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| Status |
Public on Feb 06, 2014 |
| Title |
Identification of transcription factor binding sites from ChIP-seq data at high-resolution |
| Organism |
Drosophila melanogaster |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Genome-wide mapping of protein–DNA interactions is essential for a full understanding of transcriptional regulation. A precise map of binding sites for transcription factors, core transcriptional machinery is vital for deciphering the gene regulatory networks that underlie various biological processes. Chromatin immunoprecipitation followed by sequencing (ChIP–seq) is a technique for genome-wide profiling of DNA-binding proteins. However, our conventional ChIP–seq occasionally gives wider peaks which might be due to overlapping binding sites of two or more transcription factors. Therefore, to improve the resolution of our conventional ChIP–seq which have DNA-protein footprint of ~100 bp, we decreased the size of DNA-protein footprint to ~ 50 bp by DNaseI digestion of whole cell extract (WCE).
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| Overall design |
ChIP-seq for Twist transcription factor in Drosophila embryos
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| Contributor(s) |
Bafna S, Bardet AF, Steinmann J, Stark A, Zeitlinger J |
| Citation(s) |
23980024 |
| Submission date |
Sep 06, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Samuel Richard Meier |
| E-mail(s) |
srm@stowers.org
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| Phone |
816-926-4455
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| Organization name |
Stowers Institute for Medical Research
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| Lab |
Computational Biology
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| Street address |
1000 E 50th Street
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| City |
Kansas City |
| State/province |
MO |
| ZIP/Postal code |
64110 |
| Country |
USA |
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| Platforms (1) |
| GPL11203 |
Illumina Genome Analyzer IIx (Drosophila melanogaster) |
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| Samples (10)
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| GSM998948 |
Twist ChIP-Seq from 2-4 h wild type embryos, rep1 |
| GSM998949 |
Twist ChIP-Seq from 2-4 h wild type embryos, rep2 |
| GSM998950 |
Twist ChIP-Seq from 2-4 h wild type embryos, rep3 |
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| Relations |
| BioProject |
PRJNA174520 |
| SRA |
SRP015450 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE40664_RAW.tar |
1.4 Gb |
(http)(custom) |
TAR (of BED) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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