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Series GSE13217 Query DataSets for GSE13217
Status Public on Dec 12, 2008
Title Genome-wide profiling of salt fractions maps physical properties of chromatin
Project modENCODE
Organism Drosophila melanogaster
Experiment type Genome binding/occupancy profiling by genome tiling array
Summary We applied genome-wide profiling to successive salt-extracted fractions of micrococcal nuclease-treated Drosophila chromatin. Chromatin fractions extracted with 80mM or 150mM NaCl after digestion contain predominantly mononucleosomes and represent calssical 'active' chromatin. Profiles of these low-salt-soluble fractions display phased nucleosomes over transcriptionally active genes that are locally depleted of histone H3.3 and correspond closely to profiles of RNA polymerase II. Nearly quantitative recovery of chromatin is obtained with 600mM NaCl, however, the remaining insoluble chromatin is enriched in actively transcribed regions. Salt-insoluble chromatin likely represents oligonucleosomes that are attached to large protein complexes. Both low-salt extracted and insoluble chromatin are rich in sequences that correspond to epigenetic regulatory elements genome-wide. The presence of active chromatin at both extremes of salt solubility suggests that these salt fractions capture bound and unbound intermediates in active processes, thus providing a simple, powerful strategy for mapping epigenome dynamics.

Keywords: Chromatin affinity-purification on microarray

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, streptavidin-bound biotin-tagged histone-variant-containing chromatin to whole EDTA-extracted soluble chromatin, or oligo(dT)-primed cDNA to randomly fragmented genomic DNA from S2 cell nuclei.
Web link
Contributor(s) Henikoff S, Ahmad K
Citation(s) 19088306, 20508129
BioProject PRJNA63463
Submission date Oct 15, 2008
Last update date Aug 28, 2018
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 (2)
GPL1322 [Drosophila_2] Affymetrix Drosophila Genome 2.0 Array
GPL6888 Henikoff_Dmel_r52_ChIP tiling design
Samples (47)
GSM333832 150-600_fraction_1_(Av-N_185168-1)
GSM333833 H3.3_150_(3L_185168-2)
GSM333834 H3_150-600_(H36_185170-3)

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
GSE13217_RAW.tar 5.1 Gb (http)(custom) TAR (of BEDGRAPH, CEL, GFF, PAIR, TXT)
GSE13217_figure_GSMs.txt 1.7 Kb (ftp)(http) TXT
GSE13217_readme.txt 363 b (ftp)(http) TXT
Processed data included within Sample table

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