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Series GSE62557 Query DataSets for GSE62557
Status Public on Dec 01, 2014
Title Mapping gene regulatory networks in Drosophila eye development by large-scale transcriptome perturbations and motif inference [ChIP-Seq]
Organism Drosophila melanogaster
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Genome control is operated by transcription factors (TF) controlling their target genes by binding to promoters and enhancers. Conceptually, the interactions between TFs, their binding sites, and their functional targets are represented by gene regulatory networks (GRN). Deciphering in vivo GRNs underlying organ development in an unbiased genome-wide setting involves identifying both functional TF-gene interactions and physical TF-DNA interactions. To reverse-engineer the GRN of eye development in Drosophila, we performed RNA-seq across 72 genetic perturbations and sorted cell types, and inferred a co-expression network. Next, we derived direct TF-DNA interactions using computational motif inference, ultimately connecting 241 TFs to 5632 direct target genes through 24926 enhancers. Using this network we found network motifs, cis-regulatory codes, and new regulators of eye development. We validate the predicted target regions of Grainyhead by ChIP-seq and identify this factor as a general co-factor in the eye network, being bound to thousands of nucleosome-free regions.
 
Overall design Grh ChIP-seq performed in Drosophila 3rd instar larval eye-antennal discs.
 
Contributor(s) Potier D, Davie K, Naval Sánchez M, Haggen L, Christiaens V, Aerts S
Citation(s) 25533349
Submission date Oct 21, 2014
Last update date May 15, 2019
Contact name Stein Aerts
E-mail(s) Stein.Aerts@med.kuleuven.be
Organization name KULeuven
Department CME
Lab Laboratory of Computational Biology (LCB)
Street address 49, Herestraat
City Leuven
ZIP/Postal code 3000
Country Belgium
 
Platforms (1)
GPL13304 Illumina HiSeq 2000 (Drosophila melanogaster)
Samples (2)
GSM1528824 eye-antennal-imaginal-disc_Grh-GFP
GSM1528825 eye-antennal-imaginal-disc_input
This SubSeries is part of SuperSeries:
GSE62558 Mapping gene regulatory networks in Drosophila eye development by large-scale transcriptome perturbations and motif inference
Relations
BioProject PRJNA264410
SRA SRP049104

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
GSE62557_grh-vs-input-bdgcmp-pileup_vs_lambda.bw 126.9 Mb (ftp)(http) BW
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Raw data are available in SRA
Processed data are available on Series record

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