E-GEOD-35471
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: PRJNA152351
PROVIDER: E-GEOD-35471 | ExpressionAtlas | 2015-09-22
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-GEOD-35471-analysis-methods.tsv | Tabular | |||
| E-GEOD-35471-atlasExperimentSummary.Rdata | Rdata | |||
| E-GEOD-35471-configuration.xml | Xml | |||
| E-GEOD-35471-percentile-ranks.tsv | Tabular | |||
| E-GEOD-35471.condensed-sdrf.tsv | Tabular |
Items per page: 5 1 - 5 of 50 |
Similar Datasets
Project description:Growth of the drosophila eye imaginal discs is controlled by the activation of Notch in the dorsal-ventral boundary. Overexpression in the eye disc of the Notch ligand Delta together with lola and pipsqueak from the GS(2)88A8 line induces tumoral growth. We used microarray to analyze the expression profile of tumoral discs. Antennal-eye discs of Drosophila L3 larvae were selected for RNA extraction and hybridization on Affymetrix microarrayas. Two genetic conditions were analyzed: tumoral eye discs (ey-Gal4 GS(2)88A8 UAS-Dl) and control eye discs (GS(2)88A8 UAS-Dl). Three different biological replicates of each condition, each one consisting on 300 hundred pairs of eye discs, were analyzed.
2012-02-20 | E-GEOD-35471 | biostudies-arrayexpress
Project description:Purpose: While studying possible interaction between ras and hsrω genes we found that down- or up- regulation hsrω RNA levels results in further enhancement in activity hyperactive Ras protein in eye discs of Drosophila melanogaster. In order to find out reason underlying this phenomena we checked difference in gene expression between eye discs expressing activated Ras along with alterations in hsrω RNA levels and those expressing activated Ras alone. Method: Eye disc RNA profiles of wandering late third instar larvae of sev-GAL4>UAS-GFP, sev-GAL4>UAS-hsrωRNAi, sev-GAL4>EP3037, sev-GAL4>UAS-RasV12, sev-GAL4>UAS-hsrωRNAi UAS-RasV12 and sev-GAL4>EP3037 UAS-RasV12 were generated by sequencing, in triplicate, using Illumina Hiseq2500 platform using 50bp pair-end reads, 12 samples per lane and each sample run across 2 lanes. This resulted in a sequencing depth of ~20 million reads. The resulting sequencing FastQ files were mapped to the Drosophila genome (dm6) using Tophat with Bowtie. The aligned SAM/BAM file for each was processed for guided transcript assembly using Cufflink 2.1.1 and gene counts were determined. Mapped reads were assembled using Cufflinks. Transcripts from all samples were subjected to Cuffmerge to get final transcriptome assembly across samples. In order to ascertain differential expression of gene transcripts between different samples, Cuffdiff 2.1.1 was used (Trapnell et al., 2012). Result: Using an optimized data analysis workflow, we mapped about 20 million sequence reads per sample to the Drosophila genome (dm6) and identified 15,905 transcripts with TopHat workflow in each genotypes studied. The sev-GAL4 driven expression of activated Ras in eye discs resulted in differential expression of many genes, with 374 genes being down-regulated and 138 up-regulated, when compared with those in sev-GAL4>UAS-GFP eye discs. Compared to only Ras expressing eye discs in case of down regulation of hsrω RNA in activated Ras background 148 gene were up-regulated while 434 were down-regulated. In eye discs expressing activated Ras alongwith over expression of hsrω RNA, 192 genes were up-regulated and 470 down-regulated compared to only activated Ras expressing eye discs. Some of these (11 genes) were validated using qRT-PCR. Conclusion: In activated Ras expressing eye discs, besides the expected increase in levels of transcripts of genes involved in cell growth, proliferation and differentiation, transcripts of many genes involved in RNA biosynthesis, metabolism and processing were up-regulated when compared with sev-GAL4>UAS-GFP eye discs. Levels of transcripts of none of the known members of Ras/Raf/MAPK signaling pathway were found to be significantly affected by changes in hsrω transcript levels in activated Ras expression background. Interestingly, several sn/snoRNAs along with a scaRNAs and some members of the RNA processing machinery were differentially expressed in activated Ras background and were further affected when the hsrω RNA levels were down-or up-regulated. In addition, while down-regulation of hsrω activity resulted in up-regulation of a few positive modulators of Ras signaling pathway, up-regulation of these transcripts caused down-regulation of the negative regulators of Ras/Raf/MAPK pathway, and thus resulting in increase in Ras activity in either cases.
2018-11-30 | GSE107529 | GEO
Project description:Purpose: To compare transcriptomic changes in 3rd instar larval eye discs following sev-GAL4 driven down- or up- regulation of hsrω lncRNAs. Method: Eye disc total RNA profiles of wandering late third instar larvae of sev-GAL4>UAS-GFP, sev-GAL4>UAS-hsrωRNAi, sev-GAL4>EP3037 were generated by sequencing, in duplicate, using Illumina Hiseq2500 platform using 50bp pair-end reads, 6 samples per lane and each sample run across 2 lanes. This resulted in a sequencing depth of ~20 million reads. The resulting sequencing FastQ files were mapped to the Drosophila genome (dm6) using Tophat with Bowtie. The aligned SAM/BAM file for each was processed for guided transcript assembly using Cufflink 2.1.1 and gene counts were determined. Mapped reads were assembled using Cufflinks. Transcripts from all samples were subjected to Cuffmerge to get final transcriptome assembly across samples. In order to ascertain differential expression of gene transcripts between different samples, Cuffdiff 2.1.1 was used (Trapnell et al., 2012). Result: Using an optimized data analysis workflow, we mapped about 20 million sequence reads per sample to the Drosophila genome (dm6) and identified 15,905 transcripts with TopHat workflow in each genotypes studied. The sev-GAL4 driven expression of RNAi for hsromega gene transcripts in eye discs resulted in differential expression of many genes, with 409 genes being down-regulated and 100 up-regulated, when compared with those in sev-GAL4>UAS-GFP eye discs. Compared to control eye discs in case of up regulation of hsrω RNA, 66 gene were up-regulated while 635 were down-regulated. Some of these (11 genes) were validated using qRT-PCR. Conclusion: Analysis of RNA-seq data revealed that a large proportion of transcripts were indeed similarly affected by down- or up-regulation of hsrω RNA in normal as well as activated Ras expression background. A comparison of transcriptomes of sev-GAL4>hsrωRNAi and sev-GAL4>EP3037 eye discs revealed that in each case the number of genes down regulated was more than those up-regulated. Interestingly, while 319 genes were commonly down regulated and 15 were commonly up-regulated in the two genotypes, only 2 genes showed opposing trends between sev-GAL4>UAS-hsrωRNAi and sev-GAL4>EP3037 eye discs.
2018-12-31 | GSE116476 | GEO
Project description:Wild-type Drosophila melanogaster expressing nuclear GFP-KASH fusion protein in photoreceptors for cell type-specific gene expression profiling (Rh1-Gal4>UAS-GFPKASH ; Genotype = w1118;; P{w+mC=[UAS-GFP-Msp300KASH}attP2, P{ry+t7.2=rh1-GAL4}3, ry506) were raised in 12:12h light:dark cycle at 25°C. Flies were aged for 10 or 40 days post-eclosion, and eyes were harvested from male flies for global quantitative proteomic analysis. Significantly changed proteins were identified that may contribute to age-associated retinal degeneration and loss of visual function in the aging Drosophila eye.
2021-07-23 | PXD027090 | Pride
Project description:To probe mechanistic determinants of Yki function in mitochondrial biogenesis, we conducted a genome-wide microarray experiment, and specifically compared expression patterns of genes from control (GMR gal4) and Yorkie over-expressing (GMR gal4; UAS yki) pupal eye discs. The above mentioned genotypes were grown at 29 deg C and at about 40 hrs after pupariation, the pupal eye discs were dissected. RNA was extracted from the pupal eye discs, purified and used to generate microarray probes that were hybridized to the Drosophila genome 2 arrays (Affymetrix). The Gene Chip Operating system (Affymetrix) and dCHIP program (Harvard University) were used to generate pairwise comparisons between the transcription profiles of control and Yorkie over-expressing discs.
2011-12-20 | E-GEOD-26700 | biostudies-arrayexpress
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
Project description:To probe mechanistic determinants of Yki function in mitochondrial biogenesis, we conducted a genome-wide microarray experiment, and specifically compared expression patterns of genes from control (GMR gal4) and Yorkie over-expressing (GMR gal4; UAS yki) pupal eye discs.
2011-12-20 | GSE26700 | GEO
Project description:We investigated the changes in gene expression in response to reduced levels of Ecdysoneless (Ecd) in the developing wing disc of Drosophila. To do this we utilized the GAL4/UAS system to express UAS-ecd-RNAi in the nubbin-domain (nub-Gal4, UAS-mRFP, UAS-ecd-RNAi) of the wing disc and used Nub-Gal4/+ wing discs as controls. We quantified transcriptomic expression analysis from four biological replicates for both experimental groups
2024-01-31 | GSE203127 | GEO
Project description:Growth of the drosophila eye imaginal discs is controlled by the activation of Notch in the dorsal-ventral boundary. Overexpression in the eye disc of the Notch ligand Delta together with lola and pipsqueak from the GS(2)88A8 line induces tumoral growth. We used microarray to analyze the expression profile of tumoral discs.
2012-02-20 | GSE35471 | GEO
Project description:We investigated the changes in gene expression in response to reduced levels of Ecdysoneless (Ecd), and the role of Xrp1 in induction of transcriptional changes upon loss of Ecd in the developing wing disc of Drosophila. To do this we utilized the GAL4/UAS system to express UAS-ecd-RNAi alone and in combination with UAS-xrp1-RNAi in the nubbin-domain (nub-Gal4, UAS-mRFP, UAS-ecd-RNAi and nub-Gal4, UAS-mRFP, UAS-ecd-RNAi, xrp1-RNAi) of the wing disc and used nub-Gal4, UAS-mRFP wing discs as controls. We quantified transcriptomic expression analysis from four biological replicates for both experimental groups
2024-01-31 | GSE213298 | GEO