Reporte GEO

-#Fecha:2019-03-28 18:00:11.720155		
+#Fecha:2019-04-04 19:53:05.727162		
 #Archivo	Metadato	Contenido
 #Archivo	Metadato	Contenido
 GSE88979_family.xml	!Sample_characteristics_ch1	genotype: <Gtype>ompR-8myc</Gtype>
 GSE88979_family.xml	!Sample_characteristics_ch1	genotype: <Gtype>ompR-8myc</Gtype>
 GSE88979_family.xml	!Sample_characteristics_ch1	chip antibody: <Anti>anti-myc</Anti> (Santa Cruz Biotech, sc-28207)
 GSE88979_family.xml	!Sample_characteristics_ch1	chip antibody: <Anti>anti-myc</Anti> (Santa Cruz Biotech, sc-28207)
@@ -8647,30 +8647,6 @@ GSE93506_family.xml	!Sample_title	<Name>PurR_Adenine_1</Name>
 GSE93506_family.xml	!Sample_title	<Name>PurR_Adenine_2</Name>
 GSE93506_family.xml	!Sample_title	<Name>PurR_Adenine_2</Name>
 GSE93506_family.xml	!Sample_title	<Name>PurR_glucose_1</Name>
 GSE93506_family.xml	!Sample_title	<Name>PurR_glucose_1</Name>
 GSE93506_family.xml	!Sample_title	<Name>PurR_glucose_2</Name>
 GSE93506_family.xml	!Sample_title	<Name>PurR_glucose_2</Name>
-borrame.txt	!Sample_characteristics_ch1	growth condition: <Supp>Adenine</Supp>
-borrame.txt	!Sample_characteristics_ch1	genotype: <Gtype>PurR-8myc</Gtype>
-borrame.txt	!Sample_characteristics_ch1	chip antibody: <Anti>9E10 Myc tag</Anti> antibody
-borrame.txt	!Sample_characteristics_ch1	growth condition: <Supp>Adenine</Supp>
-borrame.txt	!Sample_characteristics_ch1	genotype: <Gtype>PurR-8myc</Gtype>
-borrame.txt	!Sample_characteristics_ch1	chip antibody: <Anti>9E10 Myc tag</Anti> antibody
-borrame.txt	!Sample_characteristics_ch1	growth condition: <Supp>glucose</Supp>
-borrame.txt	!Sample_characteristics_ch1	genotype: <Gtype>PurR-8myc</Gtype>
-borrame.txt	!Sample_characteristics_ch1	chip antibody: <Anti>9E10 Myc tag</Anti> antibody
-borrame.txt	!Sample_characteristics_ch1	growth condition: <Supp>glucose</Supp>
-borrame.txt	!Sample_characteristics_ch1	genotype: <Gtype>PurR-8myc</Gtype>
-borrame.txt	!Sample_characteristics_ch1	chip antibody: <Anti>9E10 Myc tag</Anti> antibody
-borrame.txt	!Sample_growth_protocol_ch1	E. coli strains harboring PurR-8myc were grown in minimal M9 medium supplemented with glucose (2 g/L) then inoculated into 100mL of fresh <Med>M9 minimal medium</Med> supplemented with <Supp>100ug/L adenine</Supp>.
-borrame.txt	!Sample_growth_protocol_ch1	E. coli strains harboring PurR-8myc were grown in minimal M9 medium supplemented with glucose (2 g/L) then inoculated into 100mL of fresh <Med>M9 minimal medium</Med> supplemented with <Supp>100ug/L adenine</Supp>.
-borrame.txt	!Sample_growth_protocol_ch1	E. coli strains harboring PurR-8myc were grown in minimal M9 medium supplemented with glucose (2 g/L) then inoculated into 100mL of fresh <Med>M9 minimal medium</Med>.
-borrame.txt	!Sample_growth_protocol_ch1	E. coli strains harboring PurR-8myc were grown in minimal M9 medium supplemented with glucose (2 g/L) then inoculated into 100mL of fresh <Med>M9 minimal medium</Med>.
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_title	<Name>PurR_Adenine_1</Name>
-borrame.txt	!Sample_title	<Name>PurR_Adenine_2</Name>
-borrame.txt	!Sample_title	<Name>PurR_glucose_1</Name>
-borrame.txt	!Sample_title	<Name>PurR_glucose_2</Name>
 GSE26589_family.xml	!Sample_characteristics_ch1	genotype/variation: <Gtype>WT</Gtype>
 GSE26589_family.xml	!Sample_characteristics_ch1	genotype/variation: <Gtype>WT</Gtype>
 GSE26589_family.xml	!Sample_characteristics_ch1	agent: <Supp>Fe</Supp>
 GSE26589_family.xml	!Sample_characteristics_ch1	agent: <Supp>Fe</Supp>
 GSE26589_family.xml	!Sample_characteristics_ch1	genotype/variation: <Gtype>WT</Gtype>
 GSE26589_family.xml	!Sample_characteristics_ch1	genotype/variation: <Gtype>WT</Gtype>
@@ -9759,70 +9735,6 @@ GSE93506_family.xml	!Sample_title	<Name>Δfur with Fe 1 (RNA-seq)</Name>
 GSE93506_family.xml	!Sample_title	<Name>Δfur with Fe 2 (RNA-seq)</Name>
 GSE93506_family.xml	!Sample_title	<Name>Δfur with Fe 2 (RNA-seq)</Name>
 GSE93506_family.xml	!Sample_title	<Name>Δfur with DPD 1 (RNA-seq)</Name>
 GSE93506_family.xml	!Sample_title	<Name>Δfur with DPD 1 (RNA-seq)</Name>
 GSE93506_family.xml	!Sample_title	<Name>Δfur with DPD 2 (RNA-seq)</Name>
 GSE93506_family.xml	!Sample_title	<Name>Δfur with DPD 2 (RNA-seq)</Name>
-borrame.txt	!Sample_characteristics_ch1	genotype/variation: <Gtype>WT</Gtype>
-borrame.txt	!Sample_characteristics_ch1	agent: <Supp>Fe</Supp>
-borrame.txt	!Sample_characteristics_ch1	genotype/variation: <Gtype>WT</Gtype>
-borrame.txt	!Sample_characteristics_ch1	agent: <Supp>Fe</Supp>
-borrame.txt	!Sample_characteristics_ch1	genotype/variation: <Gtype>WT</Gtype>
-borrame.txt	!Sample_characteristics_ch1	agent: <Supp>DPD</Supp>
-borrame.txt	!Sample_characteristics_ch1	genotype/variation: <Gtype>WT</Gtype>
-borrame.txt	!Sample_characteristics_ch1	agent: <Supp>DPD</Supp>
-borrame.txt	!Sample_characteristics_ch1	genotype/variation: <Gtype>Δfur</Gtype>
-borrame.txt	!Sample_characteristics_ch1	agent: <Supp>Fe</Supp>
-borrame.txt	!Sample_characteristics_ch1	genotype/variation: <Gtype>Δfur</Gtype>
-borrame.txt	!Sample_characteristics_ch1	agent: <Supp>Fe</Supp>
-borrame.txt	!Sample_characteristics_ch1	genotype/variation: <Gtype>Δfur</Gtype>
-borrame.txt	!Sample_characteristics_ch1	agent: <Supp>DPD</Supp>
-borrame.txt	!Sample_characteristics_ch1	genotype/variation: <Gtype>Δfur</Gtype>
-borrame.txt	!Sample_characteristics_ch1	agent: <Supp>DPD</Supp>
-borrame.txt	!Sample_data_processing	Sequenced reads were mapped onto <Gversion>NC_000913</Gversion> reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S
-borrame.txt	!Sample_data_processing	Genome_build: <Gversion>ASM584v2</Gversion>
-borrame.txt	!Sample_data_processing	Sequenced reads were mapped onto <Gversion>NC_000913</Gversion> reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S
-borrame.txt	!Sample_data_processing	Genome_build: <Gversion>ASM584v2</Gversion>
-borrame.txt	!Sample_data_processing	Sequenced reads were mapped onto <Gversion>NC_000913</Gversion> reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S
-borrame.txt	!Sample_data_processing	Genome_build: <Gversion>ASM584v2</Gversion>
-borrame.txt	!Sample_data_processing	Sequenced reads were mapped onto <Gversion>NC_000913</Gversion> reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S
-borrame.txt	!Sample_data_processing	Genome_build: <Gversion>ASM584v2</Gversion>
-borrame.txt	!Sample_data_processing	Sequenced reads were mapped onto <Gversion>NC_000913</Gversion> reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S
-borrame.txt	!Sample_data_processing	Genome_build: <Gversion>ASM584v2</Gversion>
-borrame.txt	!Sample_data_processing	Sequenced reads were mapped onto <Gversion>NC_000913</Gversion> reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S
-borrame.txt	!Sample_data_processing	Genome_build: <Gversion>ASM584v2</Gversion>
-borrame.txt	!Sample_data_processing	Sequenced reads were mapped onto <Gversion>NC_000913</Gversion> reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S
-borrame.txt	!Sample_data_processing	Genome_build: <Gversion>ASM584v2</Gversion>
-borrame.txt	!Sample_data_processing	Sequenced reads were mapped onto <Gversion>NC_000913</Gversion> reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S
-borrame.txt	!Sample_data_processing	Genome_build: <Gversion>ASM584v2</Gversion>
-borrame.txt	!Sample_growth_protocol_ch1	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, <Supp>0.1mM of FeCl2</Supp> 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.
-borrame.txt	!Sample_growth_protocol_ch1	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, <Supp>0.1mM of FeCl2</Supp> 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.
-borrame.txt	!Sample_growth_protocol_ch1	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, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, <Supp>0.2mM of DPD</Supp> were added at early-log phase and continued to culture for additional 2h.
-borrame.txt	!Sample_growth_protocol_ch1	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, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, <Supp>0.2mM of DPD</Supp> were added at early-log phase and continued to culture for additional 2h.
-borrame.txt	!Sample_growth_protocol_ch1	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, <Supp>0.1mM of FeCl2</Supp> 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.
-borrame.txt	!Sample_growth_protocol_ch1	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, <Supp>0.1mM of FeCl2</Supp> 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.
-borrame.txt	!Sample_growth_protocol_ch1	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, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, <Supp>0.2mM of DPD</Supp> were added at early-log phase and continued to culture for additional 2h.
-borrame.txt	!Sample_growth_protocol_ch1	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, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, <Supp>0.2mM of DPD</Supp> were added at early-log phase and continued to culture for additional 2h.
-borrame.txt	!Sample_library_strategy	<Technique>RNA-Seq</Technique>
-borrame.txt	!Sample_library_strategy	<Technique>RNA-Seq</Technique>
-borrame.txt	!Sample_library_strategy	<Technique>RNA-Seq</Technique>
-borrame.txt	!Sample_library_strategy	<Technique>RNA-Seq</Technique>
-borrame.txt	!Sample_library_strategy	<Technique>RNA-Seq</Technique>
-borrame.txt	!Sample_library_strategy	<Technique>RNA-Seq</Technique>
-borrame.txt	!Sample_library_strategy	<Technique>RNA-Seq</Technique>
-borrame.txt	!Sample_library_strategy	<Technique>RNA-Seq</Technique>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_title	<Name>WT with Fe 1 (RNA-seq)</Name>
-borrame.txt	!Sample_title	<Name>WT with Fe 2 (RNA-seq)</Name>
-borrame.txt	!Sample_title	<Name>WT with DPD 1 (RNA-seq)</Name>
-borrame.txt	!Sample_title	<Name>WT with DPD 2 (RNA-seq)</Name>
-borrame.txt	!Sample_title	<Name>Δfur with Fe 1 (RNA-seq)</Name>
-borrame.txt	!Sample_title	<Name>Δfur with Fe 2 (RNA-seq)</Name>
-borrame.txt	!Sample_title	<Name>Δfur with DPD 1 (RNA-seq)</Name>
-borrame.txt	!Sample_title	<Name>Δfur with DPD 2 (RNA-seq)</Name>
 GSE26589_family.xml	!Sample_characteristics_ch1	genotype/variation: <Gtype>lacking the transcription factor Fur</Gtype>
 GSE26589_family.xml	!Sample_characteristics_ch1	genotype/variation: <Gtype>lacking the transcription factor Fur</Gtype>
 GSE26589_family.xml	!Sample_characteristics_ch1	ip antibody: <Anti>affinity purified anti-Fur antibody</Anti>
 GSE26589_family.xml	!Sample_characteristics_ch1	ip antibody: <Anti>affinity purified anti-Fur antibody</Anti>
 GSE26589_family.xml	!Sample_extract_protocol_ch1	Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final) was added to the <Phase>mid-log</Phase> cultures followed by formaldehyde to 1% final and anaerobic sparging was continued for 10 min. Cold 2.5 M glycine was added to 100mM and the mixture was incubated at 4 °C with anaerobic sparging for 30 minutes to stop the crosslinking. Cells were spun at 3500 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C. Cell pellets (from initial 250 mL of culture) were thawed and resuspended in 250 μL of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 1% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng/ml), micrococcal nuclease (50 units), 20 μM CaCl2,1.2 mM KCl, 0.3 mM NaCl, 6 mM sucrose, and 10 μM DTT. EDTA was added to 10 mM to stop the micrococcal nuclease and the samples were spun down to remove cell debris. The lysate was then precleared through incubation with a 50/50 slurry of sepharose protein A beads in IP buffer for 2-3 hours at 4 °C. The beads were removed by centrifugation and antibody was added to the pre-cleared lysate for an overnight incubation. The next day, 30 μl of a 50/50 slurry of sepharose protein A beads in IP buffer was added to the lysate to capture antibody-protein-DNA complex for one hour at 4 °C. Beads were then washed once with 1 ml of LiCl wash buffer (100 mM Tris pH 8, 250 mM LiCl, 2% TritonX-100), twice with 600 mM NaCl wash buffer (100 mM Tris pH 8, 600 mM NaCl, 2% TritonX-100), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100), and twice with TE. Elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) was added after the final wash step, and beads were incubated at 65 °C for 30 minutes to remove the crosslinked protein-DNA complexes from the beads. After centrifugation to remove the beads, the samples were incubated overnight at 65 °C to reverse the protein-DNA formaldehyde crosslinks. DNA was purified using Qiagen’s PCR Purification kit and eluted to a final volume of 50 μl with EB.
 GSE26589_family.xml	!Sample_extract_protocol_ch1	Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final) was added to the <Phase>mid-log</Phase> cultures followed by formaldehyde to 1% final and anaerobic sparging was continued for 10 min. Cold 2.5 M glycine was added to 100mM and the mixture was incubated at 4 °C with anaerobic sparging for 30 minutes to stop the crosslinking. Cells were spun at 3500 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C. Cell pellets (from initial 250 mL of culture) were thawed and resuspended in 250 μL of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 1% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng/ml), micrococcal nuclease (50 units), 20 μM CaCl2,1.2 mM KCl, 0.3 mM NaCl, 6 mM sucrose, and 10 μM DTT. EDTA was added to 10 mM to stop the micrococcal nuclease and the samples were spun down to remove cell debris. The lysate was then precleared through incubation with a 50/50 slurry of sepharose protein A beads in IP buffer for 2-3 hours at 4 °C. The beads were removed by centrifugation and antibody was added to the pre-cleared lysate for an overnight incubation. The next day, 30 μl of a 50/50 slurry of sepharose protein A beads in IP buffer was added to the lysate to capture antibody-protein-DNA complex for one hour at 4 °C. Beads were then washed once with 1 ml of LiCl wash buffer (100 mM Tris pH 8, 250 mM LiCl, 2% TritonX-100), twice with 600 mM NaCl wash buffer (100 mM Tris pH 8, 600 mM NaCl, 2% TritonX-100), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100), and twice with TE. Elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) was added after the final wash step, and beads were incubated at 65 °C for 30 minutes to remove the crosslinked protein-DNA complexes from the beads. After centrifugation to remove the beads, the samples were incubated overnight at 65 °C to reverse the protein-DNA formaldehyde crosslinks. DNA was purified using Qiagen’s PCR Purification kit and eluted to a final volume of 50 μl with EB.
@@ -9931,12 +9843,6 @@ GSE93506_family.xml	!Sample_extract_protocol_ch1	Sodium phosphate (1/100 vol. of
 GSE93506_family.xml	!Sample_growth_protocol_ch1	Cultures grown in <Med>MOPS minimal glucose media</Med> containing <Supp>10 µM FeSO4</Supp>
 GSE93506_family.xml	!Sample_growth_protocol_ch1	Cultures grown in <Med>MOPS minimal glucose media</Med> containing <Supp>10 µM FeSO4</Supp>
 GSE93506_family.xml	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
 GSE93506_family.xml	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
 GSE93506_family.xml	!Sample_title	<Name>∆fur Anaerobic [IP vs nput]</Name>
 GSE93506_family.xml	!Sample_title	<Name>∆fur Anaerobic [IP vs nput]</Name>
-borrame.txt	!Sample_characteristics_ch1	genotype/variation: <Gtype>lacking the transcription factor Fur</Gtype>
-borrame.txt	!Sample_characteristics_ch1	ip antibody: <Anti>affinity purified anti-Fur antibody</Anti>
-borrame.txt	!Sample_extract_protocol_ch1	Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final) was added to the <Phase>mid-log</Phase> cultures followed by formaldehyde to 1% final and anaerobic sparging was continued for 10 min. Cold 2.5 M glycine was added to 100mM and the mixture was incubated at 4 °C with anaerobic sparging for 30 minutes to stop the crosslinking. Cells were spun at 3500 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C. Cell pellets (from initial 250 mL of culture) were thawed and resuspended in 250 μL of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 1% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng/ml), micrococcal nuclease (50 units), 20 μM CaCl2,1.2 mM KCl, 0.3 mM NaCl, 6 mM sucrose, and 10 μM DTT. EDTA was added to 10 mM to stop the micrococcal nuclease and the samples were spun down to remove cell debris. The lysate was then precleared through incubation with a 50/50 slurry of sepharose protein A beads in IP buffer for 2-3 hours at 4 °C. The beads were removed by centrifugation and antibody was added to the pre-cleared lysate for an overnight incubation. The next day, 30 μl of a 50/50 slurry of sepharose protein A beads in IP buffer was added to the lysate to capture antibody-protein-DNA complex for one hour at 4 °C. Beads were then washed once with 1 ml of LiCl wash buffer (100 mM Tris pH 8, 250 mM LiCl, 2% TritonX-100), twice with 600 mM NaCl wash buffer (100 mM Tris pH 8, 600 mM NaCl, 2% TritonX-100), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100), and twice with TE. Elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) was added after the final wash step, and beads were incubated at 65 °C for 30 minutes to remove the crosslinked protein-DNA complexes from the beads. After centrifugation to remove the beads, the samples were incubated overnight at 65 °C to reverse the protein-DNA formaldehyde crosslinks. DNA was purified using Qiagen’s PCR Purification kit and eluted to a final volume of 50 μl with EB.
-borrame.txt	!Sample_growth_protocol_ch1	Cultures grown in <Med>MOPS minimal glucose media</Med> containing <Supp>10 µM FeSO4</Supp>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_title	<Name>∆fur Anaerobic [IP vs nput]</Name>
 GSE26054_family.xml	!Sample_characteristics_ch1	genotype: <Gtype>ArgR-8myc</Gtype>
 GSE26054_family.xml	!Sample_characteristics_ch1	genotype: <Gtype>ArgR-8myc</Gtype>
 GSE26054_family.xml	!Sample_characteristics_ch1	antibody: <Anti>9E10 Myc tag</Anti> antibody
 GSE26054_family.xml	!Sample_characteristics_ch1	antibody: <Anti>9E10 Myc tag</Anti> antibody
 GSE26054_family.xml	!Sample_characteristics_ch1	treatment: <Med>glucose (2 g/L) minimal W2 medium</Med> supplemented with <Supp>1g/L arginine</Supp>.
 GSE26054_family.xml	!Sample_characteristics_ch1	treatment: <Med>glucose (2 g/L) minimal W2 medium</Med> supplemented with <Supp>1g/L arginine</Supp>.
@@ -11077,66 +10983,6 @@ GSE93506_family.xml	!Sample_title	<Name>Lrp_NH4Cl_2</Name>
 GSE93506_family.xml	!Sample_title	<Name>Lrp_NH4Cl_3</Name>
 GSE93506_family.xml	!Sample_title	<Name>Lrp_NH4Cl_3</Name>
 GSE93506_family.xml	!Sample_title	<Name>TrpR_Trp</Name>
 GSE93506_family.xml	!Sample_title	<Name>TrpR_Trp</Name>
 GSE93506_family.xml	!Sample_title	<Name>TrpR_glucose</Name>
 GSE93506_family.xml	!Sample_title	<Name>TrpR_glucose</Name>
-borrame.txt	!Sample_characteristics_ch1	genotype: <Gtype>ArgR-8myc</Gtype>
-borrame.txt	!Sample_characteristics_ch1	antibody: <Anti>9E10 Myc tag</Anti> antibody
-borrame.txt	!Sample_characteristics_ch1	treatment: <Med>glucose (2 g/L) minimal W2 medium</Med> supplemented with <Supp>1g/L arginine</Supp>.
-borrame.txt	!Sample_characteristics_ch1	genotype: <Gtype>ArgR-8myc</Gtype>
-borrame.txt	!Sample_characteristics_ch1	antibody: <Anti>9E10 Myc tag</Anti> antibody
-borrame.txt	!Sample_characteristics_ch1	treatment: <Med>glucose (2 g/L) minimal W2 medium</Med> supplemented with <Supp>1g/L arginine</Supp>.
-borrame.txt	!Sample_characteristics_ch1	genotype: <Gtype>ArgR-8myc</Gtype>
-borrame.txt	!Sample_characteristics_ch1	antibody: <Anti>9E10 Myc tag</Anti> antibody
-borrame.txt	!Sample_characteristics_ch1	treatment: <Med>glucose (2 g/L) minimal W2 medium</Med> supplemented with <Supp>2g/L glutamine</Supp>.
-borrame.txt	!Sample_characteristics_ch1	genotype: <Gtype>ArgR-8myc</Gtype>
-borrame.txt	!Sample_characteristics_ch1	antibody: <Anti>9E10 Myc tag</Anti> antibody
-borrame.txt	!Sample_characteristics_ch1	treatment: <Med>glucose (2 g/L) minimal W2 medium</Med> supplemented with <Supp>2g/L glutamine</Supp>.
-borrame.txt	!Sample_characteristics_ch1	genotype: <Gtype>Lrp-8myc</Gtype>
-borrame.txt	!Sample_characteristics_ch1	antibody: <Anti>9E10 Myc tag</Anti> antibody
-borrame.txt	!Sample_characteristics_ch1	treatment: <Med>glucose (2 g/L) minimal M9 medium</Med> supplemented with <Supp>10 mM leucine</Supp>.
-borrame.txt	!Sample_characteristics_ch1	genotype: <Gtype>Lrp-8myc</Gtype>
-borrame.txt	!Sample_characteristics_ch1	antibody: <Anti>9E10 Myc tag</Anti> antibody
-borrame.txt	!Sample_characteristics_ch1	treatment: <Med>glucose (2 g/L) minimal M9 medium</Med> supplemented with <Supp>10 mM leucine</Supp>.
-borrame.txt	!Sample_characteristics_ch1	genotype: <Gtype>Lrp-8myc</Gtype>
-borrame.txt	!Sample_characteristics_ch1	antibody: <Anti>9E10 Myc tag</Anti> antibody
-borrame.txt	!Sample_characteristics_ch1	treatment: <Med>glucose (2 g/L) minimal M9 medium</Med> supplemented with <Supp>10 mM leucine</Supp>.
-borrame.txt	!Sample_characteristics_ch1	genotype: <Gtype>Lrp-8myc</Gtype>
-borrame.txt	!Sample_characteristics_ch1	antibody: <Anti>9E10 Myc tag</Anti> antibody
-borrame.txt	!Sample_characteristics_ch1	treatment: <Med>glucose (2 g/L) minimal M9 medium</Med> supplemented without <Supp>10 mM leucine</Supp>.
-borrame.txt	!Sample_characteristics_ch1	genotype: <Gtype>Lrp-8myc</Gtype>
-borrame.txt	!Sample_characteristics_ch1	antibody: <Anti>9E10 Myc tag</Anti> antibody
-borrame.txt	!Sample_characteristics_ch1	treatment: <Med>glucose (2 g/L) minimal M9 medium</Med> supplemented without <Supp>10 mM leucine</Supp>.
-borrame.txt	!Sample_characteristics_ch1	genotype: <Gtype>Lrp-8myc</Gtype>
-borrame.txt	!Sample_characteristics_ch1	antibody: <Anti>9E10 Myc tag</Anti> antibody
-borrame.txt	!Sample_characteristics_ch1	treatment: <Med>glucose (2 g/L) minimal M9 medium</Med> supplemented without <Supp>10 mM leucine</Supp>.
-borrame.txt	!Sample_characteristics_ch1	genotype: <Gtype>TrpR-8myc</Gtype>
-borrame.txt	!Sample_characteristics_ch1	antibody: <Anti>9E10 Myc tag</Anti> antibody
-borrame.txt	!Sample_characteristics_ch1	treatment: <Med>glucose (2 g/L) minimal M9 medium</Med> supplemented with <Supp>20 mg/L tryptophan</Supp>.
-borrame.txt	!Sample_characteristics_ch1	genotype: <Gtype>TrpR-8myc</Gtype>
-borrame.txt	!Sample_characteristics_ch1	antibody: <Anti>9E10 Myc tag</Anti> antibody
-borrame.txt	!Sample_characteristics_ch1	treatment: <Med>glucose (2 g/L) minimal M9 medium</Med> supplemented without <Supp>20 mg/L tryptophan</Supp>.
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Name>Escherichia coli str. K-12 substr. MG1655</Name>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_title	<Name>ArgR_Arginine_1</Name>
-borrame.txt	!Sample_title	<Name>ArgR_Arginine_2</Name>
-borrame.txt	!Sample_title	<Name>ArgR_NH4Cl_1</Name>
-borrame.txt	!Sample_title	<Name>ArgR_NH4Cl_2</Name>
-borrame.txt	!Sample_title	<Name>Lrp_Leu_1</Name>
-borrame.txt	!Sample_title	<Name>Lrp_Leu_2</Name>
-borrame.txt	!Sample_title	<Name>Lrp_Leu_3</Name>
-borrame.txt	!Sample_title	<Name>Lrp_NH4Cl_1</Name>
-borrame.txt	!Sample_title	<Name>Lrp_NH4Cl_2</Name>
-borrame.txt	!Sample_title	<Name>Lrp_NH4Cl_3</Name>
-borrame.txt	!Sample_title	<Name>TrpR_Trp</Name>
-borrame.txt	!Sample_title	<Name>TrpR_glucose</Name>
 GSE26054_family.xml	!Sample_characteristics_ch1	genotype/variation: <Gtype>wild type</Gtype>
 GSE26054_family.xml	!Sample_characteristics_ch1	genotype/variation: <Gtype>wild type</Gtype>
 GSE26054_family.xml	!Sample_characteristics_ch1	culture condition: <Air>Aerobic</Air> cultures
 GSE26054_family.xml	!Sample_characteristics_ch1	culture condition: <Air>Aerobic</Air> cultures
 GSE26054_family.xml	!Sample_characteristics_ch1	genotype/variation: <Gtype>wild type</Gtype>
 GSE26054_family.xml	!Sample_characteristics_ch1	genotype/variation: <Gtype>wild type</Gtype>
@@ -12537,76 +12383,6 @@ GSE93506_family.xml	!Sample_title	<Name>∆fur ∆ryhB Anaerobic A</Name>
 GSE93506_family.xml	!Sample_title	<Name>∆fur ∆ryhB Anaerobic B</Name>
 GSE93506_family.xml	!Sample_title	<Name>∆fur ∆ryhB Anaerobic B</Name>
 GSE93506_family.xml	!Sample_title	<Name>∆ryhB Aerobic</Name>
 GSE93506_family.xml	!Sample_title	<Name>∆ryhB Aerobic</Name>
 GSE93506_family.xml	!Sample_title	<Name>∆ryhB Anaerobic</Name>
 GSE93506_family.xml	!Sample_title	<Name>∆ryhB Anaerobic</Name>
-borrame.txt	!Sample_characteristics_ch1	genotype/variation: <Gtype>wild type</Gtype>
-borrame.txt	!Sample_characteristics_ch1	culture condition: <Air>Aerobic</Air> cultures
-borrame.txt	!Sample_characteristics_ch1	genotype/variation: <Gtype>wild type</Gtype>
-borrame.txt	!Sample_characteristics_ch1	culture condition: <Air>Aerobic</Air> cultures
-borrame.txt	!Sample_characteristics_ch1	genotype/variation: <Gtype>wild type</Gtype>
-borrame.txt	!Sample_characteristics_ch1	culture condition: <Air>Anaerobic</Air> cultures
-borrame.txt	!Sample_characteristics_ch1	genotype/variation: <Gtype>wild type</Gtype>
-borrame.txt	!Sample_characteristics_ch1	culture condition: <Air>Anaerobic</Air> cultures
-borrame.txt	!Sample_characteristics_ch1	genotype/variation: <Gtype>lacking the transcription factor Fur</Gtype>
-borrame.txt	!Sample_characteristics_ch1	culture condition: <Air>Aerobic</Air> cultures
-borrame.txt	!Sample_characteristics_ch1	genotype/variation: <Gtype>lacking the transcription factor Fur</Gtype>
-borrame.txt	!Sample_characteristics_ch1	culture condition: <Air>Aerobic</Air> cultures
-borrame.txt	!Sample_characteristics_ch1	genotype/variation: <Gtype>lacking the transcription factor Fur</Gtype>
-borrame.txt	!Sample_characteristics_ch1	culture condition: <Air>Anaerobic</Air> cultures
-borrame.txt	!Sample_characteristics_ch1	genotype/variation: <Gtype>lacking the transcription factor Fur</Gtype>
-borrame.txt	!Sample_characteristics_ch1	culture condition: <Air>Anaerobic</Air> cultures
-borrame.txt	!Sample_characteristics_ch1	genotype/variation: <Gtype>lacking the transcription factor Fur and the small RNA RyhB</Gtype>
-borrame.txt	!Sample_characteristics_ch1	culture condition: <Air>Aerobic</Air> cultures
-borrame.txt	!Sample_characteristics_ch1	genotype/variation: <Gtype>lacking the transcription factor Fur and the small RNA RyhB</Gtype>
-borrame.txt	!Sample_characteristics_ch1	culture condition: <Air>Aerobic</Air> cultures
-borrame.txt	!Sample_characteristics_ch1	genotype/variation: <Gtype>lacking the transcription factor Fur and the small RNA RyhB</Gtype>
-borrame.txt	!Sample_characteristics_ch1	culture condition: <Air>Anaerobic</Air> cultures
-borrame.txt	!Sample_characteristics_ch1	genotype/variation: <Gtype>lacking the transcription factor Fur and the small RNA RyhB</Gtype>
-borrame.txt	!Sample_characteristics_ch1	culture condition: <Air>Anaerobic</Air> cultures
-borrame.txt	!Sample_characteristics_ch1	genotype/variation: <Gtype>lacking the small RNA RyhB</Gtype>
-borrame.txt	!Sample_characteristics_ch1	culture condition: <Air>Aerobic</Air> cultures
-borrame.txt	!Sample_characteristics_ch1	genotype/variation: <Gtype>lacking the small RNA RyhB</Gtype>
-borrame.txt	!Sample_characteristics_ch1	culture condition: <Air>Anaerobic</Air> cultures
-borrame.txt	!Sample_growth_protocol_ch1	Cells were grown <Air>aerobically (70% N2, 25% O2, and 5% CO2)</Air> or anaerobically (95% N2 and 5% CO2) until <Phase>mid-log phase</Phase> (<OD>OD600 of ~0.3-0.35</OD>) in <Med>MOPS minimal glucose media</Med> containing <Supp>10 µM FeSO4</Supp>.
-borrame.txt	!Sample_growth_protocol_ch1	Cells were grown <Air>aerobically (70% N2, 25% O2, and 5% CO2)</Air> or anaerobically (95% N2 and 5% CO2) until <Phase>mid-log phase</Phase> (<OD>OD600 of ~0.3-0.35</OD>) in <Med>MOPS minimal glucose media</Med> containing <Supp>10 µM FeSO4</Supp>.
-borrame.txt	!Sample_growth_protocol_ch1	Cells were grown aerobically (70% N2, 25% O2, and 5% CO2) or <Air>anaerobically (95% N2 and 5% CO2)</Air> until <Phase>mid-log phase</Phase> (<OD>OD600 of ~0.3-0.35</OD>) in <Med>MOPS minimal glucose media</Med> containing <Supp>10 µM FeSO4</Supp>.
-borrame.txt	!Sample_growth_protocol_ch1	Cells were grown aerobically (70% N2, 25% O2, and 5% CO2) or <Air>anaerobically (95% N2 and 5% CO2)</Air> until <Phase>mid-log phase</Phase> (<OD>OD600 of ~0.3-0.35</OD>) in <Med>MOPS minimal glucose media</Med> containing <Supp>10 µM FeSO4</Supp>.
-borrame.txt	!Sample_growth_protocol_ch1	Cells were grown <Air>aerobically (70% N2, 25% O2, and 5% CO2)</Air> or anaerobically (95% N2 and 5% CO2) until <Phase>mid-log phase</Phase> (<OD>OD600 of ~0.3-0.35</OD>) in <Med>MOPS minimal glucose media</Med> containing <Supp>10 µM FeSO4</Supp>.
-borrame.txt	!Sample_growth_protocol_ch1	Cells were grown <Air>aerobically (70% N2, 25% O2, and 5% CO2)</Air> or anaerobically (95% N2 and 5% CO2) until <Phase>mid-log phase</Phase> (<OD>OD600 of ~0.3-0.35</OD>) in <Med>MOPS minimal glucose media</Med> containing <Supp>10 µM FeSO4</Supp>.
-borrame.txt	!Sample_growth_protocol_ch1	Cells were grown aerobically (70% N2, 25% O2, and 5% CO2) or <Air>anaerobically (95% N2 and 5% CO2)</Air> until <Phase>mid-log phase</Phase> (<OD>OD600 of ~0.3-0.35</OD>) in <Med>MOPS minimal glucose media</Med> containing <Supp>10 µM FeSO4</Supp>.
-borrame.txt	!Sample_growth_protocol_ch1	Cells were grown aerobically (70% N2, 25% O2, and 5% CO2) or <Air>anaerobically (95% N2 and 5% CO2)</Air> until <Phase>mid-log phase</Phase> (<OD>OD600 of ~0.3-0.35</OD>) in <Med>MOPS minimal glucose media</Med> containing <Supp>10 µM FeSO4</Supp>.
-borrame.txt	!Sample_growth_protocol_ch1	Cells were grown <Air>aerobically (70% N2, 25% O2, and 5% CO2)</Air> or anaerobically (95% N2 and 5% CO2) until <Phase>mid-log phase</Phase> (<OD>OD600 of ~0.3-0.35</OD>) in <Med>MOPS minimal glucose media</Med> containing <Supp>10 µM FeSO4</Supp>.
-borrame.txt	!Sample_growth_protocol_ch1	Cells were grown <Air>aerobically (70% N2, 25% O2, and 5% CO2)</Air> or anaerobically (95% N2 and 5% CO2) until <Phase>mid-log phase</Phase> (<OD>OD600 of ~0.3-0.35</OD>) in <Med>MOPS minimal glucose media</Med> containing <Supp>10 µM FeSO4</Supp>.
-borrame.txt	!Sample_growth_protocol_ch1	Cells were grown aerobically (70% N2, 25% O2, and 5% CO2) or <Air>anaerobically (95% N2 and 5% CO2)</Air> until <Phase>mid-log phase</Phase> (<OD>OD600 of ~0.3-0.35</OD>) in <Med>MOPS minimal glucose media</Med> containing <Supp>10 µM FeSO4</Supp>.
-borrame.txt	!Sample_growth_protocol_ch1	Cells were grown aerobically (70% N2, 25% O2, and 5% CO2) or <Air>anaerobically (95% N2 and 5% CO2)</Air> until <Phase>mid-log phase</Phase> (<OD>OD600 of ~0.3-0.35</OD>) in <Med>MOPS minimal glucose media</Med> containing <Supp>10 µM FeSO4</Supp>.
-borrame.txt	!Sample_growth_protocol_ch1	Cells were grown <Air>aerobically (70% N2, 25% O2, and 5% CO2)</Air> or anaerobically (95% N2 and 5% CO2) until <Phase>mid-log phase</Phase> (<OD>OD600 of ~0.3-0.35</OD>) in <Med>MOPS minimal glucose media</Med> containing <Supp>10 µM FeSO4</Supp>.
-borrame.txt	!Sample_growth_protocol_ch1	Cells were grown aerobically (70% N2, 25% O2, and 5% CO2) or <Air>anaerobically (95% N2 and 5% CO2)</Air> until <Phase>mid-log phase</Phase> (<OD>OD600 of ~0.3-0.35</OD>) in <Med>MOPS minimal glucose media</Med> containing <Supp>10 µM FeSO4</Supp>.
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_title	<Name>Wild-type Aerobic A</Name>
-borrame.txt	!Sample_title	<Name>Wild-type Aerobic B</Name>
-borrame.txt	!Sample_title	<Name>Wild-type Anaerobic A</Name>
-borrame.txt	!Sample_title	<Name>Wild-type Anaerobic B</Name>
-borrame.txt	!Sample_title	<Name>∆fur Aerobic A</Name>
-borrame.txt	!Sample_title	<Name>∆fur Aerobic B</Name>
-borrame.txt	!Sample_title	<Name>∆fur Anaerobic A</Name>
-borrame.txt	!Sample_title	<Name>∆fur Anaerobic B</Name>
-borrame.txt	!Sample_title	<Name>∆fur ∆ryhB Aerobic A</Name>
-borrame.txt	!Sample_title	<Name>∆fur ∆ryhB Aerobic B</Name>
-borrame.txt	!Sample_title	<Name>∆fur ∆ryhB Anaerobic A</Name>
-borrame.txt	!Sample_title	<Name>∆fur ∆ryhB Anaerobic B</Name>
-borrame.txt	!Sample_title	<Name>∆ryhB Aerobic</Name>
-borrame.txt	!Sample_title	<Name>∆ryhB Anaerobic</Name>
 GSE11230_family.xml	!Sample_characteristics_ch1	Escherichia coli, expressing <Gtype>NsrR</Gtype> with a C-terminal <Gtype>Flag-tag</Gtype>, was grown <Air>anaerobically</Air> in <Med>L broth</Med> supplemented with <Supp>glucose</Supp>.  
 GSE11230_family.xml	!Sample_characteristics_ch1	Escherichia coli, expressing <Gtype>NsrR</Gtype> with a C-terminal <Gtype>Flag-tag</Gtype>, was grown <Air>anaerobically</Air> in <Med>L broth</Med> supplemented with <Supp>glucose</Supp>.  
 GSE11230_family.xml	!Sample_characteristics_ch1	Escherichia coli, expressing <Gtype>NsrR</Gtype> with a C-terminal <Gtype>Flag-tag</Gtype>, was grown <Air>anaerobically</Air> in <Med>L broth</Med> supplemented with <Supp>glucose</Supp> and <Supp>nitrate</Supp>. 
 GSE11230_family.xml	!Sample_characteristics_ch1	Escherichia coli, expressing <Gtype>NsrR</Gtype> with a C-terminal <Gtype>Flag-tag</Gtype>, was grown <Air>anaerobically</Air> in <Med>L broth</Med> supplemented with <Supp>glucose</Supp> and <Supp>nitrate</Supp>. 
 GSE11230_family.xml	!Sample_characteristics_ch1	Escherichia coli, expressing <Gtype>NsrR</Gtype> with a C-terminal <Gtype>Flag-tag</Gtype>, was grown <Air>anaerobically</Air> in <Med>L broth</Med> supplemented with <Supp>glucose</Supp> and <Supp>nitrate</Supp>. 
 GSE11230_family.xml	!Sample_characteristics_ch1	Escherichia coli, expressing <Gtype>NsrR</Gtype> with a C-terminal <Gtype>Flag-tag</Gtype>, was grown <Air>anaerobically</Air> in <Med>L broth</Med> supplemented with <Supp>glucose</Supp> and <Supp>nitrate</Supp>. 
@@ -12922,21 +12698,6 @@ GSE93506_family.xml	!Sample_organism_ch2	<Orgn>Escherichia coli</Orgn>
 GSE93506_family.xml	!Sample_title	<Name>NsrR_Flagtag_rep2</Name>
 GSE93506_family.xml	!Sample_title	<Name>NsrR_Flagtag_rep2</Name>
 GSE93506_family.xml	!Sample_title	<Name>NsrR_Flagtag_rep3</Name>
 GSE93506_family.xml	!Sample_title	<Name>NsrR_Flagtag_rep3</Name>
 GSE93506_family.xml	!Sample_title	<Name>NsrR_Flagtag_rep1</Name>
 GSE93506_family.xml	!Sample_title	<Name>NsrR_Flagtag_rep1</Name>
-borrame.txt	!Sample_characteristics_ch1	Escherichia coli, expressing <Gtype>NsrR</Gtype> with a C-terminal <Gtype>Flag-tag</Gtype>, was grown <Air>anaerobically</Air> in <Med>L broth</Med> supplemented with <Supp>glucose</Supp>.  
-borrame.txt	!Sample_characteristics_ch1	Escherichia coli, expressing <Gtype>NsrR</Gtype> with a C-terminal <Gtype>Flag-tag</Gtype>, was grown <Air>anaerobically</Air> in <Med>L broth</Med> supplemented with <Supp>glucose</Supp> and <Supp>nitrate</Supp>. 
-borrame.txt	!Sample_characteristics_ch1	Escherichia coli, expressing <Gtype>NsrR</Gtype> with a C-terminal <Gtype>Flag-tag</Gtype>, was grown <Air>anaerobically</Air> in <Med>L broth</Med> supplemented with <Supp>glucose</Supp> and <Supp>nitrate</Supp>. 
-borrame.txt	!Sample_characteristics_ch2	Escherichia coli, expressing <Gtype>NsrR</Gtype> with a C-terminal <Gtype>Flag-tag</Gtype>, was grown <Air>anaerobically</Air> in <Med>L broth</Med> supplemented with <Supp>glucose</Supp> and <Supp>nitrate</Supp>.  
-borrame.txt	!Sample_characteristics_ch2	Escherichia coli, expressing <Gtype>NsrR</Gtype> with a C-terminal <Gtype>Flag-tag</Gtype>, was grown <Air>anaerobically</Air> in <Med>L broth</Med> supplemented with <Supp>glucose</Supp>.
-borrame.txt	!Sample_characteristics_ch2	Escherichia coli, expressing <Gtype>NsrR</Gtype> with a C-terminal <Gtype>Flag-tag</Gtype>, was grown <Air>anaerobically</Air> in <Med>L broth</Med> supplemented with <Supp>glucose</Supp>. 
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli</Orgn>
-borrame.txt	!Sample_organism_ch2	<Orgn>Escherichia coli</Orgn>
-borrame.txt	!Sample_organism_ch2	<Orgn>Escherichia coli</Orgn>
-borrame.txt	!Sample_organism_ch2	<Orgn>Escherichia coli</Orgn>
-borrame.txt	!Sample_title	<Name>NsrR_Flagtag_rep2</Name>
-borrame.txt	!Sample_title	<Name>NsrR_Flagtag_rep3</Name>
-borrame.txt	!Sample_title	<Name>NsrR_Flagtag_rep1</Name>
 GSE11230_family.xml	!Sample_characteristics_ch1	genotype/variation: <Gtype>fur-8myc</Gtype>
 GSE11230_family.xml	!Sample_characteristics_ch1	genotype/variation: <Gtype>fur-8myc</Gtype>
 GSE11230_family.xml	!Sample_characteristics_ch1	chip antibody: <Anti>anti-myc</Anti> (Santa Cruz Biotech, sc-28207)
 GSE11230_family.xml	!Sample_characteristics_ch1	chip antibody: <Anti>anti-myc</Anti> (Santa Cruz Biotech, sc-28207)
 GSE11230_family.xml	!Sample_characteristics_ch1	agent: <Supp>Fe</Supp>
 GSE11230_family.xml	!Sample_characteristics_ch1	agent: <Supp>Fe</Supp>
@@ -15697,126 +15458,6 @@ GSE93506_family.xml	!Sample_title	<Name>RpoB with DPD 1 (ChIP-exo)</Name>
 GSE93506_family.xml	!Sample_title	<Name>RpoB with DPD 2 (ChIP-exo)</Name>
 GSE93506_family.xml	!Sample_title	<Name>RpoB with DPD 2 (ChIP-exo)</Name>
 GSE93506_family.xml	!Sample_title	<Name>RpoB with DPD and rifampicin 1 (ChIP-exo)</Name>
 GSE93506_family.xml	!Sample_title	<Name>RpoB with DPD and rifampicin 1 (ChIP-exo)</Name>
 GSE93506_family.xml	!Sample_title	<Name>RpoB with DPD and rifampicin 2 (ChIP-exo)</Name>
 GSE93506_family.xml	!Sample_title	<Name>RpoB with DPD and rifampicin 2 (ChIP-exo)</Name>
-borrame.txt	!Sample_characteristics_ch1	genotype/variation: <Gtype>fur-8myc</Gtype>
-borrame.txt	!Sample_characteristics_ch1	chip antibody: <Anti>anti-myc</Anti> (Santa Cruz Biotech, sc-28207)
-borrame.txt	!Sample_characteristics_ch1	agent: <Supp>Fe</Supp>
-borrame.txt	!Sample_characteristics_ch1	genotype/variation: <Gtype>fur-8myc</Gtype>
-borrame.txt	!Sample_characteristics_ch1	chip antibody: <Anti>anti-myc</Anti> (Santa Cruz Biotech, sc-28207)
-borrame.txt	!Sample_characteristics_ch1	agent: <Supp>Fe</Supp>
-borrame.txt	!Sample_characteristics_ch1	genotype/variation: <Gtype>fur-8myc</Gtype>
-borrame.txt	!Sample_characteristics_ch1	chip antibody: <Anti>anti-myc</Anti> (Santa Cruz Biotech, sc-28207)
-borrame.txt	!Sample_characteristics_ch1	agent: <Supp>DPD</Supp>
-borrame.txt	!Sample_characteristics_ch1	genotype/variation: <Gtype>fur-8myc</Gtype>
-borrame.txt	!Sample_characteristics_ch1	chip antibody: <Anti>anti-myc</Anti> (Santa Cruz Biotech, sc-28207)
-borrame.txt	!Sample_characteristics_ch1	agent: <Supp>DPD</Supp>
-borrame.txt	!Sample_characteristics_ch1	genotype/variation: <Gtype>WT</Gtype>
-borrame.txt	!Sample_characteristics_ch1	chip antibody: <Anti>anti-RpoB</Anti> (Neoclone, WP002)
-borrame.txt	!Sample_characteristics_ch1	agent: <Supp>Fe</Supp>
-borrame.txt	!Sample_characteristics_ch1	genotype/variation: <Gtype>WT</Gtype>
-borrame.txt	!Sample_characteristics_ch1	chip antibody: <Anti>anti-RpoB</Anti> (Neoclone, WP002)
-borrame.txt	!Sample_characteristics_ch1	agent: <Supp>Fe</Supp>
-borrame.txt	!Sample_characteristics_ch1	genotype/variation: <Gtype>WT</Gtype>
-borrame.txt	!Sample_characteristics_ch1	chip antibody: <Anti>anti-RpoB</Anti> (Neoclone, WP002)
-borrame.txt	!Sample_characteristics_ch1	agent: <Supp>Fe and rifampicin</Supp>
-borrame.txt	!Sample_characteristics_ch1	genotype/variation: <Gtype>WT</Gtype>
-borrame.txt	!Sample_characteristics_ch1	chip antibody: <Anti>anti-RpoB</Anti> (Neoclone, WP002)
-borrame.txt	!Sample_characteristics_ch1	agent: <Supp>Fe and rifampicin</Supp>
-borrame.txt	!Sample_characteristics_ch1	genotype/variation: <Gtype>WT</Gtype>
-borrame.txt	!Sample_characteristics_ch1	chip antibody: <Anti>anti-RpoB</Anti> (Neoclone, WP002)
-borrame.txt	!Sample_characteristics_ch1	agent: <Supp>DPD</Supp>
-borrame.txt	!Sample_characteristics_ch1	genotype/variation: <Gtype>WT</Gtype>
-borrame.txt	!Sample_characteristics_ch1	chip antibody: <Anti>anti-RpoB</Anti> (Neoclone, WP002)
-borrame.txt	!Sample_characteristics_ch1	agent: <Supp>DPD</Supp>
-borrame.txt	!Sample_characteristics_ch1	genotype/variation: <Gtype>WT</Gtype>
-borrame.txt	!Sample_characteristics_ch1	chip antibody: <Anti>anti-RpoB</Anti> (Neoclone, WP002)
-borrame.txt	!Sample_characteristics_ch1	agent: <Supp>DPD and rifampicin</Supp>
-borrame.txt	!Sample_characteristics_ch1	genotype/variation: <Gtype>WT</Gtype>
-borrame.txt	!Sample_characteristics_ch1	chip antibody: <Anti>anti-RpoB</Anti> (Neoclone, WP002)
-borrame.txt	!Sample_characteristics_ch1	agent: <Supp>DPD and rifampicin</Supp>
-borrame.txt	!Sample_data_processing	library strategy: <Technique>ChIP-exo</Technique>
-borrame.txt	!Sample_data_processing	ChIP-exo reads were aligned to the <Gversion>NC_000913 </Gversion>genome reference sequence using using bowtie v1.0.0 with parameters  -S
-borrame.txt	!Sample_data_processing	Genome_build: <Gversion>ASM584v2</Gversion>
-borrame.txt	!Sample_data_processing	library strategy: <Technique>ChIP-exo</Technique>
-borrame.txt	!Sample_data_processing	ChIP-exo reads were aligned to the <Gversion>NC_000913</Gversion> genome reference sequence using using bowtie v1.0.0 with parameters  -S
-borrame.txt	!Sample_data_processing	Genome_build: <Gversion>ASM584v2</Gversion>
-borrame.txt	!Sample_data_processing	library strategy: <Technique>ChIP-exo</Technique>
-borrame.txt	!Sample_data_processing	ChIP-exo reads were aligned to the <Gversion>NC_000913</Gversion> genome reference sequence using using bowtie v1.0.0 with parameters  -S
-borrame.txt	!Sample_data_processing	Genome_build: <Gversion>ASM584v2</Gversion>
-borrame.txt	!Sample_data_processing	library strategy: <Technique>ChIP-exo</Technique>
-borrame.txt	!Sample_data_processing	ChIP-exo reads were aligned to the <Gversion>NC_000913</Gversion> genome reference sequence using using bowtie v1.0.0 with parameters  -S
-borrame.txt	!Sample_data_processing	Genome_build: <Gversion>ASM584v2</Gversion>
-borrame.txt	!Sample_data_processing	library strategy: <Technique>ChIP-exo</Technique>
-borrame.txt	!Sample_data_processing	ChIP-exo reads were aligned to the <Gversion>NC_000913</Gversion> genome reference sequence using using bowtie v1.0.0 with parameters  -S
-borrame.txt	!Sample_data_processing	Genome_build: <Gversion>ASM584v2</Gversion>
-borrame.txt	!Sample_data_processing	library strategy: <Technique>ChIP-exo</Technique>
-borrame.txt	!Sample_data_processing	ChIP-exo reads were aligned to the <Gversion>NC_000913</Gversion> genome reference sequence using using bowtie v1.0.0 with parameters  -S
-borrame.txt	!Sample_data_processing	Genome_build: <Gversion>ASM584v2</Gversion>
-borrame.txt	!Sample_data_processing	library strategy: <Technique>ChIP-exo</Technique>
-borrame.txt	!Sample_data_processing	ChIP-exo reads were aligned to the <Gversion>NC_000913</Gversion> genome reference sequence using using bowtie v1.0.0 with parameters  -S
-borrame.txt	!Sample_data_processing	Genome_build: <Gversion>ASM584v2</Gversion>
-borrame.txt	!Sample_data_processing	library strategy: <Technique>ChIP-exo</Technique>
-borrame.txt	!Sample_data_processing	ChIP-exo reads were aligned to the <Gversion>NC_000913</Gversion> genome reference sequence using using bowtie v1.0.0 with parameters  -S
-borrame.txt	!Sample_data_processing	Genome_build: <Gversion>ASM584v2</Gversion>
-borrame.txt	!Sample_data_processing	library strategy: <Technique>ChIP-exo</Technique>
-borrame.txt	!Sample_data_processing	ChIP-exo reads were aligned to the <Gversion>NC_000913</Gversion> genome reference sequence using using bowtie v1.0.0 with parameters  -S
-borrame.txt	!Sample_data_processing	Genome_build: <Gversion>ASM584v2</Gversion>
-borrame.txt	!Sample_data_processing	library strategy: <Technique>ChIP-exo</Technique>
-borrame.txt	!Sample_data_processing	ChIP-exo reads were aligned to the <Gversion>NC_000913</Gversion> genome reference sequence using using bowtie v1.0.0 with parameters  -S
-borrame.txt	!Sample_data_processing	Genome_build: <Gversion>ASM584v2</Gversion>
-borrame.txt	!Sample_data_processing	library strategy: <Technique>ChIP-exo</Technique>
-borrame.txt	!Sample_data_processing	ChIP-exo reads were aligned to the <Gversion>NC_000913</Gversion> genome reference sequence using using bowtie v1.0.0 with parameters  -S
-borrame.txt	!Sample_data_processing	Genome_build: <Gversion>ASM584v2</Gversion>
-borrame.txt	!Sample_data_processing	library strategy: <Technique>ChIP-exo</Technique>
-borrame.txt	!Sample_data_processing	ChIP-exo reads were aligned to the <Gversion>NC_000913</Gversion> genome reference sequence using using bowtie v1.0.0 with parameters  -S
-borrame.txt	!Sample_data_processing	Genome_build: <Gversion>ASM584v2</Gversion>
-borrame.txt	!Sample_growth_protocol_ch1	E. coli K-12 MG1655 WT and Fur-8-myc tagged strains 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, <Supp>0.1mM of FeCl2</Supp> 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 <Supp>2h</Supp>. For the rifampicin-treated cultures, the rifampicin dissolved in methanol was added to a final concentration of 150 mg/mL at mid-log phase and stirred for 20 min.
-borrame.txt	!Sample_growth_protocol_ch1	E. coli K-12 MG1655 WT and Fur-8-myc tagged strains 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, <Supp>0.1mM of FeCl2</Supp> 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 <Supp>2h</Supp>. For the rifampicin-treated cultures, the rifampicin dissolved in methanol was added to a final concentration of 150 mg/mL at mid-log phase and stirred for 20 min.
-borrame.txt	!Sample_growth_protocol_ch1	E. coli K-12 MG1655 WT and Fur-8-myc tagged strains 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, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, <Supp>0.2mM of DPD</Supp> were added at early-log phase and continued to culture for additional <Supp>2h</Supp>. For the rifampicin-treated cultures, the rifampicin dissolved in methanol was added to a final concentration of 150 mg/mL at mid-log phase and stirred for 20 min.
-borrame.txt	!Sample_growth_protocol_ch1	E. coli K-12 MG1655 WT and Fur-8-myc tagged strains 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, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, <Supp>0.2mM of DPD</Supp> were added at early-log phase and continued to culture for additional <Supp>2h</Supp>. For the rifampicin-treated cultures, the rifampicin dissolved in methanol was added to a final concentration of 150 mg/mL at mid-log phase and stirred for 20 min.
-borrame.txt	!Sample_growth_protocol_ch1	E. coli K-12 MG1655 WT and Fur-8-myc tagged strains 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, <Supp>0.1mM of FeCl2</Supp> 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 <Supp>2h</Supp>. For the rifampicin-treated cultures, the rifampicin dissolved in methanol was added to a final concentration of 150 mg/mL at mid-log phase and stirred for 20 min.
-borrame.txt	!Sample_growth_protocol_ch1	E. coli K-12 MG1655 WT and Fur-8-myc tagged strains 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, <Supp>0.1mM of FeCl2</Supp> 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 <Supp>2h</Supp>. For the rifampicin-treated cultures, the rifampicin dissolved in methanol was added to a final concentration of 150 mg/mL at mid-log phase and stirred for 20 min.
-borrame.txt	!Sample_growth_protocol_ch1	E. coli K-12 MG1655 WT and Fur-8-myc tagged strains 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, <Supp>0.1mM of FeCl2</Supp> 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 <Supp>2h</Supp>. For the rifampicin-treated cultures, the <Supp>rifampicin dissolved in methanol</Supp> was added to a final concentration of <Supp>150 mg/mL</Supp> at mid-log phase and stirred for <Supp>20 min</Supp>.
-borrame.txt	!Sample_growth_protocol_ch1	E. coli K-12 MG1655 WT and Fur-8-myc tagged strains 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, <Supp>0.1mM of FeCl2</Supp> 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 <Supp>2h</Supp>. For the rifampicin-treated cultures, the <Supp>rifampicin dissolved in methanol</Supp> was added to a final concentration of <Supp>150 mg/mL</Supp> at mid-log phase and stirred for <Supp>20 min</Supp>.
-borrame.txt	!Sample_growth_protocol_ch1	E. coli K-12 MG1655 WT and Fur-8-myc tagged strains 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, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, <Supp>0.2mM of DPD</Supp> were added at early-log phase and continued to culture for additional <Supp>2h</Supp>. For the rifampicin-treated cultures, the rifampicin dissolved in methanol was added to a final concentration of 150 mg/mL at mid-log phase and stirred for 20 min.
-borrame.txt	!Sample_growth_protocol_ch1	E. coli K-12 MG1655 WT and Fur-8-myc tagged strains 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, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, <Supp>0.2mM of DPD</Supp> were added at early-log phase and continued to culture for additional <Supp>2h</Supp>. For the rifampicin-treated cultures, the rifampicin dissolved in methanol was added to a final concentration of 150 mg/mL at mid-log phase and stirred for 20 min.
-borrame.txt	!Sample_growth_protocol_ch1	E. coli K-12 MG1655 WT and Fur-8-myc tagged strains 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, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, <Supp>0.2mM of DPD</Supp> were added at early-log phase and continued to culture for additional <Supp>2h</Supp>. For the rifampicin-treated cultures, the <Supp>rifampicin dissolved in methanol</Supp> was added to a final concentration of <Supp>150 mg/mL</Supp> at mid-log phase and stirred for <Supp>20 min</Supp>.
-borrame.txt	!Sample_growth_protocol_ch1	E. coli K-12 MG1655 WT and Fur-8-myc tagged strains 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, 0.1mM of FeCl2 were treated from the beginning of culture, and for DPD treated cells, <Supp>0.2mM of DPD</Supp> were added at early-log phase and continued to culture for additional <Supp>2h</Supp>. For the rifampicin-treated cultures, the <Supp>rifampicin dissolved in methanol</Supp> was added to a final concentration of <Supp>150 mg/mL</Supp> at mid-log phase and stirred for <Supp>20 min</Supp>.
-borrame.txt	!Sample_library_strategy	<Technique>ChIP-Seq</Technique>
-borrame.txt	!Sample_library_strategy	<Gversion>ChIP-Seq</Gversion>
-borrame.txt	!Sample_library_strategy	<Technique>ChIP-Seq</Technique>
-borrame.txt	!Sample_library_strategy	<Gversion>ChIP-Seq</Gversion>
-borrame.txt	!Sample_library_strategy	<Technique>ChIP-Seq</Technique>
-borrame.txt	!Sample_library_strategy	<Technique>ChIP-Seq</Technique>
-borrame.txt	!Sample_library_strategy	<Technique>ChIP-Seq</Technique>
-borrame.txt	!Sample_library_strategy	<Technique>ChIP-Seq</Technique>
-borrame.txt	!Sample_library_strategy	<Technique>ChIP-Seq</Technique>
-borrame.txt	!Sample_library_strategy	<Technique>ChIP-Seq</Technique>
-borrame.txt	!Sample_library_strategy	<Technique>ChIP-Seq</Technique>
-borrame.txt	!Sample_library_strategy	<Technique>ChIP-Seq</Technique>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_title	<Name>Fur with Fe 1 (ChIP-exo)</Name>
-borrame.txt	!Sample_title	<Name>Fur with Fe 2 (ChIP-exo)</Name>
-borrame.txt	!Sample_title	<Name>Fur with DPD 1 (ChIP-exo)</Name>
-borrame.txt	!Sample_title	<Name>Fur with DPD 2 (ChIP-exo)</Name>
-borrame.txt	!Sample_title	<Name>RpoB with Fe 1 (ChIP-exo)</Name>
-borrame.txt	!Sample_title	<Name>RpoB with Fe 2 (ChIP-exo)</Name>
-borrame.txt	!Sample_title	<Name>RpoB with Fe and rifampicin 1 (ChIP-exo)</Name>
-borrame.txt	!Sample_title	<Name>RpoB with Fe and rifampicin 2 (ChIP-exo)</Name>
-borrame.txt	!Sample_title	<Name>RpoB with DPD 1 (ChIP-exo)</Name>
-borrame.txt	!Sample_title	<Name>RpoB with DPD 2 (ChIP-exo)</Name>
-borrame.txt	!Sample_title	<Name>RpoB with DPD and rifampicin 1 (ChIP-exo)</Name>
-borrame.txt	!Sample_title	<Name>RpoB with DPD and rifampicin 2 (ChIP-exo)</Name>
 GSE11230_family.xml	!Sample_characteristics_ch1	genotype: <Gtype>wildtype</Gtype>
 GSE11230_family.xml	!Sample_characteristics_ch1	genotype: <Gtype>wildtype</Gtype>
 GSE11230_family.xml	!Sample_characteristics_ch1	chip antibody: <Anti>RNA polymerase subunit β</Anti>
 GSE11230_family.xml	!Sample_characteristics_ch1	chip antibody: <Anti>RNA polymerase subunit β</Anti>
 GSE11230_family.xml	!Sample_characteristics_ch1	genotype: <Gtype>wildtype</Gtype>
 GSE11230_family.xml	!Sample_characteristics_ch1	genotype: <Gtype>wildtype</Gtype>
@@ -17689,84 +17330,6 @@ GSE93506_family.xml	!Sample_title	<Name>σ32 30°C rep1</Name>
 GSE93506_family.xml	!Sample_title	<Name>σ32 30°C rep2</Name>
 GSE93506_family.xml	!Sample_title	<Name>σ32 30°C rep2</Name>
 GSE93506_family.xml	!Sample_title	<Name>σ32 30°C short RNase</Name>
 GSE93506_family.xml	!Sample_title	<Name>σ32 30°C short RNase</Name>
 GSE93506_family.xml	!Sample_title	<Name>σ32 43°C short RNase</Name>
 GSE93506_family.xml	!Sample_title	<Name>σ32 43°C short RNase</Name>
-borrame.txt	!Sample_characteristics_ch1	genotype: <Gtype>wildtype</Gtype>
-borrame.txt	!Sample_characteristics_ch1	chip antibody: <Anti>RNA polymerase subunit β</Anti>
-borrame.txt	!Sample_characteristics_ch1	genotype: <Gtype>wildtype</Gtype>
-borrame.txt	!Sample_characteristics_ch1	chip antibody: <Anti>RNA polymerase subunit β</Anti>
-borrame.txt	!Sample_characteristics_ch1	genotype: <Gtype>wildtype</Gtype>
-borrame.txt	!Sample_characteristics_ch1	chip antibody: <Anti>SeqA</Anti>
-borrame.txt	!Sample_characteristics_ch1	genotype: <Gtype>wildtype</Gtype>
-borrame.txt	!Sample_characteristics_ch1	chip antibody: <Anti>SeqA</Anti>
-borrame.txt	!Sample_characteristics_ch1	genotype: <Gtype>wildtype</Gtype>
-borrame.txt	!Sample_characteristics_ch1	chip antibody: <Anti>SeqA</Anti>
-borrame.txt	!Sample_characteristics_ch1	genotype: <Gtype>wildtype</Gtype>
-borrame.txt	!Sample_characteristics_ch1	chip antibody: <Anti>SeqA</Anti>
-borrame.txt	!Sample_characteristics_ch1	genotype: <Gtype>ΔseqA</Gtype>
-borrame.txt	!Sample_characteristics_ch1	chip antibody: <Anti>SeqA</Anti>
-borrame.txt	!Sample_characteristics_ch1	genotype: <Gtype>ΔseqA</Gtype>
-borrame.txt	!Sample_characteristics_ch1	chip antibody: <Anti>SeqA</Anti>
-borrame.txt	!Sample_characteristics_ch1	genotype: <Gtype>wildtype</Gtype>
-borrame.txt	!Sample_characteristics_ch1	genotype: <Gtype>wildtype</Gtype>
-borrame.txt	!Sample_characteristics_ch1	chip antibody: <Anti>σ32</Anti>
-borrame.txt	!Sample_characteristics_ch1	genotype: <Gtype>wildtype</Gtype>
-borrame.txt	!Sample_characteristics_ch1	chip antibody: <Anti>σ32</Anti>
-borrame.txt	!Sample_characteristics_ch1	genotype: <Gtype>wildtype</Gtype>
-borrame.txt	!Sample_characteristics_ch1	chip antibody: <Anti>σ32</Anti>
-borrame.txt	!Sample_characteristics_ch1	genotype: <Gtype>wildtype</Gtype>
-borrame.txt	!Sample_characteristics_ch1	chip antibody: <Anti>σ32</Anti>
-borrame.txt	!Sample_characteristics_ch1	genotype: <Gtype>wildtype</Gtype>
-borrame.txt	!Sample_characteristics_ch1	chip antibody: <Anti>σ32</Anti>
-borrame.txt	!Sample_characteristics_ch1	genotype: <Gtype>wildtype</Gtype>
-borrame.txt	!Sample_characteristics_ch1	chip antibody: <Anti>σ32</Anti>
-borrame.txt	!Sample_growth_protocol_ch1	Cells were grown at <Temp>37 °C</Temp> to an <OD>OD600 of about 0.15</OD> in 50 ml <Med>LB</Med> (+ <Supp>0.2% glucose</Supp>) before crosslinking.
-borrame.txt	!Sample_growth_protocol_ch1	Cells were grown at <Temp>37 °C</Temp> to an <OD>OD600 of about 0.15</OD> in 50 ml <Med>LB</Med> (+ <Supp>0.2% glucose</Supp>) before crosslinking.
-borrame.txt	!Sample_growth_protocol_ch1	Cells were grown at <Temp>37 °C</Temp> to an <OD>OD600 of about 0.15</OD> in 50 ml <Med>LB</Med> (+ <Supp>0.2% glucose</Supp>) before crosslinking.
-borrame.txt	!Sample_growth_protocol_ch1	Cells were grown at <Temp>37 °C</Temp> to an <OD>OD600 of about 0.15</OD> in 50 ml <Med>LB</Med> (+ <Supp>0.2% glucose</Supp>) before crosslinking.
-borrame.txt	!Sample_growth_protocol_ch1	Cells were grown at <Temp>37 °C</Temp> to an <OD>OD600 of about 0.15</OD> in 50 ml <Med>LB</Med> (+ <Supp>0.2% glucose</Supp>) before crosslinking.
-borrame.txt	!Sample_growth_protocol_ch1	Cells were grown at <Temp>37 °C</Temp> to an <OD>OD600 of about 0.15</OD> in 50 ml <Med>LB</Med> (+ <Supp>0.2% glucose</Supp>) before crosslinking.
-borrame.txt	!Sample_growth_protocol_ch1	Cells were grown at <Temp>37 °C</Temp> to an <OD>OD600 of about 0.15</OD> in 50 ml <Med>LB</Med> (+ <Supp>0.2% glucose</Supp>) before crosslinking.
-borrame.txt	!Sample_growth_protocol_ch1	Cells were grown at <Temp>37 °C</Temp> to an <OD>OD600 of about 0.15</OD> in 50 ml <Med>LB</Med> (+ <Supp>0.2% glucose</Supp>) before crosslinking.
-borrame.txt	!Sample_growth_protocol_ch1	Cells were grown at <Temp>37 °C</Temp> to an <OD>OD600 of about 0.15</OD> in 100 ml <Med>LB</Med> (+ <Supp>0.2% glucose</Supp>).
-borrame.txt	!Sample_growth_protocol_ch1	Cells were grown in 65 ml LB medium at 30 °C to an <OD>OD600 of about 0.3</OD>. Subsequently 30 ml of culture were transformed to a pre warmed <Vess>flask</Vess> at <Temp>43 °C</Temp> and the remainder kept at <Temp>30 °C (see control sample)</Temp>.
-borrame.txt	!Sample_growth_protocol_ch1	Cells were grown in 65 ml LB medium at 30 °C to an <OD>OD600 of about 0.3</OD>. Subsequently 30 ml of culture were transformed to a pre warmed <Vess>flask</Vess> at <Temp>43 °C</Temp> and the remainder kept at <Temp>30 °C (see control sample)</Temp>.
-borrame.txt	!Sample_growth_protocol_ch1	Cells were grown in 65 ml LB medium at 30 °C to an <OD>OD600 of about 0.3</OD>. Subsequently 30 ml of culture were transformed to a pre warmed <Vess>flask</Vess> at <Temp>43 °C (see heat sample)</Temp> and the remainder kept at <Temp>30 °C</Temp>.
-borrame.txt	!Sample_growth_protocol_ch1	Cells were grown in 65 ml LB medium at 30 °C to an <OD>OD600 of about 0.3</OD>. Subsequently 30 ml of culture were transformed to a pre warmed <Vess>flask</Vess> at <Temp>43 °C (see heat sample)</Temp> and the remainder kept at <Temp>30 °C</Temp>.
-borrame.txt	!Sample_growth_protocol_ch1	Cells were grown in 65 ml LB medium at 30 °C to an <OD>OD600 of about 0.3</OD>. Subsequently 30 ml of culture were transformed to a pre warmed <Vess>flask</Vess> at <Temp>43 °C (see heat sample)</Temp> and the remainder kept at <Temp>30 °C</Temp>.
-borrame.txt	!Sample_growth_protocol_ch1	Cells were grown in 65 ml LB medium at 30 °C to an <OD>OD600 of about 0.3</OD>. Subsequently 30 ml of culture were transformed to a pre warmed <Vess>flask</Vess> at <Temp>43 °C</Temp> and the remainder kept at <Temp>30 °C (see control sample)</Temp>.
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
-borrame.txt	!Sample_source_name_ch1	<Name>σ32 ChIP DNA, heat</Name>
-borrame.txt	!Sample_source_name_ch1	<Name>σ32 ChIP DNA, heat</Name>
-borrame.txt	!Sample_source_name_ch1	<Name>σ32 ChIP DNA, control</Name>
-borrame.txt	!Sample_source_name_ch1	<Name>σ32 ChIP DNA, control</Name>
-borrame.txt	!Sample_title	<Name>RNAP old rep1</Name>
-borrame.txt	!Sample_title	<Name>RNAP old rep2</Name>
-borrame.txt	!Sample_title	<Name>SeqA old rep1</Name>
-borrame.txt	!Sample_title	<Name>SeqA old rep2</Name>
-borrame.txt	!Sample_title	<Name>SeqA new rep1</Name>
-borrame.txt	!Sample_title	<Name>SeqA new rep2</Name>
-borrame.txt	!Sample_title	<Name>SeqA old deltaSeqA</Name>
-borrame.txt	!Sample_title	<Name>SeqA new deltaSeqA</Name>
-borrame.txt	!Sample_title	<Name>Crosslink</Name>
-borrame.txt	!Sample_title	<Name>σ32 43°C rep1</Name>
-borrame.txt	!Sample_title	<Name>σ32 43°C rep2</Name>
-borrame.txt	!Sample_title	<Name>σ32 30°C rep1</Name>
-borrame.txt	!Sample_title	<Name>σ32 30°C rep2</Name>
-borrame.txt	!Sample_title	<Name>σ32 30°C short RNase</Name>
-borrame.txt	!Sample_title	<Name>σ32 43°C short RNase</Name>
 GSE11230_family.xml	!Sample_characteristics_ch1	genoype: <Gtype>Wild-Type</Gtype>
 GSE11230_family.xml	!Sample_characteristics_ch1	genoype: <Gtype>Wild-Type</Gtype>
 GSE11230_family.xml	!Sample_characteristics_ch1	growth condition: <Air>anaerobic</Air>
 GSE11230_family.xml	!Sample_characteristics_ch1	growth condition: <Air>anaerobic</Air>
 GSE11230_family.xml	!Sample_characteristics_ch1	strain: <Strain>K-12</Strain>
 GSE11230_family.xml	!Sample_characteristics_ch1	strain: <Strain>K-12</Strain>
@@ -18617,40 +18180,6 @@ GSE93506_family.xml	!Sample_title	<Name>Ecoli_wild-type_rep1_anaerobic</Name>
 GSE93506_family.xml	!Sample_title	<Name>Ecoli_wild-type_rep2_anaerobic</Name>
 GSE93506_family.xml	!Sample_title	<Name>Ecoli_wild-type_rep2_anaerobic</Name>
 GSE93506_family.xml	!Sample_title	<Name>Ecoli_dFNR_rep1_anaerobic</Name>
 GSE93506_family.xml	!Sample_title	<Name>Ecoli_dFNR_rep1_anaerobic</Name>
 GSE93506_family.xml	!Sample_title	<Name>Ecoli_dFNR_rep2_anaerobic</Name>
 GSE93506_family.xml	!Sample_title	<Name>Ecoli_dFNR_rep2_anaerobic</Name>
-borrame.txt	!Sample_characteristics_ch1	genoype: <Gtype>Wild-Type</Gtype>
-borrame.txt	!Sample_characteristics_ch1	growth condition: <Air>anaerobic</Air>
-borrame.txt	!Sample_characteristics_ch1	strain: <Strain>K-12</Strain>
-borrame.txt	!Sample_characteristics_ch1	genoype: <Gtype>Wild-Type</Gtype>
-borrame.txt	!Sample_characteristics_ch1	growth condition: <Air>anaerobic</Air>
-borrame.txt	!Sample_characteristics_ch1	strain: <Strain>K-12</Strain>
-borrame.txt	!Sample_characteristics_ch1	genoype: <Gtype>dFNR</Gtype>
-borrame.txt	!Sample_characteristics_ch1	growth condition: <Air>anaerobic</Air>
-borrame.txt	!Sample_characteristics_ch1	strain: <Strain>K-12</Strain>
-borrame.txt	!Sample_characteristics_ch1	genoype: <Gtype>dFNR</Gtype>
-borrame.txt	!Sample_characteristics_ch1	growth condition: <Air>anaerobic</Air>
-borrame.txt	!Sample_characteristics_ch1	strain: <Strain>K-12</Strain>
-borrame.txt	!Sample_data_processing	Resulting reads were aligned to the published E. coli K-12 MG1655 genome (<Gversion>U00096.2</Gversion>) using the software package SOAP (Li et al, 2009), allowing no more than two mismatches (Supplemental File).  Reads aligning to repeated elements in the genome (e.g. rRNA) were removed from analysis.  For reads that had no mapping locations for the first 36 bp, the 3-30 bp subsequences were used in the subsequent mapping to the reference genome.  Reads that had unique mapping locations and did not match annotated rRNA genes were used for further analysis.  For each gene, the tag density was estimated as the number of aligned sequencing tags divided by gene size in kb.  Per-gene tag density was normalized using quantile normalization (Supplemental Files).  The tag density data were analyzed for statistically significant differential expression using BaySeq (Hardcastle &amp; Kelly, 2010) with a FDR of 0.01, and genes were organized into operons using data from EcoCyc (Keseler et al, 2011).
-borrame.txt	!Sample_data_processing	Resulting reads were aligned to the published E. coli K-12 MG1655 genome (<Gversion>U00096.2</Gversion>) using the software package SOAP (Li et al, 2009), allowing no more than two mismatches (Supplemental File).  Reads aligning to repeated elements in the genome (e.g. rRNA) were removed from analysis.  For reads that had no mapping locations for the first 36 bp, the 3-30 bp subsequences were used in the subsequent mapping to the reference genome.  Reads that had unique mapping locations and did not match annotated rRNA genes were used for further analysis.  For each gene, the tag density was estimated as the number of aligned sequencing tags divided by gene size in kb.  Per-gene tag density was normalized using quantile normalization (Supplemental Files).  The tag density data were analyzed for statistically significant differential expression using BaySeq (Hardcastle &amp; Kelly, 2010) with a FDR of 0.01, and genes were organized into operons using data from EcoCyc (Keseler et al, 2011).
-borrame.txt	!Sample_data_processing	Resulting reads were aligned to the published E. coli K-12 MG1655 genome (<Gversion>U00096.2</Gversion>) using the software package SOAP (Li et al, 2009), allowing no more than two mismatches (Supplemental File).  Reads aligning to repeated elements in the genome (e.g. rRNA) were removed from analysis.  For reads that had no mapping locations for the first 36 bp, the 3-30 bp subsequences were used in the subsequent mapping to the reference genome.  Reads that had unique mapping locations and did not match annotated rRNA genes were used for further analysis.  For each gene, the tag density was estimated as the number of aligned sequencing tags divided by gene size in kb.  Per-gene tag density was normalized using quantile normalization (Supplemental Files).  The tag density data were analyzed for statistically significant differential expression using BaySeq (Hardcastle &amp; Kelly, 2010) with a FDR of 0.01, and genes were organized into operons using data from EcoCyc (Keseler et al, 2011).
-borrame.txt	!Sample_data_processing	Resulting reads were aligned to the published E. coli K-12 MG1655 genome (<Gversion>U00096.2</Gversion>) using the software package SOAP (Li et al, 2009), allowing no more than two mismatches (Supplemental File).  Reads aligning to repeated elements in the genome (e.g. rRNA) were removed from analysis.  For reads that had no mapping locations for the first 36 bp, the 3-30 bp subsequences were used in the subsequent mapping to the reference genome.  Reads that had unique mapping locations and did not match annotated rRNA genes were used for further analysis.  For each gene, the tag density was estimated as the number of aligned sequencing tags divided by gene size in kb.  Per-gene tag density was normalized using quantile normalization (Supplemental Files).  The tag density data were analyzed for statistically significant differential expression using BaySeq (Hardcastle &amp; Kelly, 2010) with a FDR of 0.01, and genes were organized into operons using data from EcoCyc (Keseler et al, 2011).
-borrame.txt	!Sample_growth_protocol_ch1	Escherichia coli MG1655 K-12 WT and ∆fnr were grown to <Phase>mid-log phase </Phase>(<OD>O.D.600nm 0.3</OD>) <Air>anerobically (95% N2, 5% CO2)</Air> at <Temp>37°C </Temp>in <Med>MOPS</Med> +<Supp>0.2% glucose</Supp> media (Ref).
-borrame.txt	!Sample_growth_protocol_ch1	Escherichia coli MG1655 K-12 WT and ∆fnr were grown to <Phase>mid-log phase </Phase>(<OD>O.D.600nm 0.3</OD>) <Air>anerobically (95% N2, 5% CO2)</Air> at <Temp>37°C </Temp>in <Med>MOPS</Med> +<Supp>0.2% glucose</Supp> media (Ref).
-borrame.txt	!Sample_growth_protocol_ch1	Escherichia coli MG1655 K-12 WT and ∆fnr were grown to <Phase>mid-log phase </Phase>(<OD>O.D.600nm 0.3</OD>) <Air>anerobically (95% N2, 5% CO2)</Air> at <Temp>37°C </Temp>in <Med>MOPS</Med> +<Supp>0.2% glucose</Supp> media (Ref).
-borrame.txt	!Sample_growth_protocol_ch1	Escherichia coli MG1655 K-12 WT and ∆fnr were grown to <Phase>mid-log phase </Phase>(<OD>O.D.600nm 0.3</OD>) <Air>anerobically (95% N2, 5% CO2)</Air> at <Temp>37°C </Temp>in <Med>MOPS</Med> +<Supp>0.2% glucose</Supp> media (Ref).
-borrame.txt	!Sample_library_strategy	<Technique>RNA-Seq</Technique>
-borrame.txt	!Sample_library_strategy	<Technique>RNA-Seq</Technique>
-borrame.txt	!Sample_library_strategy	<Technique>RNA-Seq</Technique>
-borrame.txt	!Sample_library_strategy	<Technique>RNA-Seq</Technique>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655star</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655star</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655star</Orgn>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli str. K-12 substr. MG1655star</Orgn>
-borrame.txt	!Sample_source_name_ch1	Escherichia coli MG1655 K-12 <Gtype>dFNR (PK4854)</Gtype>
-borrame.txt	!Sample_source_name_ch1	Escherichia coli MG1655 K-12 <Gtype>dFNR (PK4854)</Gtype>
-borrame.txt	!Sample_title	<Name>Ecoli_wild-type_rep1_anaerobic</Name>
-borrame.txt	!Sample_title	<Name>Ecoli_wild-type_rep2_anaerobic</Name>
-borrame.txt	!Sample_title	<Name>Ecoli_dFNR_rep1_anaerobic</Name>
-borrame.txt	!Sample_title	<Name>Ecoli_dFNR_rep2_anaerobic</Name>
 GSE11230_family.xml	!Sample_data_processing	All sequencing reads were mapped to E. coli MG1655 reference genome (<Gversion>NC_000913</Gversion>) using CLC Genomics Workbench5 with the length fraction of 0.9 and the similarity of 0.99.
 GSE11230_family.xml	!Sample_data_processing	All sequencing reads were mapped to E. coli MG1655 reference genome (<Gversion>NC_000913</Gversion>) using CLC Genomics Workbench5 with the length fraction of 0.9 and the similarity of 0.99.
 GSE11230_family.xml	!Sample_data_processing	All sequencing reads were mapped to E. coli MG1655 reference genome (<Gversion>NC_000913</Gversion>) using CLC Genomics Workbench5 with the length fraction of 0.9 and the similarity of 0.99.
 GSE11230_family.xml	!Sample_data_processing	All sequencing reads were mapped to E. coli MG1655 reference genome (<Gversion>NC_000913</Gversion>) using CLC Genomics Workbench5 with the length fraction of 0.9 and the similarity of 0.99.
 GSE11230_family.xml	!Sample_library_strategy	<Technique>ChIP-Seq</Technique>
 GSE11230_family.xml	!Sample_library_strategy	<Technique>ChIP-Seq</Technique>
@@ -18859,11 +18388,3 @@ GSE93506_family.xml	!Sample_organism_ch1	<Orgn>Escherichia coli</Orgn> str. <Str
 GSE93506_family.xml	!Sample_organism_ch1	<Orgn>Escherichia coli</Orgn> str. <Strain>K-12</Strain> substr. <Substrain>MG1655</Substrain>
 GSE93506_family.xml	!Sample_organism_ch1	<Orgn>Escherichia coli</Orgn> str. <Strain>K-12</Strain> substr. <Substrain>MG1655</Substrain>
 GSE93506_family.xml	!Sample_treatment_protocol_ch1	The cultured cells were inoculated with 1:100 dilution into 50 mL of the fresh <Med>M9 medium</Med> containing <Supp>2 g/L glucose</Supp> in either the <Supp>presence or absence of 1 g/L arginine</Supp> and continued to culture at <Temp>37°C</Temp> until reaching an appropriate cell density (<OD>OD600 ≈ 0.5</OD>).
 GSE93506_family.xml	!Sample_treatment_protocol_ch1	The cultured cells were inoculated with 1:100 dilution into 50 mL of the fresh <Med>M9 medium</Med> containing <Supp>2 g/L glucose</Supp> in either the <Supp>presence or absence of 1 g/L arginine</Supp> and continued to culture at <Temp>37°C</Temp> until reaching an appropriate cell density (<OD>OD600 ≈ 0.5</OD>).
 GSE93506_family.xml	!Sample_treatment_protocol_ch1	The cultured cells were inoculated with 1:100 dilution into 50 mL of the fresh M9 medium containing 2 g/L glucose in either the presence or <Supp>absence of 1 g/L arginine</Supp> and continued to culture at 37°C until reaching an appropriate cell density (OD600 ≈ 0.5).
 GSE93506_family.xml	!Sample_treatment_protocol_ch1	The cultured cells were inoculated with 1:100 dilution into 50 mL of the fresh M9 medium containing 2 g/L glucose in either the presence or <Supp>absence of 1 g/L arginine</Supp> and continued to culture at 37°C until reaching an appropriate cell density (OD600 ≈ 0.5).
-borrame.txt	!Sample_data_processing	All sequencing reads were mapped to E. coli MG1655 reference genome (<Gversion>NC_000913</Gversion>) using CLC Genomics Workbench5 with the length fraction of 0.9 and the similarity of 0.99.
-borrame.txt	!Sample_data_processing	All sequencing reads were mapped to E. coli MG1655 reference genome (<Gversion>NC_000913</Gversion>) using CLC Genomics Workbench5 with the length fraction of 0.9 and the similarity of 0.99.
-borrame.txt	!Sample_library_strategy	<Technique>ChIP-Seq</Technique>
-borrame.txt	!Sample_library_strategy	<Technique>ChIP-Seq</Technique>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli</Orgn> str. <Strain>K-12</Strain> substr. <Substrain>MG1655</Substrain>
-borrame.txt	!Sample_organism_ch1	<Orgn>Escherichia coli</Orgn> str. <Strain>K-12</Strain> substr. <Substrain>MG1655</Substrain>
-borrame.txt	!Sample_treatment_protocol_ch1	The cultured cells were inoculated with 1:100 dilution into 50 mL of the fresh <Med>M9 medium</Med> containing <Supp>2 g/L glucose</Supp> in either the <Supp>presence or absence of 1 g/L arginine</Supp> and continued to culture at <Temp>37°C</Temp> until reaching an appropriate cell density (<OD>OD600 ≈ 0.5</OD>).
-borrame.txt	!Sample_treatment_protocol_ch1	The cultured cells were inoculated with 1:100 dilution into 50 mL of the fresh M9 medium containing 2 g/L glucose in either the presence or <Supp>absence of 1 g/L arginine</Supp> and continued to culture at 37°C until reaching an appropriate cell density (OD600 ≈ 0.5).