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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.

ORGANISM(S): Xenopus tropicalis

PROVIDER: GSE19413 | GEO | 2009/12/17

SECONDARY ACCESSION(S): PRJNA121789

REPOSITORIES: GEO

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

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