E-GEOD-24978
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: PRJNA131911
PROVIDER: E-GEOD-24978 | ExpressionAtlas | 2014-09-05
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-GEOD-24978-analysis-methods.tsv | Tabular | |||
| E-GEOD-24978-atlasExperimentSummary.Rdata | Rdata | |||
| E-GEOD-24978-configuration.xml | Xml | |||
| E-GEOD-24978-percentile-ranks.tsv | Tabular | |||
| E-GEOD-24978.condensed-sdrf.tsv | Tabular |
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Project description:PSC overexpression can cause phenotypes specifically in an rbf1 mutant background, likely due to a sensitization to PSC-induced phenotypes. The goal of this study is to understand the interaction between rbf1 hypomorphic mutation and the overexpression of Polycomb group gene Posterior sex combs. We used Drosophila larval eye imaginal discs that were mutant for rbf1 or overexpressing PSC and compared these to control larval eye discs to assess changes in gene expression. We identified a common set of genes that are deregulated when rbf1 is mutated or when PSC is overexpressed. RNA was extracted from eye imaginal discs dissected from third instar Drosophila larvae. Samples were amplified and hybridized to Affymetrix Drosophila Genome 2.0 Array. To better understand the effects of rbf1 mutation and PSC overexpression, we compared the gene expression of rbf1 mutant eye discs and eye discs overexpressing PSC to control eye discs.
2014-09-30 | E-GEOD-38430 | biostudies-arrayexpress
Project description:PSC overexpression can cause phenotypes specifically in an rbf1 mutant background, likely due to a sensitization to PSC-induced phenotypes. The goal of this study is to understand the interaction between rbf1 hypomorphic mutation and the overexpression of Polycomb group gene Posterior sex combs. We used Drosophila larval eye imaginal discs that were mutant for rbf1 or overexpressing PSC and compared these to control larval eye discs to assess changes in gene expression. We identified a common set of genes that are deregulated when rbf1 is mutated or when PSC is overexpressed.
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Project description:Apoptosis is an important process to eliminate cells from tissue which have incurred irreparable DNA damage. While dE2F1/dDP complexes respond to such damage by transcriptionally activating apoptotic genes, previous data suggests that activation of the previously characterized apoptotic target genes of dE2F1/dDP alone may not be the only gene regulation important for gamma irradiation-induced apoptosis. Here we report that following irradiation in dDP mutant 3rd instar larval eye imaginal discs, many genes important for oxidative phosphorylation are down-regulated, which are not down-regulated following irradiation in wild type eye discs. Biological triplicates of wild type, dDP mutant and de2f1, deleted in the posterior, eye discs were untreated or irradiated with 40Gy of gamma radiation. Total RNA was extracted by Trizol from untreated eye discs and from irradiated eye discs 4h after irradiation. RNA was column purified. PCR amplified RNAs were hybridized on Affymetrix Drosophila Genome 2.0 Array.
2013-11-25 | E-GEOD-39389 | biostudies-arrayexpress
Project description:The goal of this study was to examine RNA expression levels in the Drosophila larval eye and antennal discs and determine whether higher levels of transcription were correlated with the ability of transgenes to drive pairing with their homologous endogenous loci between chromosomes. Additionally, RNA expression levels were compared between the eye and antennal discs to determine whether increased insulator protein expression contributed to increased pairing in the eye disc.
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Project description:Exploring downstream regulation by the transcription factor FoxO is necessary to understand its function as a tumor suppressor or promoter in different biological contexts. Here, we employed RNA-seq profiling on single clones isolated using laser capture microdissection from Drosophila larval eye imaginal discs to identify FoxO targets that restrict the proliferation of Tsc1-deficient cells under nutrient restriction (NR).
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2011-02-22 | E-GEOD-24978 | biostudies-arrayexpress
Project description:Genomic enhancers regulate spatio-temporal gene expression by recruiting specific combinations of transcription factors (TFs). When TFs are bound to active regulatory regions, they displace canonical nucleosomes, making these regions biochemically detectable as nucleosome-depleted regions or accessible/open chromatin. Here we ask whether open chromatin profiling can be used to identify the entire repertoire of active promoters and enhancers underlying tissue-specific gene expression during normal development and oncogenesis in vivo. To this end, we first compare two different approaches to detect open chromatin in vivo using the Drosophila eye primordium as a model system: FAIRE-seq, based on physical separation of open versus closed chromatin; and ATAC-seq, based on preferential integration of a transposon into open chromatin. We find that both methods reproducibly capture the tissue-specific chromatin activity of regulatory regions, including promoters, enhancers, and insulators. Using both techniques, we screened for regulatory regions that become ectopically active during Ras-dependent oncogenesis, and identified 3778 regions that become (over-)activated during tumor development. Next, we applied motif discovery to search for candidate transcription factors that could bind these regions and identified AP-1 and Stat92E as key regulators. We validated the importance of Stat92E in the development of the tumors by introducing a loss of function Stat92E mutant, which was sufficient to rescue the tumor phenotype. Additionally we tested if the predicted Stat92E responsive regulatory regions are genuine, using ectopic induction of JAK/STAT signaling in developing eye discs, and observed that similar chromatin changes indeed occurred. Finally, we determine that these are functionally significant regulatory changes, as nearby target genes are up- or down-regulated. In conclusion, we show that FAIRE-seq and ATAC-seq based open chromatin profiling, combined with motif discovery, is a straightforward approach to identify functional genomic regulatory regions, master regulators, and gene regulatory networks controlling complex in vivo processes. FAIRE-Seq in Drosophila wild type eye-antennal imaginal discs (2 wt strains); ATAC-Seq in Drosophila wild type eye-antennal imaginal discs (3 wt strains) ; FAIRE-Seq in Drosophila Ras/Scrib induced eye disc tumors (1 early and 1 late); ATAC-Seq in Drosophila Ras/Scrib induced eye disc tumors (1 early and 1 late); ATAC-Seq in Drosophila eye discs with Unpaired over-expression (2 biological replicates); CTCF ChIP-seq in Drosophila eye discs; ChIP-seq input in Drosophila eye discs
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