Sex biased gene expression in 17 weeks old chicken (ovary, testes)
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ABSTRACT:
ORGANISM(S): Gallus gallus
PROVIDER: GSE14013 | GEO | 2009/12/01
SECONDARY ACCESSION(S): PRJNA112437
REPOSITORIES: GEO
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Project description:Sex chromosomes are characterized by a non-random content of genes with preferential expression in one sex. The mechanisms which are responsible for this phenomenon are, however, largely unresolved. To elucidate selective forces shaping the Z chromosome gene content in chicken, we analyzed microarray data from adult and embryonic gonads (the latter already available in GEO Series GSE8693). Experiment Overall Design: Total RNA from gonads of 8 males and 8 females was used for hybridization to Affymetrix GeneChip® Chicken Genome Arrays. Prior to hybridization the samples were combined in equal quantities into 4 pools (4 testes/ovary samples in each pool), 2 of them representing testis and 2 ovary. Experiment Overall Design: All four GeneChips met Affymetrix quality control criteria. Furthermore, all chips were checked by methods based on probe level robust linear model fitting provided by "affyPLM" package (Bolstad, 2007). None of the chips showed any signs of abnormality.
2009-12-14 | E-GEOD-14013 | biostudies-arrayexpress
Project description:Investigatation into how genes with sex-differential expression profiles are distributed among the chromosomes in Drosophila. Assayed the expression of 14,142 predicted transcripts in competitive hybridizations and found a dramatic underrepresentation of X-chromosome genes showing high relative expression in male. This is the first report of sex-biased expression of the full (predicted) genome. Findings indicate that there is significant sex-biased expression, especially in gonads. Genes showing sex-biased gene expression profiles are likely to have sex-biased functions. Keywords: other
2003-06-02 | GSE442 | GEO
Project description:Investigation of sex-biased expression across species have relied on measurements from whole flies which sample the extensive expression differences found in the germline and gonads of females and males. We wanted to examine genes with sex-biased expression in a somatic tissue to analyze patterns of genes with sex-biased expression in the context of a tissue more phenotypically similar between females and males. We used a Nimblegen microarray designed for Drosophila melanogaster and two custom micoarrays designed for D. pseudoobscura and D. mojavensis to survey gene expression differences in heads of females and males.
2010-07-30 | GSE23309 | GEO
Project description:Purpose: Accurate identification of sex-biased genes requires precise measurement of gene expression levels in gonads. This study is designed to provide such data for various Drosophila species to enhance studies of sex-biased gene expression and evolution across the genus. Methods: Virgin flies were collected and aged 6-10 days before dissecting 2-3 replicates of testes or ovaries. Total RNA was extracted using the Arcturus® PicoPure® kit . Illumina® TruSeq® RNA library kits were used to poly-A+ select and reverse-transcribe mRNA, shear cDNA into ~120 bp fragments, and produce libraries for 1x50 bp sequencing on an Illumina GAIIx or HiSeq2000. Illumina®’s Real Time Analysis v1.13 module processed images, called bases, and provided base qualities. Reads were mapped to the current reference genomes using Bowtie v2.1.0 (Langmead and Salzberg, 2012, Nat Meth) with default settings. Differentially expressed genes were detected using Cufflinks v 2.1.0 (Trapnell et al., 2010, Nat Biotech; default settings) or edgeR (Robinson et al., 2010, Bioinformatics; full-quantile GC-content normalization and full-quantile between-sample normalization). Genes were called differentially expressed at a Benjamini-Hochberg false discovery rate of 0.01. Results: Thousands of male- and female-biased genes were detected for each species using both DE detection methods. These results provide a significant improvement in sensitivity of sex-biased gene detection relative to using whole-body RNA-sequencing data. These data provide a foundation for accurate identification of sex-biased genes throughout the Drosophila genus.
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Project description:The deletion of a single miRNA cluster, miR-17~92, is sufficient to induce primary sex reversal in XY mice. The expression of the testis determining gene, Sry, is delayed in embryonic XY miR-17~92 knockout gonads, which immediately activate the ovarian genetic program. Single cell RNA-seq analysis shows that Sertoli cell differentiation is highly reduced, delayed and unable to trigger testis differentiation. Consistent with the well-known role of miRNAs in gene regulation, the expression of target genes of miR-17~92 is not stabilized in XY mutant gonads at E11.5, affecting, in turn, the fine regulation of large gene networks involved in mammalian sex determination. Our results reveal that the miR-17~92 cluster is a novel sex-determining factor that modulates several gene networks required for accurate timing of Sry expression and Sertoli cell differentiation during testis determination and early differentiation.
2023-07-09 | GSE225676 | GEO
Project description:Purpose: Accurate identification of sex-biased genes requires precise measurement of gene expression levels in gonads. This study is designed to provide such data for various Drosophila species to enhance studies of sex-biased gene expression and evolution across the genus. Methods: Virgin flies were collected and aged 6-10 days before dissecting 2-3 replicates of testes or ovaries. Total RNA was extracted using the Arcturus® PicoPure® kit . Illumina® TruSeq® RNA library kits were used to poly-A+ select and reverse-transcribe mRNA, shear cDNA into ~120 bp fragments, and produce libraries for 1x50 bp sequencing on an Illumina GAIIx or HiSeq2000. Illumina®’s Real Time Analysis v1.13 module processed images, called bases, and provided base qualities. Reads were mapped to the current reference genomes using Bowtie v2.1.0 (Langmead and Salzberg, 2012, Nat Meth) with default settings. Differentially expressed genes were detected using Cufflinks v 2.1.0 (Trapnell et al., 2010, Nat Biotech; default settings) or edgeR (Robinson et al., 2010, Bioinformatics; full-quantile GC-content normalization and full-quantile between-sample normalization). Genes were called differentially expressed at a Benjamini-Hochberg false discovery rate of 0.01. Results: Thousands of male- and female-biased genes were detected for each species using both DE detection methods. These results provide a significant improvement in sensitivity of sex-biased gene detection relative to using whole-body RNA-sequencing data. These data provide a foundation for accurate identification of sex-biased genes throughout the Drosophila genus. Testis and ovary samples from Drosophila species were sequenced 1 x 50 bp in duplicate from 6-10 day old virgin, Wolbachia-free adult flies on an Illumina GAIIx or HiSeq2000.
2013-11-04 | E-GEOD-52058 | biostudies-arrayexpress
Project description:Investigation of sex-biased expression across species have relied on measurements from whole flies which sample the extensive expression differences found in the germline and gonads of females and males. We wanted to examine genes with sex-biased expression in a somatic tissue to analyze patterns of genes with sex-biased expression in the context of a tissue more phenotypically similar between females and males. We used a Nimblegen microarray designed for Drosophila melanogaster and two custom micoarrays designed for D. pseudoobscura and D. mojavensis to survey gene expression differences in heads of females and males. PolyA+ mRNA was isolated in quadruplicate from dissected heads of 8 day old adult females and males. Female and male mRNA were labeled with Cy3 or Cy5 dyes separately and co-hybridized to species-specific microarrays. We analyzed a total of 24 channels of data.
2010-07-30 | E-GEOD-23309 | biostudies-arrayexpress
Project description:This study evaluates the temporal pattern of gene expression in human fetal gonads covering the periods of sex differentiation and the onset of steroidogenesis in the testis, with corresponding changes in the ovary.
2017-11-29 | E-MTAB-5611 | biostudies-arrayexpress
Project description:The deletion of a single miRNA cluster, miR-17~92, is sufficient to induce primary sex reversal in XY mice. The expression of the testis determining gene, Sry, is delayed in embryonic XY miR-17~92 knockout gonads, which immediately activate the ovarian genetic program. Single cell RNA-seq analysis shows that Sertoli cell differentiation is highly reduced, delayed and unable to trigger testis differentiation. Consistent with the well-known role of miRNAs in gene regulation, the expression of target genes of miR-17~92 is not stabilized in XY mutant gonads at E11.5, affecting, in turn, the fine regulation of large gene networks involved in mammalian sex determination. Our results reveal that the miR-17~92 cluster is a novel sex-determining factor that modulates several gene networks required for accurate timing of Sry expression and Sertoli cell differentiation during testis determination and early differentiation. bulk RNA-seq, single cell RNA-seq as well as IF and other characterizations of a transgenic mice for miR-17~92 cluster
2023-07-09 | GSE225675 | GEO
Project description:As a result of sex chromosome differentiation from ancestral autosomes, male mammalian cells only contain one X chromosome. It has long been hypothesized that X-linked gene expression levels have become doubled in males to restore dosage balance between the X and autosomes, and that the resulting X overexpression in females then drove the evolution of X inactivation (XCI). However, this model has never been directly tested and patterns and mechanisms of dosage compensation across different mammals and birds generally remain little understood. We have traced the evolution of dosage compensation using extensive transcriptome data from males and females representing all major mammalian lineages and birds. Our analyses suggest that the X has become globally upregulated in marsupials but probably not in placental mammals, where instead at least a subset of autosomal genes interacting with X-linked were downregulated. Thus, different driving forces may underlie the evolution of XCI and the highly efficient equilibration of X expression levels between the sexes observed for both of these lineages. In the egg-laying monotremes and birds, which have homologous sex chromosome systems, partial upregulation of the X (Z in birds) evolved but is largely restricted to the heterogametic sex, which provides an explanation for the partially sex-biased X (Z) expression and lack of global inactivation mechanisms in these lineages. Our findings suggest that dosage reductions imposed by sex chromosome differentiation events in amniotes were resolved in strikingly different ways.
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