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Tag-seq in eye-antennal and wing imaginal discs of D.melanogaster, D.yakuba, and D.virilis; RNA-seq in wild-type and glass mutant D.melanogaster eye-antennal imaginal discs.

ABSTRACT: In this study we use Tag-sequencing in eye-antennal and wing imaginal discs across Drosophila species to determine a set of conserved eye-specific developmental genes. Next, we perform motif discovery analysis using the tool i-cisTarget, to depict the core gene developmental network underlying compound eye photoreceptor. The Glass position weight matrix appears as the most highly overrepresented motif, thus positioning Glass as a master regulator in compound eye photoreceptor development. Differential gene expression analysis by RNA-seq in D.melanogaster wild-type eye-antennal versus glass mutant [gl 60j] shows that the majority of our predicted Glass targets show strong downregulation in the glass mutant. This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Drosophila yakuba Drosophila melanogaster Drosophila virilis

PROVIDER: GSE39784 | GEO | 2012/09/21

SECONDARY ACCESSION(S): PRJNA171883

REPOSITORIES: GEO

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Tag-seq in eye-antennal and wing imaginal discs of D.melanogaster, D.yakuba, and D.virilis; RNA-seq in wild-type and glass mutant D.melanogaster eye-antennal imaginal discs.

Project description:In this study we use Tag-sequencing in eye-antennal and wing imaginal discs across Drosophila species to determine a set of conserved eye-specific developmental genes. Next, we perform motif discovery analysis using the tool i-cisTarget, to depict the core gene developmental network underlying compound eye photoreceptor. The Glass position weight matrix appears as the most highly overrepresented motif, thus positioning Glass as a master regulator in compound eye photoreceptor development. Differential gene expression analysis by RNA-seq in D.melanogaster wild-type eye-antennal versus glass mutant [gl 60j] shows that the majority of our predicted Glass targets show strong downregulation in the glass mutant. This SuperSeries is composed of the following subset Series: GSE39781: RNA-seq in wild-type and glass mutant eye-antennal discs in Drosophila melanogaster GSE39782: Tag-seq profiling in eye-antennal and wing imaginal discs of D. melanogaster, D. yakuba and D. virilis

2012-09-21 | E-GEOD-39784 | biostudies-arrayexpress

Tag-seq profiling in eye-antennal and wing imaginal discs of D. melanogaster, D. yakuba and D. virilis

Project description:The aim of this study is to identify a set of eye-specific genes across Drosophila species. Species are used as replicates to remove biological noise and identify a core set of conserved eye-developmental genes. We analyze this conserved core using the motif discovery tool i-cisTarget, and identify master regulators of retinal determination, including the Zinc Finger transcription factor Glass. Six samples were analyzed by Illumina Digital Gene Expression (DGE) using the NlaIII restriction enzyme, namely two different tissues (eye-antennal discs and wing discs) for each of the three species under study.

2012-09-21 | E-GEOD-39782 | biostudies-arrayexpress

D. melanogaster eye-antennal imaginal discs developmental transcriptome

Project description:Transcriptomes of Drosophila melanogaster eye-antennal imaginal discs at three sequential larval stages: late 2nd instar (72h after egg laying (AEL)), mid 3rd instar (96h AEL) and late 3rd instar (120h AEL).

2018-01-08 | GSE94915 | GEO

RNA-seq in wild-type and glass mutant eye-antennal discs in Drosophila melanogaster

2012-09-21 | GSE39781 | GEO

RNA-seq in wild-type and glass mutant eye-antennal discs in Drosophila melanogaster

Project description:The aim of this data set is to perform a differential expression analysis between wild type eye-antennal imaginal disc and discs that are homozygous glass mutant gl[60j]. This data set is used to validate Glass target gene predictions identified by i-cisTarget on a set of conserved eye-specific genes. RNA-seq was performed in eye-antennal imaginal discs of two D.melanogaster wild-type strains (Canton S and strain RAL-208 (Jordan et al. 2007, Ayroles et al. 2009)), representing two biological replicates; and in glass mutant (gl[60j]) discs for two technical replicates.

2012-09-21 | E-GEOD-39781 | biostudies-arrayexpress

Tag-seq profiling in eye-antennal and wing imaginal discs of D. melanogaster, D. yakuba and D. virilis

2012-09-21 | GSE39782 | GEO

Atonal and Senseless perturbations in Drosophila melanogaster eye-antennal imaginal discs.

Project description:The goal of this study is to identify co-expressed genes downstream of Atonal and Senseless. These gene lists are used as candidate target genes (technically: as foreground sets) in computational predictions of cis-regulatory elements using the cisTargetX method (http://med.kuleuven.be/cme-mg/lng/cisTargetX). Together, the gene expression results and cis-regulatory predictions, yield a gene regulatory network underlying the early events in retinal differentiation. Predicted cis-regulatory interactions have been validated extensively in vivo using enhancer reporter assays and genetic perturbations. Six samples were analyzed for Atonal gain-of-function (GOF) in the eye-antennal imaginal discs of third instar larvae of Drosophila melanogaster, namely three biological repeats for two different Gal4 drivers (Gal4/7 and AtoGal), crossed with UASato. Three samples were analyzed for Atonal loss-of-function (LOF) in the eye-antennal imaginal discs, namely three biological repeats of ato-/- larvae. Three samples were analyzed for Senseless GOF, namely three biological repeats of atoGal4 crossed with UASsens. Finally, eight control samples were analyzed, namely two biological repeats of four different lines (atoGal4, Gal4/7, UASato, and cantonS wild type).

2010-07-29 | E-GEOD-16713 | biostudies-arrayexpress

Analysis of Drosophila melanogaster Chromosome Topology in Larval Eye and Antennal Discs

Project description:The goal of this study was to examine chromosome topology in Drosophila larval eye and antennal discs by identifying topologically associating domains (TADs) across the genome. TADs were compared between the eye and antennal disc to determine whether they contribute to cell-type-specific homologous pairing and transvection.

2019-08-24 | GSE136267 | GEO

Expression data from eye antennal imaginal disc expressing either activated Ras or secreted Spitz

Project description:We have used microarrays to identify genes expressed and required for the second mitotic wave (SMW) during eye development. Eye discs expressing Spitz under the control of GMR Gal4 have no SMW as Spitz promotes G1 arrest, ectopic differentiation also occures. To control for the ectopic differentiation, Spi expressing eye antennal discs were compared to eye antennal discs expressing activated RasV12. In discs expresseding RasV12 under the control of GMRGal4 the SMW takes place normally prior to any ectopic differentiation. We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process. Keywords: Comparison of eye antennal discs of two different over expression genotypes

2007-11-14 | GSE6300 | GEO

Transcription profiling of Drosophila eye antennal imaginal disc expressing either activated Ras or secreted Spitz

Project description:We have used microarrays to identify genes expressed and required for the second mitotic wave (SMW) during eye development. Eye discs expressing Spitz under the control of GMR Gal4 have no SMW as Spitz promotes G1 arrest, ectopic differentiation also occures. To control for the ectopic differentiation, Spi expressing eye antennal discs were compared to eye antennal discs expressing activated RasV12. In discs expresseding RasV12 under the control of GMRGal4 the SMW takes place normally prior to any ectopic differentiation. We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process. Experiment Overall Design: Drosophila eye antennal imaginal discs expressing either UAS RasV12 or UAS Spi under the control of GMRGal4 were dissected from 3rd instar larvae for RNA extraction and hybridization on Affymetrix microarrays.

2008-06-14 | E-GEOD-6300 | biostudies-arrayexpress

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