"strain: RSW422 (RL1963)"	"characteristics_ch1.1"
"genotype/variation: 42 deletions, ΔnusG"	"characteristics_ch1.2"
"cell type: bacterial cells"	"characteristics_ch1.3"
"chip antibody: anti-b(RNAP) NT63"	"characteristics_ch1.4"
"chip antibody vendor: Neoclone"	"characteristics_ch1.5"
"chip antibody cat. #: W0002"	"characteristics_ch1.6"
"strain: RSW422 (RL1963)"	"characteristics_ch2.1"
"genotype/variation: 42 deletions, ΔnusG"	"characteristics_ch2.2"
"cell type: bacterial cells"	"characteristics_ch2.3"
"sample type: input DNA"	"characteristics_ch2.4"
"Datasets were normalized using locally weighted linear regression (LOWESS) normalization on raw Cy3 and Cy5 signals to correct for intensity-dependent dye effects within each array using the “normalizeWithinArrays” function in the limma package for the statistical program R (v.2.14.2)."	"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 in MOPS minimal medium with 0.2% glucose at 37 oC  in gas-sparged Roux bottles or shaking flasks to mid-log phase (OD600 ~ 0.3-0.4)."	"growth_protocol_ch1.1"
"Cells were grown in MOPS minimal medium with 0.2% glucose at 37 oC  in gas-sparged Roux bottles or shaking flasks to mid-log phase (OD600 ~ 0.3-0.4)."	"growth_protocol_ch2.1"
"Escherichia coli K-12"	"organism_ch1.1"
"Escherichia coli K-12"	"organism_ch2.1"
"RNAP ChIP DNA from MDS42 ΔnusG cells"	"source_name_ch1.1"
"Input DNA from MDS42 ΔnusG cells"	"source_name_ch2.1"
"MDS42 ΔnusG RNAP 1"	"title.1"
"Cells were cross-linked by the addition of formaldehyde at 1% final concentration with continued shaking at 37 °C for 5 min before quenching with glycine (100 mM final)."	"treatment_protocol_ch1.1"
"Cells were cross-linked by the addition of formaldehyde at 1% final concentration with continued shaking at 37 °C for 5 min before quenching with glycine (100 mM final)."	"treatment_protocol_ch2.1"
"strain: RSW422 (RL1963)"	"characteristics_ch1.1"
"genotype/variation: 42 deletions, ΔnusG"	"characteristics_ch1.2"
"cell type: bacterial cells"	"characteristics_ch1.3"
"chip antibody: anti-b(RNAP) NT63"	"characteristics_ch1.4"
"chip antibody vendor: Neoclone"	"characteristics_ch1.5"
"chip antibody cat. #: W0002"	"characteristics_ch1.6"
"strain: RSW422 (RL1963)"	"characteristics_ch2.1"
"genotype/variation: 42 deletions, ΔnusG"	"characteristics_ch2.2"
"cell type: bacterial cells"	"characteristics_ch2.3"
"sample type: input DNA"	"characteristics_ch2.4"
"Cells were grown in MOPS minimal medium with 0.2% glucose at 37 oC  in gas-sparged Roux bottles or shaking flasks to mid-log phase (OD600 ~ 0.3-0.4)."	"growth_protocol_ch1.1"
"Cells were grown in MOPS minimal medium with 0.2% glucose at 37 oC  in gas-sparged Roux bottles or shaking flasks to mid-log phase (OD600 ~ 0.3-0.4)."	"growth_protocol_ch2.1"
"Escherichia coli K-12"	"organism_ch1.1"
"Escherichia coli K-12"	"organism_ch2.1"
"RNAP ChIP DNA from MDS42 ΔnusG cells"	"source_name_ch1.1"
"Input DNA from MDS42 ΔnusG cells"	"source_name_ch2.1"
"Cells were cross-linked by the addition of formaldehyde at 1% final concentration with continued shaking at 37 °C for 5 min before quenching with glycine (100 mM final)."	"treatment_protocol_ch1.1"
"Cells were cross-linked by the addition of formaldehyde at 1% final concentration with continued shaking at 37 °C for 5 min before quenching with glycine (100 mM final)."	"treatment_protocol_ch2.1"