iPSC Hi-C: Sample 6cec01f0-83ca-4dc9-b9bf-0663914232dc
We performed in situ Hi-C on 2-5 million cells. Cells were crosslinked at a final concentration of 1% formaldehyde and quenched using 200 mM glycine. Crosslinked cells were then lysed and nuclei were digested with 100U MboI overnight at 37°C. Next, fragmented ends were biotinylated for 90min at 37°C, and the sample was diluted and proximity ligated for 4 hours at room temperature. Crosslinks were reversed by the addition of SDS, ProteinaseK, and NaCl, and allowed to incubate overnight at 68°C. Samples were then purified by ethanol precipitation, resuspended in 100uL 1X Elution Buffer, fragmented using a Covaris S2 instrument, and size selected using AmpureXP beads. Subsequently, biotinylated ligation junctions were pulled down using T1 Streptavidin beads. Hi-C libraries were prepared using streptavidin beads by performing end-repair, dA-tailing, and adapter ligation, following which PCR amplification and purification was performed. The resulting libraries were sequenced on an Illumina HiSeq 4000 machine to obtain 150bp paired-end reads. 
alignment_software
BWA-MEM