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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 24, 2008 |
| Title |
Genome-Wide Mapping of in Vivo Protein-DNA Interactions |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
In vivo protein-DNA interactions connect each transcription factor with its direct targets to form a gene network scaffold. To map these protein-DNA interactions comprehensively across entire mammalian genomes, we developed a large-scale chromatin immunoprecipitation assay (ChIPSeq) based on direct ultrahigh-throughput DNA sequencing. This sequence census method was then used to map in vivo binding of the neuron-restrictive silencer factor (NRSF; also known as REST, for repressor element–1 silencing transcription factor) to 1946 locations in the human genome. The data display sharp resolution of binding position [±50 base pairs (bp)], which facilitated our finding motifs and allowed us to identify noncanonical NRSF-binding motifs. These ChIPSeq data also have high sensitivity and specificity [ROC (receiver operator characteristic) area ≥ 0.96] and statistical confidence (P < 10−4), properties that were important for inferring new candidate interactions. These include key transcription factors in the gene network that regulates pancreatic islet cell development.
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| Overall design |
Exam NRSF binding in Jurkat T cell line
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| Contributor(s) |
Johnson DS, Mortazavi A, Myers RM, Wold B |
| Citation(s) |
17540862 |
| Submission date |
Oct 03, 2008 |
| Last update date |
Feb 21, 2019 |
| Contact name |
Shujun Luo |
| E-mail(s) |
sluo@illumina.com
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| Organization name |
Illumina inc
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| Street address |
25861 Industrial Blvd
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| City |
Hayward |
| State/province |
CA |
| ZIP/Postal code |
94545 |
| Country |
USA |
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| Platforms (1) |
| GPL9052 |
Illumina Genome Analyzer (Homo sapiens) |
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| Samples (2) |
| GSM327023 |
NRSF_ChIPSeq: Antibody: NRSF |
| GSM327024 |
NRSF_ChIPSeq: Antibody: no antibody, mock |
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| Relations |
| BioProject |
PRJNA109959 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE13047_RAW.tar |
381.8 Mb |
(http)(custom) |
TAR (of TXT) |
| GSE13047_README.txt |
465 b |
(ftp)(http) |
TXT |
| Processed data provided as supplementary file |
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