"genotype: wildtype"	"characteristics_ch1.1"
"strain: MG1655"	"characteristics_ch1.2"
"chip antibody: none"	"characteristics_ch1.3"
"genotype: wildtype"	"characteristics_ch2.1"
"strain: MG1655"	"characteristics_ch2.2"
"fraction: input DNA"	"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"
"After collecting 50 ml culture as ‘non crosslinked’ sample, the rest of the cells was crosslinked.Crosslinked and non crosslinked cells were washed and sonicated. 400 µl of the sonicated extracts were mixed with 400 µl TE buffer and incubated with 2 µl RNase A (20 mg/ml) at 42 °C for 1 h.  Next, 200 µl proteinase K (20 mg/ml) were added and samples incubated for 2 h at 42 and 6 h at 65 °C. DNA was extracted with phenol and chlorophorm"	"extract_protocol_ch1.1"
"After collecting 50 ml culture as ‘non crosslinked’ sample, the rest of the cells was crosslinked.Crosslinked and non crosslinked cells were washed and sonicated. 400 µl of the sonicated extracts were mixed with 400 µl TE buffer and incubated with 2 µl RNase A (20 mg/ml) at 42 °C for 1 h.  Next, 200 µl proteinase K (20 mg/ml) were added and samples incubated for 2 h at 42 and 6 h at 65 °C. DNA was extracted with phenol and chlorophorm"	"extract_protocol_ch2.1"
"Cells were grown at 37 °C to an OD600 of about 0.15 in 100 ml LB (+ 0.2% glucose)."	"growth_protocol_ch1.1"
"Cells were grown at 37 °C to an OD600 of about 0.15 in 100 ml LB (+ 0.2% glucose)."	"growth_protocol_ch2.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch1.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch2.1"
"Crosslinked/reversed DNA"	"source_name_ch1.1"
"Non-crosslinked DNA"	"source_name_ch2.1"
"Crosslink"	"title.1"
"genotype: wildtype"	"characteristics_ch1.1"
"strain: MG1655"	"characteristics_ch1.2"
"chip antibody: none"	"characteristics_ch1.3"
"genotype: wildtype"	"characteristics_ch2.1"
"strain: MG1655"	"characteristics_ch2.2"
"fraction: input DNA"	"characteristics_ch2.3"
"Cells were grown at 37 °C to an OD600 of about 0.15 in 100 ml LB (+ 0.2% glucose)."	"growth_protocol_ch1.1"
"Cells were grown at 37 °C to an OD600 of about 0.15 in 100 ml LB (+ 0.2% glucose)."	"growth_protocol_ch2.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch1.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch2.1"
"Crosslinked/reversed DNA"	"source_name_ch1.1"
"Non-crosslinked DNA"	"source_name_ch2.1"