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Series GSE59059 Query DataSets for GSE59059
Status Public on Dec 01, 2014
Title Mapping gene regulatory networks in Drosophila eye development by large-scale transcriptome perturbations and motif inference. [RNA-seq]
Organism Drosophila melanogaster
Experiment type Expression 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 RNA-seq gene expression profiling across Drosophila 3rd instar larval wild type tissues (brain, eye-antennal and wing discs), specific cell types from the eye-antennal disc, sorted by FACS, and genetic perturbations (TF mutants, TF over-expression, and TF RNAi knockdown).
 
Contributor(s) Potier D, Davie K, Naval Sánchez M, Haggen L, Christiaens V, Aerts S
Citation(s) 25533349
Submission date Jul 03, 2014
Last update date May 15, 2019
Contact name Delphine Potier
E-mail(s) [email protected]
Organization name CIML
Street address 163 avenue de luminy
City Marseille
ZIP/Postal code 13009
Country France
 
Platforms (1)
GPL13304 Illumina HiSeq 2000 (Drosophila melanogaster)
Samples (80)
GSM1425356 Larval_brain_WT_RAL-208
GSM1425357 Larval_brain_WT_cs
GSM1425358 wing_imaginal_disc_WT_RAL-208
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 PRJNA254224
SRA SRP044038

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

Supplementary file Size Download File type/resource
GSE59059_all_network_experiments.countstable.txt.gz 1.4 Mb (ftp)(http) TXT
GSE59059_all_network_experiments.vst.txt.gz 3.9 Mb (ftp)(http) TXT
GSE59059_eya-GFP-positive_eya-GFP-negative.countstable.txt.gz 132.5 Kb (ftp)(http) TXT
GSE59059_onecut-WTs.countstable.txt.gz 99.0 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record
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