title: GSM3359974: F123_singlecellMethyl-HiC_primed_Cell_16-19; Mus musculus; OTHER
library_construction_protocol: Cell pellets were washed with cold PBS and lysed with lysis buffer to get nuclei pellets. Nucleus were permeabilized with 0.5% SDS. DNA was in situ digested with 100 units of DpnII (NEB) overnight. The ends of restriction fragments were filled with biotinylated nucleotides and in situ ligated. After reversal of crosslinks, ligated DNA was ethanol precipitate and sheared to a length of ∼400 bp by sonication (Covaris). Sonicated products were pulled down with streptavidin beads. Library construction was then performed on beads. After adapter ligation, beads were suspended in 20ul TE buffer and subjected to bisulfite conversion with EZ DNA Methylation-Gold™ Kit (Zymo). Unmethylated lambda DNA was sonicated and ligated with the same adapter for Methyl-HiC sample and then was spiked in at 0.5% before bisulfite conversion. After conversion, streptavidin beads were removed with magnet and the supernatant were purified. Purified bisulfite converted DNA was amplified with Hifi Hotstart Uracil+Ready Mix (KAPA). Libraries were prepared according to Illumina's standard DNA library protocol, in which genomic DNA was fragmented by sonication (Covaris), end-repaired, dA-tailed and ligated to cytosine methylated Illumina TruSeq adapter.
attributes.tag: GEO Accession
attributes.value: GSM3359974