"treatment: induced DNA double strand break"	"characteristics_ch1.1"
"background strain: BW27784"	"characteristics_ch1.2"
"strain: DL5966"	"characteristics_ch1.3"
"genotype: BW27784 delta_recD lacZ::XXX mhpR::XXX proA::ISceIcs  tsx::ISceIcs  PBAD-sbcDC  lacZ:: pal246 cynX::GmR  lacIq  lacZX-"	"characteristics_ch1.4"
"Alignment: reads were mapped to bespoke reference sequence (DL4201_in_lab_reference_genome (available on series record)) using the default parameters of software Bowtie 2 (Langmead, B. and Salzberg, S.L. (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods, 9, 357-359)."	"data_processing.1"
"Raw counts of mapped reads per reference base pair were then calculated using SAMtools software (with parameter –d set to 10^6)."	"data_processing.2"
"Normalisation: Counts were normalised by applying a single, sample-specific scaling factor.  To calculate this scaling factor, we implemented the median of ratios normalisation of DESeq software (Anders, S. and Huber, W. (2010) Differential expression analysis for sequence count data. Genome Biol, 11, R106) using R."	"data_processing.3"
"Genome_build: DL4201_in_lab_reference_genome (available on series record)"	"data_processing.4"
"Supplementary_files_format_and_content: txt files of a matrix containing genome position in column 1 and number of depth of mapped reads in column 2. Also, in a CSV file of a matrix containing genome position in column 1 and subsequent coloumns with normalised number of depth of mapped reads (column names have the strain number). CSV file is on the series record."	"data_processing.5"
"Cells were collected by centrifugation and washed three times in ice-cold 1X PBS. The pellet was then re-suspended in 250 μl ChIP buffer (200 mM Tris-HCl (pH 8.0), 600 mM NaCl 4% Triton X, Complete protease inhibitor cocktail EDTA-free (Roche)). Sonication of crosslinked samples was performed using the Diagenode Bioruptor® at 30s intervals for 10 min at high amplitude. After sonication, 350 μl of ChIP buffer was added to each sample, the samples were mixed by gentle pipetting and 100 μl of each lysate was removed and stored as ‘input’. Immunoprecipitation was performed overnight at 4°C using 1/100 anti-RecA antibody (Abcam, ab63797). IP samples were then incubated with Protein G Dynabeads® (Life Technologies) for 2 h at room temperature. All samples were washed 3 times with 1 X PBS + 0.02% Tween-20 before re-suspending the Protein G dynabeads in 200 μl of TE buffer (10 mM Tris (pH 7.4), 1 mM EDTA) + 1% SDS. 100 μl of TE buffer was added to the input samples and all samples were then incubated at 65°C for 10 h to reverse formaldehyde crosslinks. DNA was isolated using the MinElute PCR purification kit (Qiagen). DNA was eluted in 50 μl of TE buffer using a 2-step elution. Samples were stored at -20°C."	"extract_protocol_ch1.1"
"All samples were processed following NEB’s protocol from the NEBNext® ChIP-Seq library preparation kit."	"extract_protocol_ch1.2"
"Cells were grown in LB media supplemented with 0.2% arabinose at 37°C to and OD600nm of 0.2-0.25"	"growth_protocol_ch1.1"
"Escherichia coli K-12"	"organism_ch1.1"
"Bacterial Cell Lysates"	"source_name_ch1.1"
"DL5699 biological repeat 2 RecA ChIP"	"title.1"
"Protein DNA interactions were crosslinked for 10 min at 22.5C with 1% formaldehyde and quenched using glycine to a final concentration of 0.5M"	"treatment_protocol_ch1.1"
"ChIP-Seq"	"library_strategy.1"
"treatment: induced DNA double strand break"	"characteristics_ch1.1"
"background strain: BW27784"	"characteristics_ch1.2"
"strain: DL5966"	"characteristics_ch1.3"
"genotype: BW27784 delta_recD lacZ::XXX mhpR::XXX proA::ISceIcs  tsx::ISceIcs  PBAD-sbcDC  lacZ:: pal246 cynX::GmR  lacIq  lacZX-"	"characteristics_ch1.4"
"Cells were grown in LB media supplemented with 0.2% arabinose at 37°C to and OD600nm of 0.2-0.25"	"growth_protocol_ch1.1"
"Escherichia coli K-12"	"organism_ch1.1"
"Bacterial Cell Lysates"	"source_name_ch1.1"
"Protein DNA interactions were crosslinked for 10 min at 22.5C with 1% formaldehyde and quenched using glycine to a final concentration of 0.5M"	"treatment_protocol_ch1.1"