Drosophila DrosDel deficiency and diploid control flies
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila melanogaster
SUBMITTER: Brian Oliver
PROVIDER: E-GEOD-31407 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Microarray data of DrosDel deficiency (Df/+) and parental strain diploid flies along with spike-in controls was performed on the Nimblegen 12-plex array platform. Samples are named in this dataset according to the following sample naming scheme: tissue_genotype shorthand_sex_biological replicate #. PolyA+ mRNA was isolated in triplicate to quadruplicate from 5 day old adult female or male whole flies. Female and male mRNA were labeled with Cy3 or Cy5 dyes separately and hybridized to Drosophila 12-plex Nimblegen arrays.
2012-04-02 | E-GEOD-31386 | biostudies-arrayexpress
Project description:The model organism Encyclopedia of DNA Elements project (modENCODE) has produced a comprehensive annotation of D. melanogaster transcript models based on an enormous amount of high-throughput experimental data. However, some transcribed elements may not be functional, and technical artifacts may lead to erroneous inference of transcription. Inter-species comparison provides confidence to predicted annotation, since transcriptional activity that has been evolutionarily conserved is likely to have an advantageous function. We have performed RNA-Seq and CAGE-Seq experiments on more than 80 samples from multiple tissues and stages of 15 Drosophila species, including 8 previously unsequenced genomes. We have found strikingly conserved sequence, expression, and splicing for the vast majority of transcript models in modENCODE annotation (e.g. 99% exons of coding sequences (CDS), 88% exons of untranslated regions (UTR), and 87% splicing events), indicating that the transcriptome annotation is of very high quality. We also describe dynamic transcriptome evolution within the Drosophila genus, including conserved promoter structure, labile positions of transcription start sites, and rapidly evolving RNA-editing events. We demonstrate how this phylogenetic approach to DNA element validation will prove useful in the annotation of other high priority genomes, especially for genomes that are less compact than Drosophila (e.g. the vast majority of vertebrate genomes). Refer to individual Series (listed below).
2013-02-25 | E-GEOD-44612 | biostudies-arrayexpress
Project description:We sequenced mRNA from whole flies of females and male of Drosophila melanogaster, D. simulans, D. yakuba, D. ananassae, D. pseudobscura, D. mojavensis, and D. virilis as part of the modENCODE project to validate novel gene models found in D. melanogaster, identify genes differentially expressed between the sexes and sex-specific alternative splicing events, and examine the evolution of gene expression. Comparison of expresssion profiles in female and male whole flies. These are the same samples used to generate the array data found in GSE6640.
2011-03-23 | E-GEOD-28078 | 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:We sequenced mRNA from head tissue of females and male of Drosophila pseudobscura to identify genes differentially expressed between the sexes and sex-specific alternative splicing events. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Comparison of expression profiles in female and male head tissue from D. pseudobscura
2010-01-26 | E-GEOD-19989 | biostudies-arrayexpress
Project description:We sequenced mRNA from head tissue of females and male of Drosophila melanogaster to identify genes differentially expressed between the sexes and sex-specific alternative splicing events. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Comparison of expression profiles in female and male head tissue from D. melanogaster
2010-04-08 | E-GEOD-20348 | biostudies-arrayexpress
Project description:We sequenced mRNA from head tissue of females and male of Drosophila mojavensis to identify genes differentially expressed between the sexes and sex-specific alternative splicing events. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Comparison of expression profiles in female and male head tissue from D. mojavensis
2010-04-11 | E-GEOD-20882 | biostudies-arrayexpress
Project description:We sequenced dissected ovaries and testes (with reproductive tracts) as well as female and male carcasses in two species of Drosophila in order to validate gene predictions from the ModENCODE project. Comparison of dissected reproductive tracts and remaining carcasses between D. simulans and D. pseudoobscura
2011-08-26 | E-GEOD-31302 | biostudies-arrayexpress
Project description:Wig-1 is a p53 target gene that encodes an RNA-binding protein involved in regulation of mRNA stability through binding to AU-rich elements (AREs). The aims of this study were to identify novel Wig-1 target mRNAs and to characterize the mechanisms of their regulation. Using a microarray approach, we identified 2447 transcripts with >4-fold differential expression between Wig-1 siRNA and control siRNA treated HCT116 cells. Among the deregulated transcripts we found a number of p53 target genes. We demonstrated that Wig-1increases 14-3-3M-OM-^C transcription while it binds to an ARE in the FAS 3M-bM-^@M-^YUTR and decreases the FAS mRNA stability. Furthermore, we show that Wig-1 depletion favours cell death rather that cell cycle arrest after DNA damage. We propose a role of Wig-1 in directing the p53 stress response towards cell cycle arrest rather than cell death through regulation of 14-3-3M-OM-^C and FAS mRNA levels. Use HEEBO microarrays to examine the effects of Wig-1 protein knockdown by siRNA silencing in HCT116 cells. 3 microarrays in total.
2014-03-01 | E-GEOD-43046 | biostudies-arrayexpress
Project description:Transcriptional profiling of head tissue of Drosophila Darkener of apricot (Doa) and found in neurons (fne) mutants was performed by RNA-SEQ in females and males. The transcriptional and post-transcriptional targets of these genes, which are involved in regulation by several processes including splicing and mRNA stability, are examined and compared to wild-type. Examination of mRNA profiles in heads of wild-type male and female adult flies are compared to mutant
2014-03-13 | E-GEOD-37811 | biostudies-arrayexpress