR5416998	GSE97406	GSM2564006	GPL16085		K100Q rep 3	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	media: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose PGCGROWTHCONDITIONS	media : <Gtype> Tryptone </Gtype> broth buffered to pH 7 supplemented with <Supp> 22 mM glucose </Supp> 	22 mM glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	glucose 120 mM	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002775
SRR5416999	GSE97406	GSM2564007	GPL16085		K100R rep 1	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8. PGCGROWTHCONDITIONS	Cells were grown in TB7 supplemented with <Supp> 22 mM glucose </Supp> until OD600 ~ 1.8 . 	22 mM glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	glucose 120 mM	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002775
SRR5416999	GSE97406	GSM2564007	GPL16085		K100R rep 1	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	media: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose PGCGROWTHCONDITIONS	media : <Gtype> Tryptone </Gtype> broth buffered to pH 7 supplemented with <Supp> 22 mM glucose </Supp> 	22 mM glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	glucose 120 mM	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002775
SRR5417000	GSE97406	GSM2564008	GPL16085		K100R rep 2	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8. PGCGROWTHCONDITIONS	Cells were grown in TB7 supplemented with <Supp> 22 mM glucose </Supp> until OD600 ~ 1.8 . 	22 mM glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	glucose 120 mM	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002775
SRR5417000	GSE97406	GSM2564008	GPL16085		K100R rep 2	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	media: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose PGCGROWTHCONDITIONS	media : <Gtype> Tryptone </Gtype> broth buffered to pH 7 supplemented with <Supp> 22 mM glucose </Supp> 	22 mM glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	glucose 120 mM	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002775
SRR5417001	GSE97406	GSM2564009	GPL16085		K100R rep 3	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	growth_protocol	Cells were grown in TB7 supplemented with 22 mM glucose until OD600 ~1.8. PGCGROWTHCONDITIONS	Cells were grown in TB7 supplemented with <Supp> 22 mM glucose </Supp> until OD600 ~ 1.8 . 	22 mM glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	glucose 120 mM	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002775
SRR5417001	GSE97406	GSM2564009	GPL16085		K100R rep 3	Role of CRP K100 positive charge on Escherichia coli global transcriptome	GPL16085: Illumina MiSeq (Escherichia coli)	characteristics	media: Tryptone broth buffered to pH 7 supplemented with 22 mM glucose PGCGROWTHCONDITIONS	media : <Gtype> Tryptone </Gtype> broth buffered to pH 7 supplemented with <Supp> 22 mM glucose </Supp> 	22 mM glucose	Medium supplement	http://pakal.ccg.unam.mx/cmendezc/automatic-extraction-growth-conditions/tree/master/extraction-geo/download/srr_htregulondb/GSE97406/GSE97406.soft.gz	glucose 120 mM	89	89	/home/egaytan/automatic-extraction-growth-conditions/mapping_MCO/input/gc_ontology_terms_v2.txt	MCO000002775