Sex-specific mRNA and miRNA expression data from Drosophila larvae, pupae and adults [miRNA]
Ontology highlight
ABSTRACT:
ORGANISM(S): synthetic construct Drosophila melanogaster
PROVIDER: GSE57321 | GEO | 2014/05/07
SECONDARY ACCESSION(S): PRJNA246267
REPOSITORIES: GEO
Similar Datasets
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.
2014-05-07 | GSE57320 | GEO
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 Hymenoptera, sex is determined by a single-locus complementary sex determining system (sl-CSD). Males are normally haploid (hemizygous at the sl-CSD locus) but if the genotype of the sl-CSD locus is homozygous, they develop into diploid males. Here, we study the effects of ploidy and the sl-CSD-locus genotype by comparing gene expression differences between haploid males, diploid males and virgin queens at three developmental stages, pupae, 1 day and 11 days after eclosion. Keywords: diploid males, sl-CSD, ploidy-spcific gene, sex-specific gene, doublesex, sex-biased gene Six-condition experiment: haploid male pupae, diploid male pupae, queen pupae, 1-day-old haploid male adults, 1-day-old diploid male adults, 1-day-old queen adults (accession number GSM1031732 - GSM1031734, GSM1031737 - GSM1031738, GSM1031740 - GSM1031742, GSM1031745 - GSM1031746; reprocessed for this study), 11-day-old haploid male adults, 11-day-old diploid male adults, 11-day-old queen adults (accession number GSM1031748 - GSM1031750, GSM1031753 - GSM1031754, GSM1031756 - GSM1031758, GSM1031761 - GSM1031762; reprocessed for this study). Biological replicates: 5 colonies (x 2 genotypes for each colony). Samples were labeled with Cy3 and were compared to the same common reference RNA labeled with Cy5.
2012-12-06 | E-GEOD-42494 | biostudies-arrayexpress
Project description:In Hymenoptera, sex is determined by a single-locus complementary sex determining system (sl-CSD). Males are normally haploid (hemizygous at the sl-CSD locus) but if the genotype of the sl-CSD locus is homozygous, they develop into diploid males. Here, we study the effects of ploidy and the sl-CSD-locus genotype by comparing gene expression differences between haploid males, diploid males and virgin queens at three developmental stages, pupae, 1 day and 11 days after eclosion. Keywords: diploid males, sl-CSD, ploidy-spcific gene, sex-specific gene, doublesex, sex-biased gene Six-condition experiment: haploid male pupae, diploid male pupae, queen pupae, 1-day-old haploid male adults, 1-day-old diploid male adults, 1-day-old queen adults (accession number GSM1031732 - GSM1031734, GSM1031737 - GSM1031738, GSM1031740 - GSM1031742, GSM1031745 - GSM1031746; reprocessed for this study), 11-day-old haploid male adults, 11-day-old diploid male adults, 11-day-old queen adults (accession number GSM1031748 - GSM1031750, GSM1031753 - GSM1031754, GSM1031756 - GSM1031758, GSM1031761 - GSM1031762; reprocessed for this study). Biological replicates: 5 colonies (x 2 genotypes for each colony). Samples were labeled with Cy3 and were compared to the same common reference RNA labeled with Cy5.
2012-12-06 | E-GEOD-42785 | biostudies-arrayexpress
Project description:In Hymenoptera, sex is determined by a single-locus complementary sex determining system (sl-CSD). Males are normally haploid (hemizygous at the sl-CSD locus) but if the genotype of the sl-CSD locus is homozygous, they develop into diploid males. Here, we study the effects of ploidy and the sl-CSD-locus genotype by comparing gene expression differences between haploid males, diploid males and virgin queens at three developmental stages, pupae, 1 day and 11 days after eclosion. Keywords: diploid males, sl-CSD, ploidy-spcific gene, sex-specific gene, doublesex, sex-biased gene Six-condition experiment: haploid male pupae, diploid male pupae, queen pupae, 1-day-old haploid male adults, 1-day-old diploid male adults, 1-day-old queen adults (accession number GSM1031732 - GSM1031734, GSM1031737 - GSM1031738, GSM1031740 - GSM1031742, GSM1031745 - GSM1031746; reprocessed for this study), 11-day-old haploid male adults, 11-day-old diploid male adults, 11-day-old queen adults (accession number GSM1031748 - GSM1031750, GSM1031753 - GSM1031754, GSM1031756 - GSM1031758, GSM1031761 - GSM1031762; reprocessed for this study). Biological replicates: 5 colonies (x 2 genotypes for each colony). Samples were labeled with Cy3 and were compared to the same common reference RNA labeled with Cy5.
2012-12-06 | E-GEOD-42779 | biostudies-arrayexpress
Project description:Sexual dimorphism depends on sex-biased gene expression, but the contributions of microRNAs (miRNAs) have not been globally assessed. We therefore produced an extensive small RNA sequencing dataset to analyse male and female miRNA expression profiles in mouse, opossum and chicken. Our analyses uncovered numerous cases of somatic sex-biased miRNA expression, especially in the mouse heart and liver. Sex-biased expression is explained by miRNA-specific regulation, including sex-biased chromatin accessibility at promoters, rather than piggybacking of intronic miRNAs on sex-biased protein-coding genes. In mouse, but not opossum and chicken, sex bias is coordinated across tissues such that autosomal testis-biased miRNAs tend to be somatically male-biased, whereas autosomal ovary-biased miRNAs are female-biased, possibly due to broad hormonal control. In chicken, which has a Z/W sex chromosome system, expression output of genes on the Z chromosome is expected to be male-biased, since there is no global dosage compensation mechanism that restores expression in ZW females after almost all genes on the W chromosome decayed. Nevertheless, we found that the dominant liver miRNA, miR-122-5p, is Z-linked but expressed in an unbiased manner, due to the unusual retention of a W-linked copy. Another Z-linked miRNA, the male-biased miR-2954-3p, shows conserved preference for dosage-sensitive genes on the Z chromosome, based on computational and experimental data from chicken and zebra finch, and acts to equalise male-to-female expression ratios of its targets. Unexpectedly, our findings thus establish miRNA regulation as a novel gene-specific dosage compensation mechanism.
2017-11-01 | GSE102062 | GEO
Project description:modENCODE_submission_757 This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Strain: Canton-S; Tissue: pupae; Replicate type: biological; Developmental Stage: Pupae 2-4d; Sex: NA; EXPERIMENTAL FACTORS: Strain: Canton-S
2012-08-09 | E-GEOD-40043 | biostudies-arrayexpress
Project description:Drosophila melanogaster undergoes a complete metamorphosis, during which time the larval male and female forms transition into sexually dimorphic, reproductive adult forms. To understand this complex morphogenetic process at a molecular-genetic level, we performed whole genome microarray analyses. In somatic tissues at 48 hour After Puparium Formation (APF), 173 sex-biased transcripts that likely function downstream of the doublesex (dsx) branch of the sex determination hierarchy were identified. The mode of regulation of the sex-specific isoforms of DSX (DSX-F and DSX-M) was examined. It was determined that for most downstream targets, DSX-F and DSX-M regulate gene expression in the same manner, but that one isoform acts as a more potent regulator. Keywords: wild type; genetic modification All microarrays were dual channel with direct comparisons of male versus female or wild type versus mutant. All samples consist of whole body pupae collected at 48 hour After Puparium Formation (APF). For each experiment, four biological replicates were analyzed in a dye-swap design.
2009-02-10 | E-GEOD-11311 | biostudies-arrayexpress
Project description:Background: Stalk-eyed flies (family Diopsidae) are a model system for studying sexual selection due to the presence of elongated and sexually dimorphic eye-stalks in many species. Recent genomic studies on these flies have revealed a neo-X chromosome and evidence of gene movement onto or off of this X chromosome. To determine if sex linkage and gene movement are related to sexual dimorphism and sexual conflict, we compared gene expression between males and females using oligonucleotide microarrays and RNA from either developing eyestalk tissue or adult heads from a dimorphic species, Teleopsis dalmanni, or from developing eyestalk tissue in a congeneric monomorphic species, T. quinqueguttata. Results: Comparison of gene expression between the sexes for 3,748 genes indicates that dosage compensation is present due to elevated expression of X-linked genes in males. However, sex-biased expression was detected in 26% of the genes present in eye-antennal imaginal discs of larval T. dalmanni. Functional annotation reveals that female-biased genes are associated with transcription, anatomical development and cell communication in the nucleus, while male-biased genes are associated with metabolism and the mitochondria. Comparison of gene expression between experiments identified 140 genes with concordant sex-biased expression in the larval and adult tissues of T. dalmanni and 17 genes with identical sex-biased expression between species. There were only five reversals of sex-biased expression across experiments. In T. dalmanni, male-biased genes are more common on autosomes than on the X while female-biased genes are more common on the X in T. quinqueguttata. Female-biased expression is especially common among genes that moved onto the ancestral X while male-biased expression is more common among genes that moved onto an autosome. Conclusions: Genes with sex-biased expression exhibit different functions in each sex as expected if sexual conflict has influenced their evolution. The strong relationship between sex-biased expression and gene movement found in this study is consistent with resolution of sexual conflict by an RNA- or DNA-mediated process that moves genes between chromosomes. Measurement of gene expression in additional species should provide a more complete picture of how gene expression change occurs over evolutionary time in these extraordinary flies. Two-condition experiment, female vs. male RNA using larval eye discs for two species (Teleopsis dalmanni, Teleopsis quinqueguttata), and adult heads for one species (Teleopsis dalmanni).
2012-04-09 | E-GEOD-37121 | biostudies-arrayexpress