GSM9316566: WSU-DLCL2 (Hi-C); Homo sapiens; Hi-C
FFPE tissue from 2-5 unstained slides cut at 5-10µm were processed using the Arima HiC+ for FFPE kit (Product Number A311038, Arima Genomics, Carlsbad, CA) as per manufacturer protocols to produce Illumina-compatible sequencing libraries. Briefly, 5µm unstained FFPE tissue sections were first de-waxed and rehydrated, and then subjected to Hi-C sample preparation using Arima HiC+ for FFPE kit.  For generation of FFPE cell blocks, 10 million cells from each cell line in standard growth conditions were harvested, washed in PBS, and fixed in 3.7% formaldehyde in phosphate-buffered saline (“10% neutral-buffered formalin”) at room temperature for 20 min, then washed 2x in PBS. Cells were then processed by the standard cell block preparation method of the University of Michigan Cytology Laboratory: cells were pelleted at 0.8 x g for 5 minutes, resuspended in warmed (50°C) HistoGel (Epredia, HG4000012) and incubated at 4°C for 30 min. The HistoGel pellet was then fixed for an additional 6 hrs at room temperature in 10% neutral-buffered formalin prior to submission for standard FFPE tissue processing and embedding. After verifying cellularity with an H&E slide, ten x 10-micron sections were cut from each block for FFPE Hi-C processing as described above. Following Hi-C sample preparation,  Illumina-compatible sequencing libraries were constructed by shearing the proximally ligated DNA and then size selecting DNA fragments using SPRI beads. The size-selected DNA fragments containing proximity ligation junctions were then enriched using Enrichment Beads (provided in the Arima HiC+ for FFPE kit) and converted to Illumina-compatible sequencing libraries. The resulting Hi-C libraries underwent standard quality control (qPCR and BioAnalyzer).