Genomics

Dataset Information

155

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. Overall design: HeLa cells were transfected with either a scrambled siRNA or one of two CTCF siRNAs (Thermo Fisher Scientific ? Life technologies) using Lipofectamine RNAiMAX (Thermo Fisher Scientific - Life technologies) and incubated for 24 hr.

INSTRUMENT(S): Illumina Genome Analyzer (Homo sapiens)

SUBMITTER: Bethany Buck-Koehntop  

PROVIDER: GSE79564 | GEO | 2016-08-24

SECONDARY ACCESSION(S): PRJNA316189

REPOSITORIES: GEO

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Publications

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

Terooatea Tommy W TW   Pozner Amir A   Buck-Koehntop Bethany A BA  

Nucleic acids research 20160822 21


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 ve  ...[more]

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