title: GSM8337514: Cdca7KO,rep1; Mus musculus; OTHER
library_construction_protocol: Genomic DNA was extracted by phenol chloroform dna extraction Preparation of genomic DNA. The cells were suspended in a buffer comprising 20 mM Tris-HCl, pH 8.0, 0.4 M NaCl, 10 mM EDTA, 0.5% SDS, and 0.1 mg/ml RNase A, and then incubated at 37℃ for 1 h. Proteinese K was added to the sample at a concentration of 1 mg/ml, and then incubated at 56℃ for overnight. The sample was treated with phenol/chloroform followed by ethanol precipitation. The genomic DNA was dissolved in TE buffer. Preparation of the library. The genomic DNA (1 µg) was sheared by sonication to 100–500 bp using a Covaris S220 and purified by AMPure XP beads (Agencourt Bioscience Corp.). Then, genomic DNA libraries were constructed by KAPA Hyper Prep Kit (Kapa Biosystems) and xGen Stubby Adapter and UDI Primers Pairs kit (Integrated DNA technologies) according to manufacturer instructions. After adapter ligation, the DNA was treated with sodium bisulfite using EZ DNA Methylation GOLD kit (Zymo Research) following the manufacturer's instructions. Enrichment for adapter-ligated DNA was carried out through 17 PCR cycles using KOD One PCR Master mix (Toyobo). The concentration of the WGBS library was quantified by KAPA Library quantification kit (Kapa Biosystems). Paired-end DNA sequencing (2 × 150 bp) was then performed using the Illumina NovaSeq X plus (Illumina). We performed two technical replicates for WGBS. Each library was sequenced with 21–24 M read pairs. MethylC-seq