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Methods Mol Biol. 2014;1150:3-20. doi: 10.1007/978-1-4939-0512-6_1.

Efficient library preparation for next-generation sequencing analysis of genome-wide epigenetic and transcriptional landscapes in embryonic stem cells.

Author information

1
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.

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.

PMID:
24743988
DOI:
10.1007/978-1-4939-0512-6_1
[Indexed for MEDLINE]

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