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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
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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.
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Overall design |
Grh ChIP-seq performed in Drosophila 3rd instar larval eye-antennal discs.
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Contributor(s) |
Potier D, Davie K, Naval Sánchez M, Haggen L, Christiaens V, Aerts S |
Citation(s) |
25533349 |
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Submission date |
Oct 21, 2014 |
Last update date |
May 15, 2019 |
Contact name |
Delphine Potier |
E-mail(s) |
potier@ciml.univ-mrs.fr
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Organization name |
CIML
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Street address |
163 avenue de luminy
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City |
Marseille |
ZIP/Postal code |
13009 |
Country |
France |
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Platforms (1) |
GPL13304 |
Illumina HiSeq 2000 (Drosophila melanogaster) |
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Samples (2) |
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This SubSeries is part of SuperSeries: |
GSE62558 |
Mapping gene regulatory networks in Drosophila eye development by large-scale transcriptome perturbations and motif inference |
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Relations |
BioProject |
PRJNA264410 |
SRA |
SRP049104 |