"genotype: MG1655 del ssrS"	"characteristics_ch1.1"
"chip antibody: RpoS (Neoclone cat. no. WP009)"	"characteristics_ch1.2"
"Reads were trimmed for quality using Trimmomatic-0.32 with a cutoff quality score of 20"	"data_processing.1"
"Raw sequence data obtained in the fastq format were aligned to the genome of E. coli K12 MG1655 (NC_000913.2) using the Burrows-Wheeler matching program BWA. Reads mapping uniquely to the genome were selected."	"data_processing.2"
"Files were coverted to .bam format using samtools"	"data_processing.3"
"The MACS2 software was used to call peaks."	"data_processing.4"
"Genome_build: NC_000913.2"	"data_processing.5"
"Supplementary_files_format_and_content: .narrowPeak files output by macs2, giving peak start and end positions, as well as fold-change, -log10pvalue, -log10qvalue, and relative summit position to peak start"	"data_processing.6"
"Cross-linked cells were harvested by centrifugation, washed thrice with ice-cold TBS (pH 7.5), resuspended in 1 ml lysis buffer [10 mM Tris (pH 8.0), 20% sucrose, 50 mM NaCl, 10 mM EDTA, 20 mg/ml lysozyme and 0.1 mg/ml RNase A] and incubated at 37°C for 30 min. After lysis, 3 ml immunoprecipitation (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% sodium dodecyl sulphate (SDS) and PMSF (final 1 mM)] was added and the DNA sheared to an average size of ~250 bp using a Bioruptor (Diagenode). Insoluble cellular matter was removed by centrifugation for 10 min at 4°C. An 800 μl aliquot was incubated with 20 μl Protein A/G UltraLink Resin (Pierce) on a rotary shaker for 45 minutes at room temperature. The supernatant was removed and incubated with mouse monoclonal antibody (Neoclone cat. no. WP009) and 30 μl Protein A/G UltraLink Resin (pre-incubated with 1mg/ml BSA in TBS), on a rotary shaker at room temperature for 90 min. Samples were washed once with IP buffer, twice with IP buffer + 500 mM NaCl, once with wash buffer [10 mM Tris (pH 8.0), 250 mM LiCl, 1 mM EDTA, 0.5% Nonidet P-40 and 0.5% sodium deoxycholate] and once with TE (pH 7.5). Immunoprecipitated complexes were eluted in 100 μl elution buffer [10 mM Tris (pH 7.5), 10 mM EDTA and 1% SDS] at 65°C for 20 min. Immunoprecipitated samples and the sheared DNA from the Bioruptor were uncrosslinked in elution buffer containing 0.8 mg/ml Pronase at 42°C for 2 h followed by 65°C for 6 h. DNA was purified using the phenol-chloroform method."	"extract_protocol_ch1.1"
"Libraries were prepared for sequencing using standard Illumina protocols"	"extract_protocol_ch1.2"
"Cells were grown at 37°C, 200 rpm in M9 glucose, for 16 hours (stationary phase)."	"growth_protocol_ch1.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch1.1"
"Bacterial cells"	"source_name_ch1.1"
"ssrS_1_IP"	"title.1"
"Formaldehyde was added to a final concentration of 1%. After incubation for 20 minutes, glycine was added to a final concentration of 0.5 M and incubated for 5 minutes."	"treatment_protocol_ch1.1"
"ChIP-Seq"	"library_strategy.1"
"genotype: MG1655 del ssrS"	"characteristics_ch1.1"
"chip antibody: RpoS (Neoclone cat. no. WP009)"	"characteristics_ch1.2"
"Cells were grown at 37°C, 200 rpm in M9 glucose, for 16 hours (stationary phase)."	"growth_protocol_ch1.1"
"Escherichia coli str. K-12 substr. MG1655"	"organism_ch1.1"
"Bacterial cells"	"source_name_ch1.1"
"Formaldehyde was added to a final concentration of 1%. After incubation for 20 minutes, glycine was added to a final concentration of 0.5 M and incubated for 5 minutes."	"treatment_protocol_ch1.1"