"strain: MG1655 K-12 WT"	"characteristics_ch1.1"
"antibody: polycolonal antiserum was raised against His6-ArcA then Affinity Purified against ArcA to yield the polyclonal antibodies used for ChIP"	"characteristics_ch1.2"
"strain: MG1655 K-12 WT"	"characteristics_ch2.1"
"Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction."	"data_processing.1"
"Cell pellets (from initial 50 ml of culture) were thawed and resuspended in 250ul of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% 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. After treatment, a distribution of DNA fragments ranging from 200-600 bp was detected by agarose-gel electrophoretic separation of a small sample that was de-crosslinked by incubation at 65 °C for >4 hr. 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 incubated with a 50/50 slurry of Sepharose protein A beads and protein G 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 and G 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 250 mM 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%SDS), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2%SDS), 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 toremove 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 50ul with EB."	"extract_protocol_ch1.1"
"Cell pellets (from initial 50 ml of culture) were thawed and resuspended in 250ul of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% 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. After treatment, a distribution of DNA fragments ranging from 200-600 bp was detected by agarose-gel electrophoretic separation of a small sample that was de-crosslinked by incubation at 65 °C for >4 hr. 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 incubated with a 50/50 slurry of Sepharose protein A beads and protein G 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 and G 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 250 mM 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%SDS), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2%SDS), 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 toremove 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 50ul with EB."	"extract_protocol_ch2.1"
"Cells were grown anaerobically (95% N2 and 5% CO2) until mid-log phase (OD600 of 0.3) and treated with 1% final volumen formaldehyde for ten minutes. Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final) was added to the mid-log 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 5000 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C."	"growth_protocol_ch1.1"
"Cells were grown anaerobically (95% N2 and 5% CO2) until mid-log phase (OD600 of 0.3) and treated with 1% final volumen formaldehyde for ten minutes. Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final) was added to the mid-log 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 5000 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C."	"growth_protocol_ch2.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch1.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch2.1"
"ArcA IP from WT Escherichia coli MG1655 K-12"	"source_name_ch1.1"
"ArcA INPUT from WT Escherichia coli MG1655 K-12"	"source_name_ch2.1"
"ArcA - Anaerobic - Affinity Purified -biological rep B"	"title.1"
"Cell pellets (from initial 50 ml of culture) were thawed and resuspended in 250ul of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% 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. After treatment, a distribution of DNA fragments ranging from 200-600 bp was detected by agarose-gel electrophoretic separation of a small sample that was de-crosslinked by incubation at 65 °C for >4 hr. 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 incubated with a 50/50 slurry of Sepharose protein A beads and protein G 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 and G 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 250 mM 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%SDS), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2%SDS), 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 toremove 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 50ul with EB."	"treatment_protocol_ch1.1"
"Cell pellets (from initial 50 ml of culture) were thawed and resuspended in 250ul of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% 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. After treatment, a distribution of DNA fragments ranging from 200-600 bp was detected by agarose-gel electrophoretic separation of a small sample that was de-crosslinked by incubation at 65 °C for >4 hr. 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 incubated with a 50/50 slurry of Sepharose protein A beads and protein G beads in IP buffer for 2-3 hours at 4 °C. The beads were removed by centrifugation and no 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 and G 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 250 mM 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%SDS), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2%SDS), 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 toremove 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 50ul with EB."	"treatment_protocol_ch2.1"
"strain: MG1655 K-12 WT"	"characteristics_ch1.1"
"antibody: polycolonal antiserum was raised against His6-ArcA then Affinity Purified against ArcA to yield the polyclonal antibodies used for ChIP"	"characteristics_ch1.2"
"strain: MG1655 K-12 WT"	"characteristics_ch2.1"
"Cells were grown anaerobically (95% N2 and 5% CO2) until mid-log phase (OD600 of 0.3) and treated with 1% final volumen formaldehyde for ten minutes. Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final) was added to the mid-log 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 5000 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C."	"growth_protocol_ch1.1"
"Cells were grown anaerobically (95% N2 and 5% CO2) until mid-log phase (OD600 of 0.3) and treated with 1% final volumen formaldehyde for ten minutes. Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final) was added to the mid-log 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 5000 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C."	"growth_protocol_ch2.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch1.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch2.1"
"ArcA IP from WT Escherichia coli MG1655 K-12"	"source_name_ch1.1"
"ArcA INPUT from WT Escherichia coli MG1655 K-12"	"source_name_ch2.1"
"Cell pellets (from initial 50 ml of culture) were thawed and resuspended in 250ul of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% 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. After treatment, a distribution of DNA fragments ranging from 200-600 bp was detected by agarose-gel electrophoretic separation of a small sample that was de-crosslinked by incubation at 65 °C for >4 hr. 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 incubated with a 50/50 slurry of Sepharose protein A beads and protein G 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 and G 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 250 mM 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%SDS), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2%SDS), 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 toremove 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 50ul with EB."	"treatment_protocol_ch1.1"
"Cell pellets (from initial 50 ml of culture) were thawed and resuspended in 250ul of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% 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. After treatment, a distribution of DNA fragments ranging from 200-600 bp was detected by agarose-gel electrophoretic separation of a small sample that was de-crosslinked by incubation at 65 °C for >4 hr. 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 incubated with a 50/50 slurry of Sepharose protein A beads and protein G beads in IP buffer for 2-3 hours at 4 °C. The beads were removed by centrifugation and no 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 and G 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 250 mM 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%SDS), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2%SDS), 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 toremove 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 50ul with EB."	"treatment_protocol_ch2.1"