RNA was harvested (i) for the ESCs using the RNeasy Plus Mini Kit (QIAGEN) including gDNA eliminator treatment according to instructions of the manufacturer; and (ii) for the EpiSCs using Trizol (Invitrogen) according to the manufacturer's recommendations. Total RNA (100 μg) was subjected to two rounds of poly(A) selection (Oligotex mRNA Mini Kit; QIAGEN), followed by DNaseI treatment (QIAGEN). mRNA (100–200 ng) was fragmented by hydrolysis (5× fragmentation buffer: 200mM Tris acetate, pH8.2, 500 mM potassium acetate and 150 mM magnesium acetate) at 94 °C for 90 s and purified (RNAeasy Minelute Kit; QIAGEN). cDNA was synthesized using 5 μg random hexamers by Superscript III Reverse Transcriptase (Invitrogen). Double-stranded cDNA synthesis was performed in second strand buffer (Invitrogen) according to the manufacturer's recommendations and purified (Minelute Reaction Cleanup Kit; QIAGEN). ChIP-Seq was performed according to Marks et al. (2012). For RNA-Seq of ESCs and EpiSCs, cDNA was prepared for sequencing by end repair of 20 ng double-stranded cDNA as measured by Qubit (Invitrogen). ChIP-Seq was performed according to Marks et al. (2012). For RNA-Seq of ESCs and EpiSCs, cDNA was prepared for sequencing by end repair of 20 ng double-stranded cDNA as measured by Qubit (Invitrogen). Adaptors were ligated to DNA fragments, followed by size selection (~300 bp) and 14 cycles of PCR amplification. Quality control of the adaptor-containing DNA libraries was performed by quantitative PCR and by running the products on an Automated Electrophoresis System (Experion, BioRad). Cluster generation and sequencing was performed using the Illumina Genome Analyzer IIx, Hi-Seq 2000 or NextSeq 500 platforms according to standard Illumina protocols. Generation of FASTQ files and demultiplexing was performed using Illumina CASAVA. All sequencing analyses were conducted based on the M. musculus NCBI m37 genome assembly (MM9; assembly July 2007).