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Series GSE15807 Query DataSets for GSE15807
Status Public on Nov 05, 2009
Title The network of targeting interactions in chromatin
Organism Drosophila melanogaster
Experiment type Genome binding/occupancy profiling by array
Genome binding/occupancy profiling by genome tiling array
Summary In eukaryotes, many chromatin proteins together regulate gene expression.
Chromatin proteins often direct the genomic binding pattern of other chromatin proteins, for example by recruitment or competition mechanisms.
The network of such targeting interactions in chromatin is complex and still poorly understood. Based on genome-wide binding maps, we constructed a network model of the targeting interactions among a broad set of 43 chromatin components in Drosophila cells. This model predicts many novel functional relationships. For example, we identified mechanisms that determine the distinct genomic binding patterns of the heterochromatin components HP3 and Su(var)3-7. We also discovered a central role for the remodeling factor Brahma in the targeting of several DNA-binding factors.
Furthermore, the interaction network consists of several sub-networks that regulate distinct groups of genes. Our network model provides a global view of the targeting interplay among dozens of chromatin components.
For this study, we used 36 published datasets, representing various chromatin components, as well as 7 newly generated DamID profiles. Additionally, we generated DamID profiles of 4 proteins and a profile of differential accessibility in Brm knockdown vs. control cells.
 
Overall design DamID experiments for multiple chromatin proteins was performed in Drosophila cell cultures. Samples were hybridized to spotted cDNA arrays. Every experiment was done at least in duplicate with one sample in the reverse dye orientation. Where indicated, one biological sample was hybridized to two arrays (a and b) in the same dye orientation; values from these arrays were first averaged before averaging dye-swapped biological replicates. Samples represent averaged results of replicates. A metadata file and a value matrix for the individual replicates are linked below as supplementary files.

Change in chromatin accessibility was probed by Dam methylase expression in white vs. brahma RNAi treated Kc167 cells. Material from two test and control experiments was isolated according to DamID procedure and co-hybridized in reverse dye orientations. Sample represents averaged results of replicates. A metadata file and a value matrix for the individual replicates are linked below as supplementary files. An additional processed data file 'GATCfragments_deltaAcc.gff' whose rows represent normalized values averaged per GATC fragment rather than normalized values per array reporter is linked below as a supplementary file.
 
Contributor(s) van Steensel B, Braunschweig U, Filion GJ, Chen M, van Bemmel JG, Ideker T
Citation(s) 20007327
Submission date Apr 23, 2009
Last update date Jun 26, 2012
Contact name Bas van Steensel
E-mail(s) b.v.steensel@nki.nl
Phone + 31 20 512 2040
Fax +31 20 669 1383
URL http://www.nki.nl/nkidep/vansteensel
Organization name Netherlands Cancer Institute
Department division of Molecular Biology
Lab van Steensel group
Street address Plesmanlaan 121
City Amsterdam
ZIP/Postal code 1066 CX
Country Netherlands
 
Platforms (2)
GPL1908 FHCRC Fly 12K v1.0
GPL8471 NimbleGen Drosophila 385k array rel4 300bp
Samples (16)
GSM397253 Embryonic Drosophila cells, Kc167 cells, Dnmt2 DamID
GSM397254 Embryonic Drosophila cells, Kc167 cells, Rpd3 DamID
GSM397255 Embryonic Drosophila cells, Kc167 cells, DSP1 DamID
Relations
BioProject PRJNA116717

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
GSE15807_GATCfragments_deltaAcc.gff.gz 3.0 Mb (ftp)(http) GFF
GSE15807_RAW.tar 167.1 Mb (http)(custom) TAR (of TXT)
GSE15807_matrix_replicates_DamID.txt.gz 2.9 Mb (ftp)(http) TXT
GSE15807_matrix_replicates_deltaAccess.txt.gz 14.7 Mb (ftp)(http) TXT
GSE15807_metadata_replicates_DamID.txt.gz 3.2 Kb (ftp)(http) TXT
GSE15807_metadata_replicates_deltaAccess.txt.gz 979 b (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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