Expression data from third instar larval eye discs
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila melanogaster
PROVIDER: GSE25267 | GEO | 2011/09/01
SECONDARY ACCESSION(S): PRJNA134809
REPOSITORIES: GEO
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Project description:Expression of dE2F1 induces proliferation and apoptosis. We sought to perform an unbiased analysis of the effect of co-expression of miR-11 We used microarrays to identify differentially regulated genes following expression of dE2F1 and/or dme-miR-11 using the GMR-Gal4 driver Drosophila third instar larvae were selected for RNA extraction and hybridization on Affymetrix microarrays. The GMR-Gal4 driver induces expression posterior to the morphogenetic furrow. We compared the gene expression profiles following induction of expression of dE2F1 + dDP and/or dme-miR-11.
2011-08-31 | E-GEOD-25267 | biostudies-arrayexpress
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2015-08-26 | GSE51724 | GEO
Project description:We used microarrays to identify genes that are differentially expressed in the absence of miR-998 expression. Drosophila third instar larvae were selected for RNA extraction and hybridization on Affymetrix microarrays. Three biological replicates for each genotype were prepared. The data was normalized using the RMA algorithm.
2015-08-26 | E-GEOD-51724 | biostudies-arrayexpress
Project description:We performed single-cell RNA-sequencing experiments to understand how the Rbf and Hippo pathways collaborate to maintain cell identity. Drosophila melanogaster photoreceptor neurons with dual mutation in Rbf[120a] and wts[x1] specify normally before abruptly dedifferentiating. We performed scRNA-Seq on w1118, Rbf[120a] single mutant, wts[x1] single mutant, and Rbf[120a] wts[x1] double mutant tissues to better understand the dedifferentiation phenotype. We identified transcriptional changes that were unique to double mutant tissue. We then validated these experiments using a novel dedifferentiation model expressing constitutively active yki[S111A,S168A,S250A] in Rbf[120a] mutant tissue using the GMR-GAL4 driver. We performed single-cell experiments on eye tissues expressing yki[S111A,S168A,S250A] in Rbf wildtype and mutant backgrounds, as well as tissues co-expressing Hth and yki. We then analyzed these experiments to determine the dedifferentiation transcriptional program.
2023-08-04 | GSE217380 | GEO
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:The importance of the role of microRNAs in gene expression and disease is well recognized. However, what is less appreciated is that almost half of miRNA genes are organized in polycistronic clusters and are therefore co-expressed. The mir-11~998 cluster consists of two miRNAs, miR-11 and miR-998. Here, we describe a novel layer of regulation that links the processing and expression of miR-998 to the presence of the mir-11 gene. We show that the presence of mir-11 in the pri-miRNA is required for processing by Drosha, and deletion of mir-11 prevents the expression of miR-998. Replacing mir-11 with an unrelated miRNA rescued miR-998 expression in vivo and in vitro, as did expressing miR-998 from a shorter, more canonical miRNA scaffold. The embedded regulation of miR-998 is functionally important because unchecked miR-998 expression in the absence of miR-11 resulted in highly penetrant pleiotropic developmental defects. We further show that this novel regulation of expression of miRNAs within a cluster is not limited to the mir-11~998 cluster and likely reflects the more general cis-regulation of expression of individual miRNAs. Thus, our results reveal a novel layer of regulation within miRNA clusters that tempers the functions of the individual miRNAs. Unlinking their expression has the potential to change the expression of multiple miRNA targets and shift biological response.
2015-11-15 | GSE73946 | GEO
Project description:Purpose: Feeding larvae of fly models of polyQ and other neurodegenerative disorders on AR or RS supplemented food substantially suppressed neurodegeneration. With a view to gain further insight into the suppression of polyQ pathology by AR or RS, we expressed the UAS-127Q transgene using the predominantly eye-specific GMR-GAL4 driver and examined the transcriptomic changes in wild type and 127Q-expressing eye discs following feeding on AR or RS. In order to find out reason underlying the suppression of neurodegeneration by feeding of AR and RS, we checked difference in gene expression between eye discs expressing GMR-GAL4>UAS-127Q and wild type. Method: Eye disc RNA profiles of wandering late third instar larvae of GMR-GAL4>UAS-127Q and wild type larvae, reared on normal food or food supplemented with AR or RS since after hatching, were generated by sequencing, in triplicate, using Illumina Hiseq2500 platform using 51bp pair-end reads, 12 samples per lane and each sample run across 2 lanes of flowcell (Flowcell ID: C7K52ACXX).This resulted in a sequencing depth of 19-25 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 merge with Cuffmerge to get final transcriptome assembly across samples. In order to ascertain differential expression of transcripts between different samples, Cuffdiff 2.1.1 was used (Trapnell et al., 2012). Result: Using an optimized data analysis workflow, we mapped about 19-25 million sequence reads per sample to the Drosophila melanogaster genome (dm6) and identified 15,904 transcripts with cufflink workflow in each genotypes studied. The GMR-GAL4 driven UAS-127Q expression in eye discs reared on AR supplemented food resulted in 259 differential expression, with 147 genes being down-regulated and 112 up-regulated, when compared with those reared on normal food, however, when larvae from same genotype reared on RS supplemented food resulted in 1641 DEGs, with 846 genes being down-regulated and 795 up-regulated compared with larvae reared on normal food. In eye disc of wild type larvae reared on AR supplemented food resulted in 680 DEGs, with 470 genes being down-regulated and 205 up-regulated compared with those reared on normal food. Larvae from wild type reared on RS supplemented food resulted in 427 DEGs, with 264 genes being down-regulated and 163 up-regulated compared with those reared on normal food. Compared to only GMR-GAL4>UAS-127Q and wild type larval eye discs reared on normal food, total of 1691, with 799 gene were up-regulated while 892 were down-regulated. Conclusion: The present results not only re-inforce earlier findings from our lab that the Ayurvedic Amalaki Rasayana and Rasa-Sindoor are potent suppressors of neurodegeneration but also provide direct evidence that these general health-promoting formulations significantly alter expression of many genes in protein-aggregation-clearance pathways and thus eliminate the cause of proteinopathy so that cell death is inhibited while other normal cellular activities continue. These formulations, which have been used in Ayurvedic practice for thousands of years as health-promoting as well as curative supplements, do not have any side-effects. Therefore, we believe that these Ayurvedic formulations have a good potential to ameliorate the sufferings of polyQ and other neurodegenerative disorders.
2020-10-31 | GSE140856 | 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: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: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