Hme dip kits

For ChIP experiments, mouse ESCs stably expressing FHA-Srap1 were fixed in 1% paraformaldehyde for 10 min at 37 C, followed by quenching with 125 mM glycine for 5 min. Cells were lysed and processed using the MAGnify ChIP system (Life Sciences). For DIP, genomic DNA was isolated from Srap1 KO and matched wild-type ESCs using the DNeasy Blood and Tissue DNA kit (QIAGEN) and sonicated for a total of 6 min. Samples were processed using the MeDIP or hMeDIP kits (Active Motif) according to the manufacturer's protocol. For RNA-seq, total RNA was extracted using the Zymo RNA Clean & Concentrator (Zymo Research), followed by rRNA depletion and cDNA preparation using the KAPA Stranded RNA-Seq Kit with RiboErase. For RRBS, genomic DNA was extracted from E9.5 wild-type and Srap1 KO embryos using the DNeasy Blood and Tissue kit and digested with MspI overnight. Sizeselected (<0.7 kb) DNA fragments were subjected to bisulfite conversion using the EZ DNA Methylation-Gold kit (Zymo Research), followed by 12 cycles of PCR amplification using Kapa HiFi HotStart Uracil+ polymerase. Indexed libraries were prepared using the Kapa HyperPrep kit and purified with 0.93 Ampure XP beads (Beckman Coulter), pooled, and analyzed on an Illumina Hi-Seq2000 or NextSeq500.