|
| Status |
Public on Nov 08, 2012 |
| Title |
Genome-wide comparative ChIP-seq data of CTCF and RNA-seq data in Drosophila white prepupa on Illumina Genome Analyzer |
| Project |
modENCODE
|
| Organisms |
Drosophila melanogaster; Drosophila pseudoobscura; Drosophila simulans; Drosophila yakuba |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
|
| Summary |
This is a dataset which comprises the following two different kinds of genomic data in Drosophila species:
First, triplicate ChIP-seq data of CTCF (CCCTC binding factor) binding profiles in each of the four closely related Drosophila species : Drosophila melanogaster, Drosophila simulans, Drosophila yakuba and Drosophila pseudoobscura at white pre pupa stage;
Second, triplicate RNA-seq data of white pre pupa whole animals of three Drosophila species: Drosophila melanogaster, Drosophila simulans and Drosophila yakub. The binding site/region/peaks are called using a modified method of QuEST( please see details in our related publication). The sequence read counts and RPKM values are calculated following the method in Mortazavi et al 2008 Nature Methods paper.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
|
| |
|
| Overall design |
Examination of CTCF binding in 4 Drosophila species and their correlation with gene expression levels in the same development stages
|
| Web link |
http://www.ncbi.nlm.nih.gov/projects/geo/info/ENCODE.html
|
| |
|
| Contributor(s) |
Ni X, White KP |
| Citation(s) |
23139640 |
| |
| Submission date |
Sep 30, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Kevin P. White |
| E-mail(s) |
kpwhite@uchicago.edu
|
| Organization name |
University of Chicago
|
| Department |
Institute for Genomics and Systems Biology
|
| Street address |
900 E. 57th STR. 10th FL.
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60615 |
| Country |
USA |
| |
|
| Platforms (4)
|
| GPL9058 |
Illumina Genome Analyzer (Drosophila melanogaster) |
| GPL9394 |
Illumina Genome Analyzer (Drosophila simulans) |
| GPL9395 |
Illumina Genome Analyzer (Drosophila pseudoobscura) |
| GPL11000 |
Illumina Genome Analyzer (Drosophila yakuba) |
|
| Samples (21)
|
|
| Relations |
| SRA |
SRP003653 |
| BioProject |
PRJNA132691 |
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