GSM1625731: Ch8.B26-PM-2hrs-tech-replicate1; Mus musculus; OTHER
Cell cycle synchronized cultures were crosslinked for 10 minutes at RT in 1% formaldehyde. The reaction was quenched for 5 min at RT. We then applied 4C-seq method. Briefly, nuceli were isolated from the cross-linked cells and digested using the restriction enzyme HindIII. Fragments were ligated under dilute conditions and reversed cross-linked. The samples were then digested with DpnII and circularized. Subsequently bait specific primers were used to amplify the interaction partners and sequenced using the Illumina HiSeq 2500 platform, generating 50 bp reads. Libraries were generated by amplifying the 4C template using bait specific primers with added illumina adaptors. Bait is the genomic loci of interest whose genome-wide interactions are being measured by 4C-seq. We denote each bait by its chromosome followed by letter B and the approximate megabase-scale coordinate of the bait (e.g. Ch8.B26 means bait with a coordinate on 26th megabase of chromosome 8). Twelve baits were chosen based on their replication timing regulation and were named Ch8.B7,Ch8.B26,Ch8.B44,Ch8.B53,Ch8.B87,Ch8.B118,Ch16.B30,Ch16.B41,Ch16.B46,Ch16.B48,Ch17.B50,Ch17.B50 Coordinates are in mm9.