"genotype: wildtype"	"characteristics_ch1.1"
"strain: MG1655"	"characteristics_ch1.2"
"chip antibody: SeqA"	"characteristics_ch1.3"
"genotype: wildtype"	"characteristics_ch2.1"
"strain: MG1655"	"characteristics_ch2.2"
"fraction: input DNA, SeqA ChIP supernatant"	"characteristics_ch2.3"
"Spot intensities were extracted using the Feature Extraction software 10.5.1.1 from Applied Biosystems with a linear dye normalization correction method. The gProcessedSignal and rProcessedSignal was used for further analysis with the statistics software R. Ratios of g (sample) to r (control) were calculated after background substraction and normalized to the array wide average. Data points with a value below 0 after background subtraction were set 'null'. Data points form non-unique regions on the chromosome were excluded from analysis."	"data_processing.1"
"Cultures of E. coli MG1655 and its derivates were cross linked by addition of 27 µl of formaldehyde (37%) per ml medium (final concentration 1%). Crosslinking was performed at slow shaking (100 rpm) for 20 min followed by quenching with 0.2 ml of 2.5 M glycine per ml medium (final concentration 0.5 M). Cells were collected by centrifugation and washed twice with cold TBS (pH7.5). After resuspension in 1 ml lysis buffer (10mM Tris (pH 8.0), 20% sucrose, 50mM NaCl, 10mM EDTA, 10 mg/ml lysozyme) and incubation at 37 °C for 30 min C followed by addition of 4 ml IP buffer cells were sonicated on ice with 12 times 30 sec and 30 sec breaks at an UP 400s Ultrasonic processor (Dr. Hielscher GmbH) with 100% power. After centrifugation for 10 min at 9000 g, 800 µl aliquotes of the supernatant were stored at -20 °C. 800 µl of sonicated cell extract (see above) were incubated with 20 µl protein A/G agarose beads (Ultralink) and antibody rotating at 4 °C. Washing was done with 500 µl buffer (2 x 500 µl IP buffer [50 mM HEPES-KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X 100, 0.1 % Sodium deoxycholate, 0.1 % SDS], 1 x IP buffer with 500mM NaCl, 1 x wash buffer [10mM Tris pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% Nonidet-P40, 0.5% Sodium deoxycholate] and 1 x TE) followed by rotation at room temperature for three minutes with subsequent collection of the beads by centrifugation. For elution, 100 µl elution buffer (50 mM Tris (pH 7.5), 10 mM EDTA, 1% SDS) was added to the beads, incubated in a 65 °C water bath for 10 min and centrifuged as above. After reversion of crosslink the DNA was purified with phenol/chloroform. METHOD DETAILS are given and are important for the different arrays.  METHOD DETAILS:  For RNAP old, SeqA old and SeqA old deltaSeqA:  Cell extracts were incubated with agarose beads and antibody over night. Samples were transferred to a Spin-X centrifuge column (Costar), centrifuged for 2 min at 4.000 rpm to collect the beads on the column. The flow through was removed. Washing was by adding the described buffers to the beads on the spin column and rotation at room temperature for three minutes with subsequent collection of the beads by centrifugation as above. For elution, 100 µl elution buffer was added to the column with the beads, incubated in a 65 °C water bath for 10 min and centrifuged as above. To prepare the control DNA, 800 µl of sonicated cell extract was incubated at 65 °C over night followed by 30 min after addition of 1 µl RNase A (20 mg/ml) and extraction with phenol/chloroform.  For SeqA new, SeqA new deltaSeqA, sigma32 30°C and sigma 32 43°C:  The ChIP protocol as described above resulted in the high background signal. The following modifications were applied. First, agarose beads were not collected on a spin column but instead at the bottom of a usual 1.5 ml reaction tube. The supernatant was than removed by pipetting. Second, the control DNA was taken from the supernatant resulting from centrifugation of the precipitated chromatin beads processed further as the immuno precipitated DNA after elution. Third, before addition of proteinase K sample and control DNA were incubated with RNase A (50 µg/ml) for at least 90 min at 42 °C. Incubation of 800 µl cell extract with σ32- or SeqA antiserum was for 1 h at 4 °C.  For sigma32 30°C short RNase and  sigma32 30°C short RNase:  The ChIP protocol was as described for sigma 32 30°C and sigma 32 43°C but with a shorter RNase A incubation for only 30 instead of 90 min."	"extract_protocol_ch1.1"
"Cultures of E. coli MG1655 and its derivates were cross linked by addition of 27 µl of formaldehyde (37%) per ml medium (final concentration 1%). Crosslinking was performed at slow shaking (100 rpm) for 20 min followed by quenching with 0.2 ml of 2.5 M glycine per ml medium (final concentration 0.5 M). Cells were collected by centrifugation and washed twice with cold TBS (pH7.5). After resuspension in 1 ml lysis buffer (10mM Tris (pH 8.0), 20% sucrose, 50mM NaCl, 10mM EDTA, 10 mg/ml lysozyme) and incubation at 37 °C for 30 min C followed by addition of 4 ml IP buffer cells were sonicated on ice with 12 times 30 sec and 30 sec breaks at an UP 400s Ultrasonic processor (Dr. Hielscher GmbH) with 100% power. After centrifugation for 10 min at 9000 g, 800 µl aliquotes of the supernatant were stored at -20 °C. 800 µl of sonicated cell extract (see above) were incubated with 20 µl protein A/G agarose beads (Ultralink) and antibody rotating at 4 °C. Washing was done with 500 µl buffer (2 x 500 µl IP buffer [50 mM HEPES-KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X 100, 0.1 % Sodium deoxycholate, 0.1 % SDS], 1 x IP buffer with 500mM NaCl, 1 x wash buffer [10mM Tris pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% Nonidet-P40, 0.5% Sodium deoxycholate] and 1 x TE) followed by rotation at room temperature for three minutes with subsequent collection of the beads by centrifugation. For elution, 100 µl elution buffer (50 mM Tris (pH 7.5), 10 mM EDTA, 1% SDS) was added to the beads, incubated in a 65 °C water bath for 10 min and centrifuged as above. After reversion of crosslink the DNA was purified with phenol/chloroform. METHOD DETAILS are given and are important for the different arrays.  METHOD DETAILS:  For RNAP old, SeqA old and SeqA old deltaSeqA:  Cell extracts were incubated with agarose beads and antibody over night. Samples were transferred to a Spin-X centrifuge column (Costar), centrifuged for 2 min at 4.000 rpm to collect the beads on the column. The flow through was removed. Washing was by adding the described buffers to the beads on the spin column and rotation at room temperature for three minutes with subsequent collection of the beads by centrifugation as above. For elution, 100 µl elution buffer was added to the column with the beads, incubated in a 65 °C water bath for 10 min and centrifuged as above. To prepare the control DNA, 800 µl of sonicated cell extract was incubated at 65 °C over night followed by 30 min after addition of 1 µl RNase A (20 mg/ml) and extraction with phenol/chloroform.  For SeqA new, SeqA new deltaSeqA, sigma32 30°C and sigma 32 43°C:  The ChIP protocol as described above resulted in the high background signal. The following modifications were applied. First, agarose beads were not collected on a spin column but instead at the bottom of a usual 1.5 ml reaction tube. The supernatant was than removed by pipetting. Second, the control DNA was taken from the supernatant resulting from centrifugation of the precipitated chromatin beads processed further as the immuno precipitated DNA after elution. Third, before addition of proteinase K sample and control DNA were incubated with RNase A (50 µg/ml) for at least 90 min at 42 °C. Incubation of 800 µl cell extract with σ32- or SeqA antiserum was for 1 h at 4 °C.  For sigma32 30°C short RNase and  sigma32 30°C short RNase:  The ChIP protocol was as described for sigma 32 30°C and sigma 32 43°C but with a shorter RNase A incubation for only 30 instead of 90 min."	"extract_protocol_ch2.1"
"Cells were grown at 37 °C to an OD600 of about 0.15 in 50 ml LB (+ 0.2% glucose) before crosslinking."	"growth_protocol_ch1.1"
"Cells were grown at 37 °C to an OD600 of about 0.15 in 50 ml LB (+ 0.2% glucose) before crosslinking."	"growth_protocol_ch2.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch1.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch2.1"
"SeqA ChIP DNA, new protocol"	"source_name_ch1.1"
"Input DNA from SeqA ChIP supernatant"	"source_name_ch2.1"
"SeqA new rep1"	"title.1"
"genotype: wildtype"	"characteristics_ch1.1"
"strain: MG1655"	"characteristics_ch1.2"
"chip antibody: SeqA"	"characteristics_ch1.3"
"genotype: wildtype"	"characteristics_ch2.1"
"strain: MG1655"	"characteristics_ch2.2"
"fraction: input DNA, SeqA ChIP supernatant"	"characteristics_ch2.3"
"Cells were grown at 37 °C to an OD600 of about 0.15 in 50 ml LB (+ 0.2% glucose) before crosslinking."	"growth_protocol_ch1.1"
"Cells were grown at 37 °C to an OD600 of about 0.15 in 50 ml LB (+ 0.2% glucose) before crosslinking."	"growth_protocol_ch2.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch1.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch2.1"
"SeqA ChIP DNA, new protocol"	"source_name_ch1.1"
"Input DNA from SeqA ChIP supernatant"	"source_name_ch2.1"