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Mir, A.A. ; Dyar, K.A. ; Greulich, F. ; Quagliarini, F. ; Jouffe, C. ; Hubert, M. J. ; Hemmer, M.C. ; Uhlenhaut, N.H.

In Vivo ChIP-Seq of nuclear receptors: A rough guide to transform frozen tissues into high-confidence genome-wide binding profiles.

In: Nuclear Receptors. Berlin [u.a.]: Springer, 2019. 39-70 (Methods Mol. Biol. ; 1966)
DOI PMC
Open Access Green as soon as Postprint is submitted to ZB.
Chromatin immunoprecipitation coupled to next generation sequencing (ChIP-seq) is a powerful tool to map context-dependent genome-wide binding of nuclear hormone receptors and their coregulators. This information can provide important mechanistic insight into where, when and how DNA–protein interactions are linked to target gene regulation. Here we describe a simple, yet reliable ChIP-seq method, including nuclear isolation from frozen tissue samples, cross-linking DNA–protein complexes, chromatin shearing, immunoprecipitation, and purification of ChIP DNA. We also include a standard ChIP-seq data analysis pipeline to elaborate and analyze raw single-end or paired-end sequencing data, including quality control steps, peak calling, annotation, and motif enrichment.
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Publication type Article: Edited volume or book chapter
Keywords Chip-seq ; Chromatin Immunoprecipitation ; Data Analysis ; In Vivo ; Nuclear Receptors
ISSN (print) / ISBN 1064-3745
e-ISSN 1940-6029
Book Volume Title Nuclear Receptors
Journal Methods in Molecular Biology
Quellenangaben Volume: 1966, Issue: , Pages: 39-70 Article Number: , Supplement: ,
Publisher Springer
Publishing Place Berlin [u.a.]
Reviewing status Peer reviewed
Institute(s) Institute of Diabetes and Cancer (IDC)