Ab137034

ChIP using anti-Ssrp1 (ab137034, Abcam) or anti-USP7 (A300–033A, Bethyl) was performed as described above. ChIP DNA (2 ng) was used for the ChIP-seq library which was prepared by Novogene Corporation. Each library was sequenced by Novogene Corporation, resulting in pair-ended 150 bp reads with ChIP input as control. The adapter sequences and low-quality 3′ ends of reads were removed with Cutadapt and mapped to the mouse mm10 genome assembly using Bowtie2 (46 (link)). The ChIP-seq correlation coefficient was determined by Deeptools (47 (link)). Due to the close correlation between Ssrp1 ChIP duplicate, we merged the two Ssrp1 duplicates for downstream analysis. Enrichment of ChIP-seq signal was also generated by Deeptools. Ssrp1 binding peaks were predicted by Macs2 (48 (link)). MERVL-int center information was inferred from RepeatMasker annotation file from UCSC genome browser (49 (link)).

ChIP was performed essentially as described previously (3 (link)). Briefly, ESCs were cross-linked by 1% formaldehyde for 10 min at room temperature and quenched by 200 mM glycine for 5 min. Soluble chromatin was obtained after cell lysis and sonication. Then samples were pre-cleared and incubated with 3–5 μg antibody loaded protein G MagBeads (L00274, GenScript) at 4°C overnight. Subsequently, the immunoprecipitated DNA was decrosslinked, purified and analyzed by qPCR. ChIP-qPCR was done with anti-Ssrp1 antibody (ab137034, Abcam), anti-USP7 antibody (A300–033A, Bethyl) or anti-H2Bub antibody (#5546, Cell Signaling Technology).