ChIP-seq of human embryonic stem cells during cell cycle progression

The experiment was designed to look into changes in key transcription factors (TFs) binding sites during cell cycle progression in human embryonic stem cells (hESCs). For this, 1 million FUCCI hESCs are sorted in Early G1 (EG1), Late G1 (LG1), and S/G2/M phases in duplicates for each experiment, and chromatin immunoprecipitation was performed for the TFs CTCF, OCT4, NANOG, SOX2, RING1B. Library preparation and sequencing were performed at the Wellcome Trust Sanger Institute next-generation sequencing facility. Size selection was applied, and fragments between 100bp and 400bp (average length of 200bp) were used to prepare barcoded sequencing libraries using NEBNext Sample Prep Kit1 (NEB) following manufacturer's instructions. Equimolar amounts of each library were pooled, and 10 samples/lane were multiplexed on Illumina HiSeq 2000, 2 X 75bp paired-end reads.