GSM3380629: ActD treated cells rep1; Homo sapiens; Hi-C
Hi-C libraries were generated with the in-situ ligation using the HindIII restriction enzyme (PMID: 28435001), Briefly, after crosslinking the cells with 1% formaldehyde for 10 minutes at room temperature, the nuclei were extracted by dounce homogenization. Next, the chromatin was digested with HindIII either in the presence of 500μg RNase A (Qiagen #19101), or 30U of RNase Inhibitor (NEB, #M0314L).  These samples that are treated after formaldehyde crosslinking (aXL) are referred as “aXL RNase A” and “aXL CTRL”, respectively. The bXL samples were processed according to the original protocol(PMID: 28435001). The digested chromatin was then end-labelled with biotin-14-dCTP (Thermo Fisher 19519016), and in-situ ligation was performed. Extraction of the DNA was performed by phenol-chloroform extraction, and the biotin was removed from unligated ends, followed by shearing of the DNA by using a Covaris S220 instrument to 100-500bp size range. After A-tailing, biotin pull-down and adapter ligation, paired-end sequencing was performed on a HiSeq instrument. Hi-C libraries for each condition were generated in two biological replicates.
GEO Accession
GSM3380629