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| Status |
Public on Oct 29, 2008 |
| Title |
Differential gene expression analysis in the larval heart of Drosophila |
| Organism |
Drosophila melanogaster |
| Experiment type |
Expression profiling by array
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| Summary |
The abstract of the manuscript titled "Identification of co-regulated genes and cis-regulatory modules in Drosophila contractile cardiomyocytes" is given below:
"Understanding how sets of genes are co-regulated to generate cell diversity during metazoan development is a major challenge. This requires the identification of tightly co-expressed genes in a given developmental process, of the responsible cis-regulatory modules, and of the combination of trans-acting transcription factors. We chose the Drosophila cardiac tube to address this issue. The cardiac tube is composed of a rostral aorta and a caudal heart, with distinct morphologies and functions and its development is controlled by conserved transcription factors.
Our goal was to identify heart specific expressed genes and to use a combination of genetic and bioinformatic tools to identify and characterize their heart cis-regulatory modules (CRMs). By combined candidate gene approach and microarray experiments, we found 15 different genes that are specifically co-expressed in the contractile cardiomyocytes of the heart. Potential heart-specific CRMs were retrieved from evolutionary conserved non-coding sequences that were ranked according to an integrated score based on combinations of conserved occurrences of potential binding sites for transcription factors known to be expressed in the cardiovascular system, namely Abd-A, Tin, GATA, Mef2, Hand, and T-box factors. Candidate CRMs were then tested in vivo by generating nGFP reporter construct transgenic flies, allowing the identification of three heart enhancers precisely reproducing endogenous gene expression in the heart.
We identified 15 genes that are tightly co-regulated in the contractile cardiomyocytes of the heart and for three of them found the responsible enhancer through computational predictions. A computational post-analysis suggests that different combinations of heart transcription factors may regulate these enhancers and permits to further refine the in silico identification of heart-specific CRMs."
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| Overall design |
In the present study, we described two distinct whole-genome microarray experiments to identify differentially expressed genes in the drosophila larval heart (or dorsal vessel) :
1) comparison of the transcriptome of heart (posterior part) versus aorta (anterior part) from the third instar larval cardiac organ,
2) comparison of the transcriptome of the entire larval dorsal vessel to that of sibling whole larvae.
For each microarray experiment, 4 biological replicates were used through a dye-switch (or biological dye-swap) microarray experimental design in which they were labelled so that each of two conditions has half the samples tagged with Cy3 dyes (2 with Cy3) and the other half with Cy5 dyes (2 with Cy5), then independently hybridized in a reverse and balanced way on dual-channel microarrays (4 arrays). A graphical representation of the design used on this study is showed in the associated manuscript.
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| Contributor(s) |
Tevy MF, Zeitouni B, Aerts S, Potier D, Tosi E, Buontempo F, Hassem BA, Sémériva M, Capovilla M, Perrin L |
| Citation missing |
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| |
| Submission date |
Aug 25, 2008 |
| Last update date |
Jan 18, 2013 |
| Contact name |
Bruno ZEITOUNI |
| E-mail(s) |
zeitouni@ibdml.univ-mrs.fr, perrin@ibdml.univ-mrs.fr
|
| Phone |
+33491269611
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| Fax |
+33491820682
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| Organization name |
CNRS
|
| Department |
UMR 6216
|
| Lab |
Institut de Biologie du Développement de Marseille (IBDML)
|
| Street address |
Campus de Luminy Case 907
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| City |
MARSEILLE Cedex 9 |
| ZIP/Postal code |
13288 |
| Country |
France |
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| Platforms (1) |
| GPL5112 |
MLRG/DrosoIndac Drosophila melanogaster 15K |
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| Samples (8)
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| GSM315306 |
Larval Heart vs Larval Aorta rep4 |
| GSM315307 |
Larval Dorsal Vessel vs Whole Larvae rep1 |
| GSM315308 |
Larval Dorsal Vessel vs Whole Larvae rep2 |
| GSM315309 |
Whole Larvae vs Larval Dorsal Vessel rep3 |
| GSM315310 |
Whole Larvae vs Larval Dorsal Vessel rep4 |
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| Relations |
| BioProject |
PRJNA112895 |
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