ChIP-Seq Data Analysis: Identification of Protein–DNA Binding Sites with SISSRs Peak-Finder

Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 802)

Abstract

Protein–DNA interactions play key roles in determining gene-expression programs during cellular development and differentiation. Chromatin immunoprecipitation (ChIP) is the most widely used assay for probing such interactions. With recent advances in sequencing technology, ChIP-Seq, an approach that combines ChIP and next-generation parallel sequencing is fast becoming the method of choice for mapping protein–DNA interactions on a genome-wide scale. Here, we briefly review the ChIP-Seq approach for mapping protein–DNA interactions and describe the use of the SISSRs peak-finder, a software tool for precise identification of protein–DNA binding sites from sequencing data generated using ChIP-Seq.

Key words

ChIP-Seq SISSRs Protein–DNA interaction Binding sites Transcription factor Next-generation sequencing Genomics 

Notes

Acknowledgments

This work was supported by the Intramural Research Program of the National Institutes of Health, National Institute of Environmental Health Sciences (Project number ES102625–02 to R.J.).

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.National Institutes of Environmental Health Sciences, National Institutes of HealthResearch Triangle ParkUSA
  2. 2.Centre for Modeling and SimulationUniversity of PunePuneIndia

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