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ChIP-chip Designs to Interrogate the Xenopus Embryo Genome for Transcription Factor Binding and Epigenetic Regulation


ABSTRACT: Background: Chromatin immunoprecipitation combined with genome tile path microarrays or deep sequencing can be used to study genome-wide epigenetic profiles and the transcription factor binding repertoire. Although well studied in a variety of cell lines, these genome-wide profiles have so far been little explored in vertebrate embryos. Principal findings: Here we report on two genome tile path ChIP-chip designs for interrogating the Xenopus tropicalis genome. In particular, a whole-genome microarray design was used to identify active promoters by close proximity to histone H3 lysine 4 trimethylation. A second microarray design features these experimentally derived promoter regions in addition to currently annotated 5’ ends of genes. Conclusions: A whole-genome and a dedicated promoter microarray design was developed which can be used to study epigenetic phenomena and transcription factor binding in developing Xenopus embryos. H3K4me3 and TBP ChIP-chip on Xenopus tropicalis tiling arrays

ORGANISM(S): Xenopus (Silurana) tropicalis

SUBMITTER: Robert Akkers 

PROVIDER: E-GEOD-19413 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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ChIP-chip designs to interrogate the genome of Xenopus embryos for transcription factor binding and epigenetic regulation.

Akkers Robert C RC   van Heeringen Simon J SJ   Manak J Robert JR   Green Roland D RD   Stunnenberg Hendrik G HG   Veenstra Gert Jan C GJ  

PloS one 20100121 1


<h4>Background</h4>Chromatin immunoprecipitation combined with genome tile path microarrays or deep sequencing can be used to study genome-wide epigenetic profiles and the transcription factor binding repertoire. Although well studied in a variety of cell lines, these genome-wide profiles have so far been little explored in vertebrate embryos.<h4>Principal findings</h4>Here we report on two genome tile path ChIP-chip designs for interrogating the Xenopus tropicalis genome. In particular, a whole  ...[more]

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