Chapter title |
Efficient library preparation for next-generation sequencing analysis of genome-wide epigenetic and transcriptional landscapes in embryonic stem cells.
|
---|---|
Chapter number | 1 |
Book title |
Stem Cell Transcriptional Networks
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Published in |
Methods in molecular biology, January 2014
|
DOI | 10.1007/978-1-4939-0512-6_1 |
Pubmed ID | |
Book ISBNs |
978-1-4939-0511-9, 978-1-4939-0512-6
|
Authors |
Benjamin L Kidder, Keji Zhao, Benjamin L. Kidder, Kidder, Benjamin L., Zhao, Keji |
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. |
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