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Series GSE24449 Query DataSets for GSE24449
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 and
Overall design Examination of CTCF binding in 4 Drosophila species and their correlation with gene expression levels in the same development stages
Web link
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
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)
Samples (21)
GSM602326 Dmel_WPP_CTCF_ChIPSeq_1, 2 and 3
GSM602327 Dmel_WPP_CTCF_Input_1
GSM602328 Dmel_WPP_CTCF_Input_2
SRA SRP003653
BioProject PRJNA132691

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE24449_RAW.tar 1.1 Gb (http)(custom) TAR (of BED, TXT, WIG)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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