Xenopus tropicalis ChIP-on-chip microarray designs


Whole genome and promoter genome tilepath designs

Chromatin immunoprecipitation (ChIP) combined with genome tile path microarrays (ChIP-chip) can be used to study genome-wide epigenetic profiles and the transcription factor binding repertoire.
Two Roche NimbleGen genome tile path ChIP-chip designs for interrogating the Xenopus tropicalis genome have been developed:
   (1) A whole-genome microarray design (5-array set), and
   (2) an experimentally defined promoter array, based on 5' ends of transcription units decorated with histone H3 lysine 4 trimethylation in gastrula stage embryos.
These microarray designs can be used to study epigenetic phenomena and transcription factor binding in developing Xenopus embryos.


Robert C. Akkers*, Simon J. van Heeringen*, J. Robert Manak, Roland D. Green, Hendrik G. Stunnenberg and Gert Jan C. Veenstra. 2010. ChIP-chip designs to interrogate the genome of Xenopus embryos for transcription factor binding and epigenetic regulation. PLoS ONE, 5, e8820 (doi:10.1371/journal.pone.0008820).
PLoS ONE Open Access         


The microarray designs can be downloaded as compressed NimbleGen design files (ndf) from the table below. These are optimized designs (v2) which include additional control probes. In addition, the small scaffolds were distributed over the five arrays of the genome-wide 5-array tile path design.

WG: Whole genome 5-array set covering the complete X.tropicalis genome, with the exclusion of of repeat-masked regions. A separate design file for each microarray (1-5).
Promoter: Single array design covering genomic regions enriched for H3K4me3 in gastrula stage embryos (i.e. experimentally verified active promoters), in addition to 5' regions of all annotated genes (JGI FilteredModels, v1).

Genome assembly: Joint Genome Institute version 4.1 (xenTro2, August 2005).

File Name: Date Created: File Size:
 Promoter_081002_XT41_H3K4me3_ChIP_v2_HX1.ndf.gz  12/18/2009 97,189 KB
 WG_080603_XT41_GV_v2_ChIP_1_HX1.ndf.gz  12/23/2009 117,725 KB
 WG_080603_XT41_GV_v2_ChIP_2_HX1.ndf.gz  1/4/2010 107,979 KB
 WG_080603_XT41_GV_v2_ChIP_3_HX1.ndf.gz  1/4/2010 111,655 KB
 WG_080603_XT41_GV_v2_ChIP_4_HX1.ndf.gz  1/4/2010 104,126 KB
 WG_080603_XT41_GV_v2_ChIP_5_HX1.ndf.gz  1/4/2010 116,345 KB

The microarray data and the earlier version of the microarray designs (v1) have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE19413.

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Radboud University Faculty of Science Radboud Institute for Molecular Life Sciences Dept. Molecular Developmental Biology