GSM4700365: RT112 sh2; Homo sapiens; Hi-C
20 million cells per condition were crosslinked with 1% formaldehyde for 10 min at room temperature. Nuclei were permeabilized. DNA was digested with MboI, the ends of the restriction fragments were labelled with biotinylated nucleotides, and then ligated. After revearsal of crosslinks, DNA was purified. Purified DNA was fragmented to obtain fragments of an average size of 300–400 bp using a Bioruptor Pico (Diagenode; 8 cycles; 20 sec ON/60 sec OFF). 3 µg of DNA per condition were used for library preparation. Biotinylated DNA was pulled down with Dynabeads MyOne T1 streptavidin beads. End-repair, A-tailing and the Illumina adaptors ligation were performed on beads. Libraries were amplified by 10 cycles of PCR and purified using AMPure XP beads. The concentration and size distribution of the Hi-C library after PCR amplification were determined using a Qbit fluorometer and visual exploration in an agarose gel. Hi-C libraries were then paired-end sequenced on an Illumina NextSeq500 (200M reads per library).
GEO Accession
GSM4700365