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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Differential gene expression in S284Y flies

ABSTRACT: RNA were extracted from 5 adult male and 5 adult female dU2AF50 wt and mutant flies grown at either the permisive (25C) or restrictive (30C) temperature for 4 days. Keywords: other

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Marco Blanchette

PROVIDER: E-GEOD-1345 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome-wide analysis reveals an unexpected function for the Drosophila splicing factor U2AF50 in the nuclear export of intronless mRNAs.

Blanchette Marco M Labourier Emmanuel E Green Richard E RE Brenner Steven E SE Rio Donald C DC

Molecular cell 20040601 6

The protein factor U2AF is an essential component required for pre-mRNA splicing. Mutations identified in the S. pombe large U2AF subunit were used to engineer transgenic Drosophila carrying temperature-sensitive U2AF large subunit alleles. Mutant recombinant U2AF heterodimers showed reduced polypyrimidine tract RNA binding at elevated temperatures. Genome-wide RNA profiling comparing wild-type and mutant strains identified more than 400 genes differentially expressed in the dU2AF50 mutant flies ...[more]

PMID: 15200955

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Differential gene expression in S284Y flies

Project description:RNA were extracted from 5 adult male and 5 adult female dU2AF50 wt and mutant flies grown at either the permisive (25C) or restrictive (30C) temperature for 4 days. Keywords: other

2004-05-25 | GSE1345 | GEO

RNA-seq analyses of kdm5 mutant flies and wt flies under normal condition and oxidative stress

Project description:Comparing the transcriptome of wildtype and kdm5 mutant flies in normal conditions revealed a total of 4787 genes that were significantly downregulated and thus require KDM5 for their activation, and 3269 upregulated genes that are normally repressed by KDM5 (p<0.05, FDR <0.05). Because kdm5 mutants are sensitive to the oxidizer paraquat, we also carried out RNA-seq from wildtype and kdm5 mutant adults in oxidative stress conditions. Paraquat treatment of wildtype flies lead to the upregulation of 2481, and downregulation of 3103 genes adult mRNA profiles of 1-3-days old wild type (WT) and kdm5 mutant under normal condition and oxitative stress were generated by deep sequencing, using Illumina HisSeq 2000.

2015-12-22 | E-GEOD-70590 | biostudies-arrayexpress

Expression data from wild type and ttk^twk mutant whole ovaries

Project description:Epithelial tube morphogenesis requires precise orchestration of cell signaling, shape, migration, and adhesion. Follicle cells in the Drosophila ovary form epithelial tubes, the lumens of which act as molds for the eggshell respiratory filaments, or dorsal appendages (DAs). The Tramtrack69 (TTK69) transcription factor controls DA lumen volume and shape by promoting tube expansion; the tramtrack mutation twin peaks (ttk^twk) reduces TTK69 levels late in oogenesis, inhibiting DA tube expansion. We used microarrays to identify differentially expressed genes in the ttk^twk mutant that are downstream of TTK69 and that play a functional role in DA tube expansion. Ovaries were dissected from female flies at 36 hours of age, to maximize the proportion of developing egg chambers undergoing DA tube expansion. Flies were raised at a constant temperature of 25C in the presence of wet yeast, to maximize the rate of egg chamber production.

2012-12-06 | E-GEOD-42758 | biostudies-arrayexpress

C. elegans heat stress time course

Project description:We sought to study the effect of heat stress on gene expression in C. elegans. We cultured CF512 animals to adulthood at 25C (at which they are sterile). We then induced heat stress by switching the culture temperature to 30C. Keywords: time-course

2004-01-18 | GSE946 | GEO

The foraging gene in Drosophila mediates metabolic as well as behavioral plasticity

Project description:The foraging gene in Drosophila, encoding PKG, is known for its importance as a natural variant affecting behavioral plasticity. Here, we demonstrate that it also affects metabolic plasticity: Rovers show a greater response to changes in their food environment than do sitters. Using metabolic profiling, we define foraging- and food-dependent changes in metabolites indicating that Rover store energy predominantly as lipids, whereas sitter variants store it as carbohydrates, Such changes are reflected in gene expression patterns, indicating an influence of foraging on regulators of insulin signaling. Combining for alleles with mutants of positive insulin signaling regulators makes Rover responses sitter-like, but does not change sitter responses. Collectively these findings suggest that the effect on metabolic plasticity of foraging works through the insulin signaling pathway. Keywords: stress response, comparative genomic hybridization, genotype by environment Design: 3 genotypes x 2 treatments x 3 replicates. Treatments were leaving flies on lab food (control) or food-depriving them overnight with access to water. Three genotypes differed in foraging alleles: Rovers are homozygous for[R] (strain: BB), sitters homozygous for[s] (strain: ee, mutant sitters homozygous for[s2] (strain:s2) . Adult flies were 6-7 days post emergence. Three samples of equal numbers of male and females were collected per combination, frozen in liquid nitrogen, and heads were sieved for RNA extraction. This Gene by Environment design tests how presence or absence of food for a short period (overnight) affects gene expression in different foraging genotypes.

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Gene Expression in Human Lung Type II Cells

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2009-12-30 | E-GEOD-19699 | biostudies-arrayexpress

Expression profile of adult Drosophila melanogaster expressing a self-replicating RNA of Sindbis virus

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2013-01-31 | E-GEOD-42726 | biostudies-arrayexpress

Expression data from Canton-S and D18 adult flies

Project description:Expression data from Canton-S and D18 adult flies

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The Drosophila Tis11 protein and its effects on mRNA expression in flies

Project description:Insects generally express one tristetraprolin family member, proteins that in mammals promote mRNA decay. The Drosophila protein, Tis11, can promote mRNA decay in cells, and its deficiency in flies results in major changes in mRNA levels. Tis11 deficiency in Drosophila results in accumulation of potentialtarget transcripts. Tis11 can affect post- transcriptional gene expression in adult flies by regulating mRNA decay. Examination of gene expression differences between wild-type, Tis11-knockout, and Tis11-mutated flies

2014-10-23 | E-GEOD-58937 | biostudies-arrayexpress

Depletion of histone deacetylase 3 antagonizes PI3K-mediated tissue overgrowth through the acetylation of histone H4 at lysine 16

Project description:Histone acetylation is one of the best studied gene modifications and has been shown to be involved in numerous important biological processes. HereinM-oM-<M-^Lwe demonstrate that Hdac3 regulates both organ and body size through the deacetylation of histone H4 at lysine 16 (H4K16ac). H4K16ac is affected by PI3K signaling cascades. Increasing H4K16ac by the depletion of Hdac3 counteracts PI3K-induced tissue overgrowth and PI3K-mediated alterations in the transcription profile. Using microarry, we compared the transcriptional profile between flies over-expressing PI3K and flies co-expressing PI3K and Hdac3 dsRNA. The findings provide further insight into the mechanism of PI3K-mediated growth and chromatin remodeling. Total RNA was isolated from Drosophila wing imaginal discs using Trizol reagent and hybridized on Affymetrix microarrays. We performed microarray gene expression profiling from drosophila 3rd wing disc of en-Gal4, PI3K overexpression, HDAC3 RNAi, and PI3K overexpression + Hdac3 RNAi.

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