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Series GSE26186 Query DataSets for GSE26186
Status Public on Jan 16, 2011
Title Broad chromosomal domains of histone modification patterns in C. elegans
Project modENCODE
Organism Caenorhabditis elegans
Experiment type Genome binding/occupancy profiling by genome tiling array
Summary Chromatin immunoprecipitation identifies specific interactions between genomic DNA and proteins, advancing our understanding of gene-level and chromosome-level regulation. Based on chromatin immunoprecipitation experiments using validated antibodies, we define the genome-wide distributions of 19 histone modifications, one histone variant, and eight chromatin-associated proteins in Caenorhabditis elegans embryos and L3 larvae. Cluster analysis identified five groups of chromatin marks with shared features: two groups correlate with gene repression, two with gene activation, and one with the X chromosome. The X chromosome displays numerous unique properties, including enrichment of monomethylated H4K20 and H3K27, which correlate with the different repressive mechanisms that operate in somatic tissues and germ cells, respectively. The data also revealed striking differences in chromatin composition between the autosomes and between chromosome arms and centers. Chromosomes I and III are globally enriched for marks of active genes, consistent with containing more highly expressed genes, compared to chromosomes II, IV, and especially V. Consistent with the absence of cytological heterochromatin and the holocentric nature of C. elegans chromosomes, markers of heterochromatin such as H3K9 methylation are not concentrated at a single region on each chromosome. Instead, H3K9 methylation is enriched on chromosome arms, coincident with zones of elevated meiotic recombination. Active genes in chromosome arms and centers have very similar histone mark distributions, suggesting that active domains in the arms are interspersed with heterochromatin-like structure. These data, which confirm and extend previous studies, allow for in-depth analysis of the organization and deployment of the C. elegans genome during development.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

This SuperSeries is composed of the SubSeries listed below.
 
Overall design Refer to individual Series.
 
Citation(s) 21177964
BioProject PRJNA135009
Submission date Dec 20, 2010
Last update date Feb 02, 2015
Contact name DCC modENCODE
E-mail(s) help@modencode.org
Phone 416-673-8579
Organization name Ontario Institute for Cancer Research
Lab modENCODE DCC
Street address MaRS Centre, South Tower, 101 College Street, Suite 800
City Toronto
State/province Ontario
ZIP/Postal code M5G 0A3
Country Canada
 
Platforms (5)
GPL4614 NimbleGen_DesignID3426_UNC_LiebLab tiling array
GPL4619 NimbleGen_DesignID3427_UNC_LiebLab tiling array
GPL7685 UNC Celegans 2.1mil HX1 (C elegans ChIP HX1)
Samples (109)
GSM147959 DPY-27 IP1 array1
GSM147967 SDC-3 IP1 array1
GSM147968 DPY-27 IP2 array1
This SuperSeries is composed of the following SubSeries:
GSE6739 ChIP-chip analysis of Dosage Compensation complex members SDC-3 and DPY-27 in C elegans wild type embryos.
GSE10201 ChIP-chip analysis of HTZ-1 and RNA Polymerase II in wildtype (N2) embryos
GSE16621 Analysis of SDC-2, DPY-26, MIX-1, DPY-27 and RNA Polymerase II ChIP-chip and RNA abundance in C. elegans

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE26186_RAW.tar 7.7 Gb (http)(custom) TAR (of GFF, GFF3, PAIR, TXT, WIG)

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