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| Status |
Public on Dec 08, 2009 |
| Title |
A native chromatin purification system for epigenomic profiling in C. elegans |
| Project |
modENCODE
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| Organism |
Caenorhabditis elegans |
| Experiment type |
Genome binding/occupancy profiling by genome tiling array
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| Summary |
We describe an in vivo chromatin purification system for genome-wide epigenetic profiling in C. elegans. In this system, we coexpressed the E. coli biotin ligase enzyme (BirA), together with the C. elegans H3.3 gene fused to BioTag, a 23-amino acid peptide serving as a biotinylation substrate for BirA, in vivo in worms. We developed methods to isolate chromatin under different salt extraction conditions, followed by affinity purification of biotinylated chromatin with streptavidin and genome-wide profiling with microarrays.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
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| Overall design |
All experiments were done using two channels per chip, comparing DNAs extracted from either salt-extracted or insoluble chromatin to whole nuclear chromatin, whole nuclear chromatin to randomly fragmented genomic DNA, streptavidin-bound biotin-tagged histone-variant-containing chromatin to salt-extracted chromatin, gel-purified mononucleosomes to whole EDTA-extracted soluble chromatin, or streptavidin-bound biotin-tagged histone-variant-containing chromatin to whole EDTA-extracted soluble chromatin to randomly fragmented DNA from embryo nuceli.
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| Web link |
http://www.ncbi.nlm.nih.gov/projects/geo/info/ENCODE.html
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| Contributor(s) |
Henikoff S, Ooi S |
| Citation(s) |
19966274 |
| BioProject |
PRJNA63461 |
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| Submission date |
Nov 04, 2009 |
| Last update date |
Jun 28, 2012 |
| Contact name |
Jorja Henikoff |
| E-mail(s) |
jorja@fhcrc.org
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| Phone |
206-667-4850
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| Organization name |
Fred Hutchinson Cancer Research Center
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| Department |
Basic Sciences
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| Lab |
Henikoff
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| Street address |
1100 Fairview AV N, A1-162
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109-1024 |
| Country |
USA |
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| Platforms (1) |
| GPL7098 |
NimbleGen C_elegans_WS170_Tiling_Iso_HX1 tiling design |
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| Samples (18)
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| Supplementary file |
Size |
Download |
File type/resource |
| GSE18898_RAW.tar |
2.5 Gb |
(http)(custom) |
TAR (of BEDGRAPH, GFF, PAIR, TXT) |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
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