GSM5962111: NM1 knockout Mouse Embryonic Fibroblast, rep3 (Hi-C); Mus musculus; Hi-C
Cells were fixed with formaldehyde, pellets were washed twice by 1X PBS and stored at -80 deg. The frozen pellets were shipped on dry ice to Genome Technology Center at NYU Langone Health, NY. All subsequent processing was performed by Genome Technology Center at NYU Langone Health using standard DNA extraction and library preparation protocols. Hi-C was performed at Genome Technology Center at NYU Langone Health, NY from cells cross-linked with formaldehyde. Experiments were performed in triplicates following the instructions from Arima Hi-C kit (Arima Genomics, San Diego, CA). Subsequently, Illumina-compatible sequencing libraries were prepared by using a modified version of KAPA HyperPrep library kit (KAPA BioSystems, Willmington, MA). Quality check steps were performed to assess the fraction of proximally ligated DNA labeled with biotin, and the optimal number of PCR reactions needed to make libraries. The libraries were loaded into an Illumina flowcell (Illumina, San Diego, CA) on a NovaSeq instrument for paired-end 50 reads.