Single array to study protein/DNA interactions in over 25,500 human promoters
- High-density 35 bp probe spacing offers more probes per promoter for the most accurate view of protein/DNA interactions
- Extensive 10 kb coverage for each promoter region ensures the most comprehensive promoter analysis
- 25-mer probes yield the most specific hybridization results available
- Economical single array design you can use in your own lab
The GeneChip® 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 GenBank®, 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 GeneChip® Human Tiling 2.0R Array Set (P/N 900772).
Data Sheets
Human Tiling Arrays (pdf, 260 KB)
Archived Presentations
Scientific Forum, 1st European ChIP-on-chip
Webinar, Six-part ChIP-on-chip Symposia Series
Application Notes
| Part # | Description | Details |
|---|---|---|
| 900775 | GeneChip® Human Promoter 1.0R Array | 2 Arrays |
| 900776 | GeneChip® Human Promoter 1.0R Array | 6 Arrays |
| 900777 | GeneChip® Human Promoter 1.0R Array | 30 Arrays |
Required Products
| Part # | Description | Details |
|---|---|---|
| 00-0211 | GeneChip® Scanner 3000 7G | See Product Page |
Related Products
| Part # | Description | Details |
|---|---|---|
| Integrated Genome Browser (IGB) | Available Via Download | |
| Affymetrix Tiling Analysis Software (TAS) | Available Via Download | |
| 900301 | Control Oligo B2, 3nM | Sufficient for 30 samples |
| 900812 | GeneChip® WT Double-Stranded DNA Terminal Labeling Kit | Sufficient for 30 reactions |
Manuals
Chromatin Immunoprecipitation Assay Protocol (pdf, 679 KB)
Tutorial
Library Files
GeneChip Tiling Arrays - Data Analysis Library File Updates
Human Promoter 1.0R Array (zip, 132 MB)
Human Promoter Array 1.0 R NCBIv36 Annotation Bundle
Human Promotor Tiling Array NCBIv36 BPMAP file
Human Promotor Tiling Array NCBIv36 probe bed file
Package Inserts
Human Promoter 1.0R Array (pdf, 489 KB)
Human Promoter 1.0R Array (pdf, 489 KB)
Additional Support
CEL Files, Human Promoter 1.0R Array (zip, 84 MB)
