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E-GEOD-40664 - Identification of transcription factor binding sites from ChIP-seq data at high-resolution

Status
Released on 6 February 2014, last updated on 18 February 2014
Organism
Drosophila melanogaster
Samples (10)
Protocols (12)
Description
Genome-wide mapping of protein–DNA interactions is essential for a full understanding of transcriptional regulation. A precise map of binding sites for transcription factors, core transcriptional machinery is vital for deciphering the gene regulatory networks that underlie various biological processes. Chromatin immunoprecipitation followed by sequencing (ChIP–seq) is a technique for genome-wide profiling of DNA-binding proteins. However, our conventional ChIP–seq occasionally gives wider peaks which might be due to overlapping binding sites of two or more transcription factors. Therefore, to improve the resolution of our conventional ChIP–seq which have DNA-protein footprint of ~100 bp, we decreased the size of DNA-protein footprint to ~ 50 bp by DNaseI digestion of whole cell extract (WCE). ChIP-seq for Twist transcription factor in Drosophila embryos
Experiment type
ChIP-seq 
Contacts
Samuel Richard Meier <srm@stowers.org>, Alexander Stark, Anais F Bardet, Jonas Steinmann, Julia Zeitlinger, Sangeeta Bafna
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
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