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Series GSE18898 Query DataSets for GSE18898
Status Public on Dec 08, 2009
Title A native chromatin purification system for epigenomic profiling in C. elegans
Project modENCODE
Organism Caenorhabditis elegans
Experiment type Genome binding/occupancy profiling by genome tiling array
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 and
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.
Web link
Contributor(s) Henikoff S, Ooi S
Citation(s) 19966274
BioProject PRJNA63461
Submission date Nov 04, 2009
Last update date Jun 28, 2012
Contact name Jorja Henikoff
Phone 206-667-4850
Organization name Fred Hutchinson Cancer Research Center
Department Basic Sciences
Lab Henikoff
Street address 1100 Fairview AV N, A1-162
City Seattle
State/province WA
ZIP/Postal code 98109-1024
Country USA
Platforms (1)
GPL7098 NimbleGen C_elegans_WS170_Tiling_Iso_HX1 tiling design
Samples (18)
GSM468560 H3.3_350mM_salt_fraction_(SOH12)
GSM468561 80mM_salt_fraction_1_(SOH18)
GSM468563 H3.3_600mM_salt_fraction_1_(SOH21)

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
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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