Sex-specific mRNA and miRNA expression data from Drosophila larvae, pupae and adults
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ABSTRACT:
ORGANISM(S): Drosophila melanogaster
SUBMITTER: Fiona Ingleby
PROVIDER: E-GEOD-57322 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Sex differences in gene expression throughout development are poorly understood, especially sex-specific expression of micro RNAs. However these patterns of gene expression could have important implications in our understanding of the underlying mechanics of sex differentiation and sexual conflict. We extract mRNA and miRNA from male and female Drosophila melanogaster from three developmental timepoints, third larval instar, pupae and adults, and examine gene expression using microarrays. We found a large number of sex-biased mRNA transcripts at each stage of development, whereas sex-biased miRNA expression was low in larvae and pupae and more prevalent in adults. We isolated 2 biological replicates of each sex at each of the three developmental timepoints and extracted mRNA and miRNA from each sample, creating 12 samples of each type of RNA which were ran on GeneChip Drosophila Genome 2.0 Affymetrix microarrays to examine mRNA expression, and GeneChip miRNA 3.0 Affymetrix microarrays to examine miRNA expression.
2014-05-07 | E-GEOD-57321 | biostudies-arrayexpress
Project description:Sex differences in gene expression throughout development are poorly understood, especially sex-specific expression of micro RNAs. However these patterns of gene expression could have important implications in our understanding of the underlying mechanics of sex differentiation and sexual conflict. We extract mRNA and miRNA from male and female Drosophila melanogaster from three developmental timepoints, third larval instar, pupae and adults, and examine gene expression using microarrays. We found a large number of sex-biased mRNA transcripts at each stage of development, whereas sex-biased miRNA expression was low in larvae and pupae and more prevalent in adults. We isolated 2 biological replicates of each sex at each of the three developmental timepoints and extracted mRNA and miRNA from each sample, creating 12 samples of each type of RNA which were ran on GeneChip Drosophila Genome 2.0 Affymetrix microarrays to examine mRNA expression, and GeneChip miRNA 3.0 Affymetrix microarrays to examine miRNA expression.
2014-05-07 | E-GEOD-57320 | biostudies-arrayexpress
Project description:In Drosophila melanogaster, mating radically transforms female physiology and behavior. Post-mating responses include an increase in the oviposition rate, a reduction in female receptivity, and an activation of the immune system . The fitness consequences of mating are similarly dramatic – females must mate once in order to produce fertile eggs, but additional matings have a clear negative effect. Previously, microarrays have been used to examine gene expression of females differing in their reproductive status with the aim of identifying genes influenced by mating. However, since only virgin and single mated females were compared, transcriptional changes associated with reproduction (under natural selection) and the effects of male-induced harm (under sexually antagonistic selection) cannot be disentangled. We partitioned these fundamentally different effects by instead examining the expression profiles of virgin, single mated and double mated females. We found substantial effects relating to reproduction and further effects that are only attributable to a second mating. Immune response genes dominate this male-induced harm effect indicating that the cost of mating may be due partly to this system's activation. We propose that both sexually antagonistic and natural selection have been important in the evolution of the innate immunity genes, thereby contributing to the sexual dimorphismand rapid evolution at these loci. Keywords: Female response to mating Female flies were flash frozen in liquid nitrogen either as virgins or 6 hours after mating and stored at -80°C until RNA extraction was performed (not more than 2 days). 8 whole flies – randomly selected within each treatment – were pooled for each extraction. Total RNA was extracted using Trizol (Invitrogen) and purified with an RNeasy Mini Kit (Qiagen). RNA quantity and quality was checked with an Agilent Bioanalyzer. According to the manufacturer's instructions, samples were prepared and hybridized to Affymetrix GeneChip Drosophila Genome 2.0 (Affymetrix, Santa Clara, CA, USA) by the Uppsala Array Platform (Uppsala, Sweden). Each experimental treatment consisted of 4 independent RNA extractions and hybridizations, giving a total of 12 arrays.
2009-02-18 | E-GEOD-12834 | biostudies-arrayexpress
Project description:Differences in the selective pressures experienced by males and females are believed to be ubiquitous in dioecious organisms and are expected to result in the evolution of sexually antagonistic alleles, thereby driving the evolution of sexual dimorphism. Negative genetic correlation for fitness between the sexes has been documented, however, the identity, number and location of loci causing this relationship are unknown. Here we show that a large proportion of Drosophila melanogaster transcripts are associated with the interaction between genomic haplotype and gender and that at least 8% of loci in the fly genome are currently evolving under sexually antagonistic selection. We measured gene expression of adult males and females of Drosophila melanogaster from 15 hemiclone lines, showing either high-male/low-female fitness, high-female/lowmale fitness or average fitness in both sexes. Data from four replicates for each sex/line are presented, giving a total of 120 arrays.
2010-02-10 | E-GEOD-17013 | biostudies-arrayexpress
Project description:Intralocus sexual conflict, where males and females have different fitness optima for the same trait, has been suggested to potentially be resolved by genomic imprinting, whereby expression in offspring is altered according to parent-of-origin. However, this idea has not yet been empirically tested. Here, we designed an experimental evolution protocol in Drosophila melanogaster which enabled us to look for imprinting effects on the X-chromosome. We enforced father-to-son transmission of the X-chromosome for many generations, and compared fitness and gene expression levels between control males, males with a control X-chromosome that had undergone one generation of father-son transmission (CDX), and males with an X-chromosome that had undergone many generations of father-son transmission (MLX). Although fitness differences were consistent with lowered fitness of males with a paternally inherited X-chromosome, expression differences suggested that this was due to deleterious maternal effects rather than imprinting. We conclude that imprinting is unlikely to resolve intralocus sexual conflict in Drosophila melanogaster. 18 samples were analyzed. There were 3 replicate populations within each of 3 treatments (Control, CDX, and MLX), and two males were analyzed from each population, for a total of 18 males.
2012-04-16 | E-GEOD-37325 | biostudies-arrayexpress
Project description:Recent evidence supports a role for RNA as a common pathogenic agent in both the “polyglutamine” and “untranslated” dominant expanded repeat disorders. One feature of all repeat sequences currently associated with disease is their predicted ability to form a hairpin secondary structure at the RNA level. In order to investigate mechanisms by which hairpin forming repeat RNAs could induce neurodegeneration, we have looked for alterations in gene transcripts as hallmarks of the cellular response to toxic hairpin repeat RNAs. Three disease associated repeat sequences - CAG, CUG and AUUCU - were specifically expressed in the neurons of Drosophila and resultant common, early, transcriptional changes assessed by microarray analyses. Transcripts that encode several components of the Akt/Gsk3-β signalling pathway were altered as a consequence of expression of these repeat RNAs, indicating that this pathway is a component of the neuronal response to these pathogenic RNAs and may represent an important common therapeutic target in this class of diseases. The heads from newly eclosed Male Drosophila were used for RNA extraction and profiling on Affymetrix Drosophile Genome 2.0 microarrays. Twenty samples were analysed, representing control and experimental lines. Two independently derived control lines were used in each exeriment, totaling 4 samples. The tri-nucleotide repeats (CAG, CUG, CAA) were represented by three independently derived two transgene insertion lines each in one experiment and two independent four transgene insertion lines each in a second experiment, totaling 15 samples. A single four transgene insertion line was analysed for AUUCU. Candidates were selected from the pool of transcripts which showed a ‘present’ call in either all independent lines for a particular repeat sequence, or in all samples for the elav- GAL4/+ control in that experiment. Where possible, T-tests were performed on raw values to determine samples that showed a significant difference with a P-value < 0.05.
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Project description:Dominantly inherited expanded repeat neurodegenerative diseases are typically caused by the expansion of existing variable copy number tandem repeat sequences in otherwise unrelated genes. Repeats located in translated regions encode polyglutamine that is thought to be the toxic agent, however in several instances the expanded repeat is in an untranslated region, necessitating multiple pathogenic pathways or an alternative common toxic agent. As numerous clinical features are shared by several of these diseases, and expanded repeat RNA is a common intermediary, RNA has been proposed as a common pathogenic agent. Various forms of repeat RNA are toxic in animal models, by multiple distinct pathways. In Drosophila, repeat-containing double-stranded RNA (rCAG.rCUG~100) toxicity is dependent on Dicer processing evident with the presence of single-stranded rCAG7, which have been detected in affected HD brains. Microarray analysis of Drosophila rCAG.rCUG~100 repeat RNA toxicity revealed perturbation of several pathways including innate immunity. Recent reports of elevated circulating cytokines prior to clinical onset, and age-dependent increased inflammatory signaling and microglia activation in the brain, suggest that immune activation precedes neuronal toxicity. Since the Toll pathway is activated by certain forms of RNA, we assessed the role of this pathway in RNA toxicity. We find that rCAG.rCUG~100 activates Toll signaling and that RNA toxicity is dependent on this pathway. The sensitivity of RNA toxicity to autophagy further implicates innate immune activation. Expression of rCAG.rCUG~100 was therefore directed in glial cells and found to be sufficient to cause neuronal dysfunction. Non-autonomous toxicity due to expanded repeat-containing double-stranded RNA mediated activation of innate immunity is therefore proposed as a candidate pathway for this group of human genetic diseases. The heads from newly eclosed male Drosophila were used for RNA extraction and profiling on Affymetrix Drosophile Genome 2.0 microarrays. Nine samples were analysed, representing control and experimental lines. Two independent lines of rCAG.rCUG~100 double-stranded RNA were analysed in triplicate. These were compared to 4xUAS control analysed in triplicate. All transgenes were expressed using the elavII-GAL4 pan-neuronal driver. Candidates were selected from the pool of transcripts which showed a 'present' call in all samples. T-tests were performed on raw values to determine samples that showed a significant difference with a P-value < 0.05.
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