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Platform GPL5082 Query DataSets for GPL5082
Status Public on Apr 13, 2007
Title [Hs_PromPR] Affymetrix Human Promoter 1.0R Array
Technology type in situ oligonucleotide
Distribution commercial
Organism Homo sapiens
Manufacturer Affymetrix
Manufacture protocol see manufacturer's web site
Catalog number 900775
 
Description The GeneChipĀ® Human Promoter 1.0R Array is designed for chromatin immunoprecipitation (ChIP) experiments. The Human Promoter Array is a single array comprised of over 4.6 million probes tiled through over 25,500 human promoter regions. Sequences used in the design of the Human Promoter array were selected from NCBI human genome assembly (Build 34). Repetitive elements were removed by RepeatMasker. Promoter regions were selected using sequence information from:

35,685 ENSEMBL genes (version 21_34d, May 14, 2004)
25,172 RefSeq mRNAs (NCBI GenBankĀ®, February 7, 2004)
47,062 complete-CDS mRNA (NCBI GenBank, December 15, 2003)

Probes are tiled at an average resolution of 35 bp, as measured from the central position of adjacent 25-mer oligos, leaving a gap of approximately 10 bp between probes. Each promoter region covers approximately 7.5 kb upstream through 2.45 kb downstream of 5' transcription start sites. For over 1,300 cancer-associated genes, coverage of promoter regions was expanded to include additional genomic content. This more extensive coverage spans from 10 kb upstream through 2.45 kb downstream of transcriptional start sites.

The array interrogates regions proximal to transcription start sites and contains probes for approximately 59 percent of CpG islands annotated by UCSC in NCBI human genome assembly (Build 34). The probes selected for the Human Promoter 1.0R Array are a subset of the probes used in the whole-genome ChIP array set, the GeneChipĀ® Human Tiling 2.0R Array Set (P/N 900772).

BPMAP and other files can be downloaded from the Affymetrix Web site below.
 
Web link http://www.affymetrix.com/products/arrays/specific/human_promoter.affx
http://www.affymetrix.com/support/technical/libraryfileupdatesmain.affx
Submission date Apr 13, 2007
Last update date Jan 21, 2015
Organization Affymetrix, Inc.
E-mail(s) geo@ncbi.nlm.nih.gov, support@affymetrix.com
Phone 888-362-2447
URL http://www.affymetrix.com/index.affx
Street address
City Santa Clara
State/province CA
ZIP/Postal code 95051
Country USA
 
Samples (608) GSM182106, GSM182107, GSM182108, GSM182109, GSM182110, GSM182111 
Series (79)
GSE7516 ChIP-chip analysis of human DREAM complex subunits in G0-arrested and S-phase synchronized cells
GSE10453 ChIP-chip from HCT116 cells with UbH2B and H3K4me2 coupled to expression analysis
GSE11413 Me-DIP-chip data from osteosarcoma cell lines

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp

Supplementary data files not provided

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