GSM8267140: Group 3 Medulloblastoma - UPN1355; Homo sapiens; Hi-C
Primary patient tumor tissue was formalin fixed and paraffin embedded according to clinical histopathology standard. Hi-C data was generated using the Arima-HiC kit, according to the manufacturer protocols. Briefly, whole genome DNA was extracted from FFPE sample and crosslinked in 2% formaldehyde. Crosslinked chromatin was digested using restriction enzyme mix for 30 min at 37C followed by 20 min at 62C.  5'-overhangs were then filled with biotinylated nucleotide (buffer/enzyme B 45 min at 25C) before the DNA fragments were  proximally ligated using buffer/enzyme C mix at 15 min at 25C. Purified ligated DNA was fragmented using Biorupter Plus (Diagenode) for goal size 400-600 bp. Biotin enrichment is then performed prior to adapter ligation. Libraries were prepared using the Illumina TruSeq adapter kit according to manufacturer specifications.