GSM3244835: d0TST_DXZ4_Cap_rep2; Mus musculus; OTHER
HYbrid Capture Hi-C (Hi-C2) probes were designed and hybridization to in-situ Hi-C libraries carried out as described previously (Sanborn et al., PNAS 2015). Probe sets were designed to enrich interactions in two regions of interest: chrX:70,370,161-71,832,975 and chrX:71,832,976-73,511,687 (mm9). Briefly, 120 bp probes were designed around the MboI restriction sites of the regions of interest as previously described 6 and custom synthesized pools of single stranded oligodeoxynucleotides ordered from CustomArray, Inc. (Bothell, WA). Single stranded DNA oligos were amplified and biotinylated in a MAXIScript T7 transcription reaction (Ambion). The resulting biotinylated RNA probes were hybridized to 250-300 ng of in situ Hi-C libraries for 24 hours at 65C. DNA hybridized to the RNA probes was pulled down by streptavidin beads (Dynabeads MyOne Streptavidin C1, Life Technologies), washed, and eluted as described (Sanborn et al., 2015). The resulting DNA was desalted using a 1X SPRI cleanup and amplified with Illumina primers for 18 cycles to prepare for sequencing.
GEO Accession
GSM3244835