"genotype: GATC-cluster::srlA"	"characteristics_ch1.1"
"strain: TWx30"	"characteristics_ch1.2"
"chip antibody: SeqA"	"characteristics_ch1.3"
"genotype: GATC-cluster::srlA"	"characteristics_ch2.1"
"strain: TWx30"	"characteristics_ch2.2"
"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."	"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."	"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"	"source_name_ch1.1"
"input DNA"	"source_name_ch2.1"
"SeqA in srlA GATC cluster rep1"	"title.1"
"genotype: GATC-cluster::srlA"	"characteristics_ch1.1"
"strain: TWx30"	"characteristics_ch1.2"
"chip antibody: SeqA"	"characteristics_ch1.3"
"genotype: GATC-cluster::srlA"	"characteristics_ch2.1"
"strain: TWx30"	"characteristics_ch2.2"
"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"	"source_name_ch1.1"
"input DNA"	"source_name_ch2.1"