Genomics

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


ABSTRACT: 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.

ORGANISM(S): Musculus  

SUBMITTER: Steven Henikoff   Peter J Skene  Jorja Henikoff 

PROVIDER: E-GEOD-67454 | ArrayExpress | 2015-06-12

SECONDARY ACCESSION(S): GSE67454SRP056749PRJNA279984

REPOSITORIES: GEO, ArrayExpress, ENA

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