|
| Status |
Public on Dec 17, 2009 |
| Title |
ChIP-chip Designs to Interrogate the Xenopus Embryo Genome for Transcription Factor Binding and Epigenetic Regulation |
| Organism |
Xenopus tropicalis |
| Experiment type |
Genome binding/occupancy profiling by genome tiling array
|
| Summary |
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.
|
| |
|
| Overall design |
H3K4me3 and TBP ChIP-chip on Xenopus tropicalis tiling arrays
|
| |
|
| Contributor(s) |
Akkers RC, van Heeringen SJ, Manak JR, Green RD, Stunnenberg HG, Veenstra GJ |
| Citation(s) |
20098671 |
| |
| Submission date |
Dec 10, 2009 |
| Last update date |
Apr 11, 2012 |
| Contact name |
Gert Jan Veenstra |
| E-mail(s) |
g.veenstra@science.ru.nl
|
| Phone |
+31 24 3610541
|
| Organization name |
Radboud University
|
| Department |
Molecular Developmental Biology
|
| Street address |
Geert Grooteplein 28
|
| City |
Nijmegen |
| ZIP/Postal code |
6525 GA |
| Country |
Netherlands |
| |
|
| Platforms (8)
|
| GPL9778 |
NimbleGen Xenopus tropicalis Whole Genome Tiling v1.0 slide 1 |
| GPL9779 |
NimbleGen Xenopus tropicalis Whole Genome Tiling v1.0 slide 2 |
| GPL9780 |
NimbleGen Xenopus tropicalis Whole Genome Tiling v1.0 slide 3 |
| GPL9781 |
NimbleGen Xenopus tropicalis Whole Genome Tiling v1.0 slide 4 |
| GPL9782 |
NimbleGen Xenopus tropicalis Whole Genome Tiling v1.0 slide 5a |
| GPL9783 |
NimbleGen Xenopus tropicalis Whole Genome Tiling v1.0 slide 5b |
| GPL9784 |
NimbleGen Xenopus tropicalis Whole Genome Tiling v1.0 slide 5c |
| GPL9785 |
NimbleGen Xenopus tropicalis Dedicated Promoter v1.0 |
|
| Samples (10)
|
|
| Relations |
| BioProject |
PRJNA121789 |
Less...
More...