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Input Strategy for Improving Analysis of ChIP-exo Data and Beyond [RNA-Seq]

ABSTRACT: Several recently emerging ChIP-seq (chromatin immunoprecipitation followed by sequencing) based methods perform chemical steps on bead-bound immunoprecipitated chromatin, posing a challenge for generating similarly treated input controls required for bioinformatics and data quality analyses. Here we present a versatile method for producing technique-specific input controls for ChIP-based methods that utilize additional bead-bound processing steps. Application of this method allowed for discovery of a novel CTCF binding motif from ChIP-exo data.

ORGANISM(S): Homo sapiens

PROVIDER: GSE79564 | GEO | 2016/08/24

SECONDARY ACCESSION(S): PRJNA316189

REPOSITORIES: GEO

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PAtCh-Cap: input strategy for improving analysis of ChIP-exo data sets and beyond

Project description:Recently, a number of advances have been implemented into the core ChIP-seq (chromatin immunoprecipitation coupled with next-generation sequencing) methodology to streamline the process, reduce costs or improve data resolution. Several of these emerging ChIP-based methods perform additional chemical steps on bead-bound immunoprecipitated chromatin, posing a challenge for generating similarly treated input controls required for artifact removal during bioinformatics analyses. Here we present a versatile method for producing technique-specific input controls for ChIP-based methods that utilize additional bead-bound processing steps. This reported method, termed protein attached chromatin capture (PAtCh-Cap), relies on the non-specific capture of chromatin-bound proteins via their carboxylate groups, leaving the DNA accessible for subsequent chemical treatments in parallel with chromatin separately immunoprecipitated for the target protein. Application of this input strategy not only significantly enhanced artifact removal from ChIP-exo data, increasing confidence in peak identification and allowing for de novo motif searching, but also afforded discovery of a novel CTCF binding motif.

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Input Strategy for Improving Analysis of ChIP-exo Data and Beyond

Project description:Input Strategy for Improving Analysis of ChIP-exo Data and Beyond

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Input Strategy for Improving Analysis of ChIP-exo Data and Beyond

Project description:This SuperSeries is composed of the SubSeries listed below.

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Project description: Not available

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