Bisulfite sequencing of genomic DNA from E. coli K12 MG1655 and the isogenic dcm- strain
Escherichia coli
To identify cytosines that are methylated in E. coli K12 MG1655, we first isolated genomic DNA from cultures grown in batch to mid-exponential, late-exponential, transition-to-stationary and stationary phases. We then treated the DNA with a commercial bisulfite reagent, which converts unmethylated cytosines to uracil, but leaves methylated residues unaffected, and produces single-stranded DNA. Following synthesis of the second strand of DNA, we carried out multiplexed DNA sequencing (Lefrancois et al. 2009) on an Illumina GA IIx system producing several million 36-mer reads.  The following gives information on sequencing tags used and the corresponding samples:  strain time-point Multiplexing_tag ALL ALL N/A  wildtype exponential TCGCTT wildtype late-exponential CAAGTT  wildtype transition GTATAG wildtype stationary TACAAG dcm- exponential CCTTGC dcm- late-exponential GCTACC dcm transition TGCCGA dcm stationary ATGGCA