SRX847840 GSM1587027 SRP052604 SRS823866 GSM1587027 ChIP-Seq GENOMIC ChIP 2×107 mouse ES cells were cross-linked with 1% formaldehyde at 25°C for 10 min and sonicated to generate chromatin fragments of 100–500 bp. Chromatin fragments from 2×107 cells were immunoprecipitated using Nanog, Oct4 and Sox2 antibody 25ng of input genomic DNA or experimental enriched DNA were utilized for each library construction. 150-300 bp DNA fragments were selected by AMPure XP Beads (Beckman Coulter) after the adapter ligation. An Agilent 2100 BioAnalyzer was used to quantify the amplified DNA, qPCR was applied to accurately quantify the library concentration. 20 pM diluted libraries were used for sequencing. 50-cycle single-end sequencings were performed using Illumina HISeq 2000. Image processing and sequence extraction were done using the standard Illumina Pipeline. Illumina HiSeq 2000 GEO Sample GSM1587027 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1587027 gds 301587027 GEO Accession GSM1587027