Genomic Analysis of DNA Double-Strand Break Repair in Escherichia coli (MFA profiles)

Counting DNA reads using whole genome sequencing is providing new insight into DNA double-strand break repair (DSBR) in the model organism Escherichia coli. We describe the application of RecA chromatin immunoprecipitation coupled to genomic DNA sequencing (RecA-ChIP-seq) and marker frequency analysis (MFA) to analyse the genomic consequences of DSBR. Comparison of MFA profiles resulting from three different methods. Two biological repeats were carried out for each of the for strains for all three methods. Two strains experienced an induced DNA double strand break (DL4184 and DL4243) and two did not (DL4201 and DL4257). Two strains are wild-type for the ruvAB gene (DL4184 and DL4201) and two strains have the ruvAB gene deleted (DL4243 and DL4257). The analysis contains four re-analysed samples from GSE117541 (GSM3302820, GSM3302821, GSM3302824 and GSM3302825).