title: Efficient library preparation for next-generation sequencing analysis of genome-wide epigenetic and transcriptional landscapes in embryonic stem cells.
abstract: Gene expression in embryonic stem (ES) cells is regulated in part by a network of transcription factors, epigenetic regulators, and histone modifications that influence the underlying chromatin in a way that is conducive or repressive for transcription. Advances in next-generation sequencing technology have allowed for the genome-wide analysis of chromatin constituents and protein-DNA interactions at high resolution in ES cells and other stem cells. While many studies have surveyed genome-wide profiles of a few factors and expression changes at a fixed time point in undifferentiated ES cells, few have utilized an integrative approach to simultaneously survey protein-DNA interactions, histone modifications, and expression programs during ES cell self-renewal and differentiation. To identify transcriptional networks that regulate pluripotency and differentiation, it is important to generate high-quality genome-wide maps of transcription factors, chromatin factors, and histone modifications and to survey global gene expression profiles. Here, to interrogate genome-wide profiles of chromatin features and to survey global gene expression programs in ES cells, we describe protocols for efficient library construction for next-generation sequencing of ChIP-Seq and RNA-Seq samples.
authors.affiliation: Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Dr., Bldg 10, 7B04, Bethesda, MD, 20892, USA, Benjamin.kidder@nih.gov.
authors.forename: Benjamin L
authors.initials: BL
authors.lastname: Kidder
authors.forename: Keji
authors.initials: K
authors.lastname: Zhao
mesh_terms: D000818:Animals; D018929:Cell Culture Techniques; D002460:Cell Line; D002843:Chromatin / Q000235:genetics; D047369:Chromatin Immunoprecipitation; D003001:Cloning, Molecular; D018076:DNA, Complementary / Q000096:biosynthesis / Q000235:genetics; D053595:Embryonic Stem Cells / Q000378:metabolism*; D044127:Epigenesis, Genetic / Q000235:genetics*; D057890:Epigenomics / Q000379:methods*; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D051379:Mice; D017423:Sequence Analysis, RNA; D013010:Sonication; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D002843:Chromatin; D018076:DNA, Complementary