title: GSM4802002: PCGBM2_S1_Hi-C; Homo sapiens; Hi-C
library_construction_protocol: For Hi-C, libraries were generated from 5 million cultured glioblastoma cell lines and disassociated mouse embryonic tissue as described in (Rao et al., 2014) with minor modifications. Briefly, in situ Hi-C consists of 7 steps: (1) crosslinking cells with formaldehyde, (2) digesting the DNA using a 4-cutter restriction enzyme (e.g., DpnII) within intact permeabilized nuclei, (3) filling in, biotinylating the resulting 5′-overhangs and ligating the blunt ends, (4) shearing the DNA, (5) pulling down the biotinylated ligation junctions with streptavidin beads, (6) library amplification and (7) analyzing these fragments using paired end sequencing. As quality control (QC) steps, we checked for efficient sonication with an agarose DNA gel and for appropriate size selection using the Agilent Bioanalyzer on final amplified libraries. For the final QC, we performed superficial sequencing on the Illumina Hiseq 2500 (~30M reads/sample) to assess quality of the libraries using percent of reads passing filter, percent of chimeric reads, and percent of forward-reverse pairs.  125bp paired-end sequencing was performed on the Illumina HiSeq 4000.