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Series GSE7118 Query DataSets for GSE7118
Status Public on Mar 01, 2007
Title Ludwig Institute/UCSD ENCODE project March 2007 Release
Project Pilot ENCODE
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by genome tiling array
Summary The readout of genome information is controlled by transcriptional regulatory elements, but a comprehensive view of the combinatorial control by these DNA sequences, which bind regulatory protein and/or the modified histones in regulating gene transcription, is clearly preliminary. We have developed an experimental strategy for comprehensive determination of such functional elements in human DNA. This strategy involves the application of genome-wide location analysis, also known as ChIP-chip, to a panel of well-characterized regulatory proteins and histones with specific modifications, known to generally associate with transcriptional regulatory elements in vivo. Identification of their genomic binding sites will allow us to determine the sequence features in the human genome that carry out transcriptional regulatory function. We have designed and produced DNA microarrays to represent all the non-repetitive sequences in the 30 million basepair ENCODE regions of the human genome to map various types of transcriptional regulatory elements in three model cell types. We have identified promoters by mapping the genomic sequences associated with RNA polymerase II and the general transcription factor TFIID in cells, enhancer elements by mapping the genomic sequences associated with transcriptional co-activators and enhancer-specific chromatin modifications, and insulators by mapping the genomic sequences associated with the insulator binding protein CTCF. The raw microarray results are released periodically prior to publication.
Keywords: ChIP-chip ENCODE
 
Overall design ChIP-chip analyses were performed for various transcription factors and chromatin modifications in various cell types. Details to be described in publications.
Web link http://www.ncbi.nlm.nih.gov/projects/geo/info/ENCODE.html
 
Contributor(s) Ren B, Glass CK, Rosenfeld MG, Webster N, Ching KA, Harp L, Ye Z, Stuart RK, Calcar SV, Kim TH, Hawkins RD, Hon G, Barrera LO, Luna R, Wang K
Citation(s) 19295514, 18927605
BioProject PRJNA63415
Submission date Feb 23, 2007
Last update date Jun 28, 2012
Contact name Bing Ren
E-mail(s) biren@ucsd.edu
Organization name Ludwig Institute for Cancer Research
Department Department of Cellular and Molecular Medicine
Lab Laboratory of Gene Regulation
Street address 9500 Gilman Drive
City La Jolla
State/province CA
ZIP/Postal code 92093-0653
Country USA
 
Platforms (2)
GPL1454 RenLab ENCODE PCR tiling array
GPL4559 ENCODE NimbleGen hg17 tiling array
Samples (124)
GSM171017 p300(C-20) IMR90 RenLab ENCODE PCR tiling array replicate 3 slide ENC1681p300
GSM171018 H3K4me1 IMR90 RenLab ENCODE PCR tiling array replicate 3 slide ENC1681H3K4me1
GSM171020 H2A.Z HeLa RenLab ENCODE PCR tiling array replicate 1 ENC1217

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
GSE7118_RAW.tar 631.0 Mb (http)(custom) TAR (of GPR, PAIR)

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