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E-GEOD-67454 - A simple method for generating high-resolution maps of genome wide protein binding

Status
Released on 12 June 2015, last updated on 21 June 2015
Organism
Drosophila melanogaster, Homo sapiens, Mus musculus
Samples (5)
Protocols (9)
Description
Chromatin immunoprecipitation (ChIP) and its derivatives are the main techniques used to determine transcription factor binding sites. However, conventional ChIP with sequencing (ChIP-seq) has problems with poor resolution and newer techniques require significant experimental alterations and complex bioinformatics. Here we build upon our high-resolution crosslinking ChIP-seq (X-ChIP-seq) method and compare it to existing methodologies. By using micrococcal nuclease, which has both endo- and exo-nuclease activity to fragment the chromatin and thereby generate precise protein-DNA footprints, high-resolution X-ChIP-seq achieves single base pair resolution of transcription factor binding. A significant advantage of this protocol is the minimal alteration to the conventional ChIP-seq workflow and simple bioinformatic processing. Using High-resolution X-ChIP-seq we determined the genome-wide binding profile of various DNA binding proteins.
Experiment type
ChIP-seq 
Contacts
Jorja Henikoff <jorja@fhcrc.org>, Peter J Skene, Steven Henikoff
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
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