GSM5764573: Hi-C KO; Mus musculus; Hi-C
Hi-C was performed as described (Rao et al., Cell 159, 1665-1680 (2014).). Primary thymocytes were isolated from Satb1 F/F:Cd4-cre mice and were formaldehyde crosslinked at 2% at room temperature for 10 min. Two biological replica per sample were prepared for Hi-C.   Hi-C libraries was prepared using the Arima HiC+ kit (Arima Genomics) exactly following the associated protocol.  Paired-end sequencing was performed by Illumina NovaSeq 6000. chromatin preparation for Hi-C experiment: Hi-C was performed using Arima-HiC Kit.  Thymocytes were collected from 2 weeks old mice in two two biological replicates each from Satb1+/+:Cd4-cre (WT) and SATB1F/F:Cd4-cre (KO) mice. Briefly, 20 million cells were fixed in 2% formaldehyde for 10 min.  These cells were processed according to the protocols described in the Arma-HiC Kit, with initial digestion with restriction enzyme cocktail. Ends were filled and labeled with biotin, and subsequently ligated. After this step, DNA is sheared and biotin-labeled fragments were pull down.  The pulled down fragments were subjected to library preparation, followed by paired-end sequencing with Nova Seq.