title: GSM5100391: HiC in iNeuron rep2; Homo sapiens; Hi-C
library_construction_protocol: In situ Hi-C consists of 7 steps: (1) crosslinking cells with formaldehyde, (2) DNA digestion using MboI, (3) filling in and marking ends with Biotin, (4) proximity ligation, (5) DNA shearing, (6) pulling down the biotinylated ligation junctions with streptavidin beads, and (7) paired end sequencing. As quality control (QC), we confirmed efficient restriction, ligation and DNA shearing with an agarose DNA gel and for appropriate size selection in using Agilent 4200 TapeStation system after steps (5) and (6). For the final QC, we performed 75 paired end sequencing on the Illumina Nextseq to assess quality of the libraries based on percent of Intra-chromosomal reads, long Range (>20Kb) reads, and Library Complexity. The HiC libraries were sequenced on 100 paired end sequencing using Illumina Novaseq 6000.