Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 496012
Title Characterization of in vivo DNA-binding events of plant transcription factors by ChIP-seq : Experimental protocol and computational analysis
Author(s) Mourik, Hilda Van; Muiño, J.M.; Pajoro, Alice; Angenent, G.C.; Kaufmann, Kerstin
Source In: Plant Functional Genomics: Methods and Protocols: Second Edition Springer New York LLC - ISBN 9781493924448 - p. 93 - 121.
DOI https://doi.org/10.1007/978-1-4939-2444-8_5
Department(s) Laboratory of Molecular Biology
PRI BIOS Plant Development Systems
Publication type Peer reviewed book chapter
Publication year 2015
Keyword(s) ChIP-seq data analysis - Chromatin immunoprecipitation - Plant transcription factors - Transcription factor DNA-binding sites
Abstract

Chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) is a powerful technique for genome-wide identification of in vivo binding sites of DNA-binding proteins. The technique had been used to study many DNA-binding proteins in a broad variety of species. The basis of the ChIP-seq technique is the ability to covalently cross-link DNA and proteins that are located in very close proximity. This allows the use of an antibody against the (tagged) protein of interest to specifically enrich DNAfragments bound by this protein. ChIP-seq can be performed using antibodies against the native protein or against tagged proteins. Using a specific antibody against a tag to immunoprecipitate tagged proteins eliminates the need for a specific antibody against the native protein and allows more experimental flexibility. In this chapter we present a complete workflow for experimental procedure and bioinformatic analysis that allows wet-lab biologists to perform and analyze ChIP-seq experiments.

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