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Wardle FC
Odom DT
Bell GW
Yuan B
Danford TW
Wiellette EL
Herbolsheimer E
Sive HL
Young RA
Smith JC

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Wardle FC
Odom DT
Bell GW
Yuan B
Danford TW
Wiellette EL
Herbolsheimer E
Sive HL
Young RA
Smith JC
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Zebrafish promoter microarrays identify actively transcribed embryonic genes

Fiona C Wardle¹ , Duncan T Odom² , George W Bell² , Bingbing Yuan², Timothy W Danford³ , Elizabeth L Wiellette²^,4 , Elizabeth Herbolsheimer² , Hazel L Sive² , Richard A Young² and James C Smith¹

¹Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Zoology, Cambridge University, Cambridge CB2 1QN, UK

²Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA

³Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Vassar Street, Cambridge, MA 02139, USA

⁴Novartis Institutes for Biomedical Research, Mass Ave, Cambridge, MA 02139, USA

author email corresponding author email

Genome Biology 2006, 7:R71doi:10.1186/gb-2006-7-8-r71


Published:	4 August 2006

Subject areas: Genome studies, Development, Model organisms

Additional files

Additional data file 1:

Anti-H3 and anti-H3K4Me3 antibodies were use to ChIP DNA from gastrula stage embryos. PCR was performed on this DNA and on whole cell extract DNA that was not immunoprecipitated with primers designed against the promoter region of rhodopsin, bactin2 and wnt11. As expected, rhodopsin, which is not expressed at gastrula stages, was not enriched over anti-H3, where as bactin2, which is expressed ubiquitously, and wnt11, which is a mesodermally expressed gene, are both enriched over H3.

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Additional data file 2:

The zebrafish ChIP-Chip protocol, giving detailed information of the experimental procedure used

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Additional data file 3:

Sequences of primers used in RT-PCR analysis and cycling conditions for each primer pair are given

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Additional data file 4:

Probes showing enrichment in ChIP-chip analysis. Each probe is given a chromosome and chromosomal position based on Zv4 zebrafish genome assembly

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Additional data file 5:

Genes and transcripts associated with a genomic region or probe that is enriched in ChIP-chip analysis

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Additional data file 6:

Genes that are reported not to be expressed at gastrula stages and indicate if the gene is bound (probes at the 5' end of the gene are enriched in ChIP-chip analysis), or not bound (probes show no significant enrichment). The table also shows the results of RT-PCR analysis on selected genes

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Additional data file 7:

genes that are reported to be expressed at the gastrula stage and indicate if the gene is bound (probes at the 5' end of the gene are enriched in ChIP-chip analysis), or not bound (probes show no significant enrichment)

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