title: GSM3204307: MEF MUT rep1; Mus musculus; OTHER
library_construction_protocol: Hi-C was performed as described in Belton et al. 2012 (PMID: 22652625) . For each Hi-C library 25 x 10^6 cells were cultured in EC10 media. The day of harvesting, cells were incubated in 22.5 mL of fresh media without serum, and cross-linked by adding 625 μL of 37% formaldehyde (1% final concentration). Plates were immediately mixed thoroughly after formaldehyde addition, and subsequently rocked every 2 minutes for exactly 10 minutes at RT. The cross-linking was quenched by addition of 1.25 mL of 2.5 M glycine. After 5 minutes at RT, plates were placed on ice for an additional 15 minutes. Cells were finally harvested by a cell lifter, transferred to a 15 mL falcon tubes, and centrifuged at 800 g for 10 min (4oC). The cell pellet was snap-frozen in liquid nitrogen, and stored at -80oC until use. Hi-C libraries were then sequenced on a HiSeq4000 (paired end reads of 100 bases each). Two biological replicates of WT and SmcHD1 null MEFs were sequenced in separate lanes, each yielding ~350 million reads per replicate. Hi-C library was constructed as described in Belton et al. 2012 (PMID: 22652625)