Expression differences between inversions and their progenitors in Drosophila melanogaster embryos
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila melanogaster
SUBMITTER: Lisa Meadows
PROVIDER: E-GEOD-21607 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:An analysis of the impact of infection by Buchnera aphidicola APS (isolated from Acyrthosiphon pisum strain LL01) on gene expression of S2 cells. All comparisons are made against a pool of RNA from S2 cells not exposed to B. aphidicola. B. aphidicola freshly isolated from the aphids, and data are collected at 1, 6 and 24 hours after exposure of S2 cells to the B. aphidicola preparation. Keywords: time course, Buchnera aphidicola APS, aphids, Drosophila melanogaster S2 cells All comparisons are made against a pool of RNA from S2 cells not exposed to B. aphidicola. B. aphidicola freshly isolated from the aphids, and data are collected at 1, 6 and 24 hours after exposure of S2 cells to the B. aphidicola preparation.
2008-12-14 | E-GEOD-11012 | biostudies-arrayexpress
Project description:To identify genes upregulated in response to Notch signalling in KC cells. Keywords: Expression analysis at a single timepoint (30' after Notch activation) KC cells were obtained from Dr Martin Zeidler. Control versus Notch activated KC cells: mRNA was extracted from KC cells incubated in the absence or presence of EDTA to activate Notch (cells were harvested 30 minutes after addition of EDTA). RNA was isolated using TRIzol (Sigma) and reverse transcription was performed with Superscript III Reverse Transcriptase (Invitrogen) and oligo-dT primers (Sigma). Control and experimental samples were labeled with Cy3 or Cy5, mixed together and hybridized on Drosophila transcriptome long-oligonucleotide microarrays (FlyChip, FL002; http://www.flychip.org.uk/services/core/FL002/). Three biological replicates and dye swaps were performed (5 arrays in total/experiment). Slides were scanned by Genepix 400B dual laser scanner (Axon) and spots were found and quantified by Dapple software.
2010-06-23 | E-GEOD-9965 | biostudies-arrayexpress
Project description:Analysis of differential gene expression in third instar Drosophila salivary glands in the absence versus presence of cohesin. ABSTRACT: Developmental abnormalities observed in Cornelia de Lange Syndrome (CdLS) have been genetically linked to mutations in the cohesin machinery. These findings raise the possibility that cohesin, in addition to its canonical function of mediating sister chromatid cohesion, might also be involved in regulating gene expression. We report that cleavage of cohesinM-CM-^Us kleisin subunit in post-mitotic Drosophila salivary glands induces major changes (both up and down) in the transcript levels of many genes. Kinetic analyses of changes in transcript levels upon cohesin cleavage reveal that a subset of genes responds to cohesin cleavage within a few hours. In addition, cohesin binds to most of these loci, suggesting that cohesin is directly regulating their expression. Amongst these genes are several that are regulated by the steroid hormone Ecdysone. Transcripts at EcR and Eip74EF, which encode an Ecdysone Receptor and an Ecdysone-regulated transcription factor, respectively, decline ten-fold within four hours of cohesin cleavage. Cytological visualization of transcription at selected Ecdysone-responsive genes reveals that puffing at Eip74EF ceases within an hour or two of cohesin cleavage, long before any decline in EcR associated with this locus. We conclude that cohesin regulates expression of a distinct set of genes, including those mediating the Ecdysone response. A heat-inducible transgene (hs-TEV) was used to induce TEV in terminally differentiated third instar Drosophila salivary glands expressing either wild type (+ cohesin) or TEV-cleavable myc10-tagged Rad21 protein (Rad21TEV, - cohesin). Total RNA was isolated from + and - cohesin salivary glands 10-12 hours after heat shock induction of TEV (7 independent biological samples each). RNA samples were converted to cDNA, labeled with Cy3 and Cy5 respectively (3x) and vice versa (4x; dye swaps), and hybridized to INDAC FL003 arrays. Analysis of seven arrays, each hybridized to an independently generated sample-pair revealed major differences in transcript levels between + and - cohesin samples.
2010-12-22 | E-GEOD-21844 | biostudies-arrayexpress
Project description:The expression profile of asense mutant neuroblasts and GMCs were compared to wildtype in order to investigate the function of Asense in neural development. Abstract of paper: Neural stem cells must strike a balance between self-renewal and multipotency, and differentiation. Identification of the transcriptional networks regulating stem cell division is an essential step in understanding how this balance is achieved. We have shown that the homeodomain transcription factor, Prospero, acts to repress self-renewal and promote differentiation. Amongst its targets are three neural stem cell transcription factors, Asense, Deadpan and Snail, of which Asense and Deadpan are repressed by Prospero. Here we identify the targets of these three factors throughout the genome. We find a large overlap in their target genes, and indeed with the targets of Prospero, with 245 genomic loci bound by all factors. Many of the genes have been implicated in vertebrate stem cell self-renewal, suggesting that this core set of genes is crucial in the switch between self-renewal and differentiation. We also show that multiply bound loci are enriched for genes previously linked to nervous system phenotypes, thereby providing a short-cut to identifying genes important for nervous system development. 8 asense mutant samples were directly compared to 8 wildtype samples. 3 out of the 8 were dye-swapped.
2010-06-25 | E-GEOD-18214 | biostudies-arrayexpress
Project description:Paper abstract: Stem cells have the remarkable ability to give rise to both self-renewing and differentiating daughter cells. Drosophila neural stem cells segregate cell-fate determinants from the self-renewing cell to the differentiating daughter at each division. Here, we show that one such determinant, the homeodomain transcription factor Prospero, regulates the choice between stem cell self-renewal and differentiation. We have identified the in vivo targets of Prospero throughout the entire genome. We show that Prospero represses genes required for self-renewal, such as stem cell fate genes and cell-cycle genes. Surprisingly, Prospero is also required to activate genes for terminal differentiation. We further show that in the absence of Prospero, differentiating daughters revert to a stem cell-like fate: they express markers of self-renewal, exhibit increased proliferation, and fail to differentiate. These results define a blueprint for the transition from stem cell self-renewal to terminal differentiation. 6 wildtype samples and 6 prospero mutant samples were hybridised to arrays against a commom reference sample (generated from whole embryo cDNA). The prospero samples were indirectly compared to the wildtype samples via the common reference. Half the wildtype and half of the prospero arrays were dye-swapped.
2010-06-25 | E-GEOD-18213 | biostudies-arrayexpress
Project description:Inversions have a breakpoint within a "neighbourhood" of testis expressed genes and the other breakpoint megabases away. The gene expression neighbourhood is therefore intact in the progenitor but disrupted in the inversion. 12 different inversion stocks, 3 or 4 biological replicates for each, including dye swaps.
2010-06-25 | E-GEOD-16616 | biostudies-arrayexpress
Project description:Inversions have a breakpoint within a "neighbourhood" of testis expressed genes and the other breakpoint megabases away. The gene expression neighbourhood is therefore intact in the progenitor but disrupted in the inversion. Keywords: Genome variation profiling by array 12 different inversion stocks, 3 or 4 biological replicates for each, including dye swaps.
2010-12-06 | E-GEOD-15565 | biostudies-arrayexpress
Project description:It is now well established that mature mammalian spermatozoa carry a population of mRNA molecules, at least some of which are transferred to the oocyte at fertilisation. However, the function of the sperm transcriptome remains largely unclear. To shed light on the evolutionary conservation of this feature of sperm biology, we analysed highly purified populations of mature sperm from the fruitfly, Drosophila melanogaster. As with mammalian sperm, we found a consistently enriched population of mRNA molecules that are not likely to be derived from contaminating somatic cells or immature sperm. Using tagged transcripts for three of the spermatozoal mRNAs, we demonstrate that they are transferred to the oocyte at fertilisation and can be detected at least until the onset of zygotic gene expression. We find a remarkable conservation in the functional annotations associated with fly and human spermatozoal mRNAs, in particular a highly significant enrichment for transcripts encoding Ribosomal Proteins. The identification of a conserved set of spermatozoal transcripts opens the possibility of using the power of Drosophila genetics to address the function of this enigmatic class of molecules. RNA extracted from three biological replicates of purified sperm (Sperm rep1, Sperm rep2 and Sperm rep3) was used as a template for oligo-dT-primed reverse transcription, amplification, labelling of dye swapped technical replicates and hybridisation to long oligonucleotides microarrays. As a control, RNA from two biological replicates of dissected adult testis plus accessory glands (Testis_rep1, Testis_rep2) was amplified, labelled (dye-swap technical replicate) and hybridised to similar arrays. To help with the spot-finding of the arrays genomic DNA was co-hybridised in some cases (this genomic DNA data was excluded from further analysis). Genes with an intensity level below 200 in at least one channel across the Sperm or Testis set were removed (5579 transcripts present in all three sperm replicates, 5358 transcripts from the testis/accessory gland samples and 4295 transcripts common to both data sets). Then the quantile normalisation was independently applied to the Sperm replicate samples and Testis replicates.
2012-04-23 | E-GEOD-33947 | biostudies-arrayexpress
Project description:We analysed the effect of the deficiency Df(2R)ED3921 and Df(2R)ED50000 on gene expression in embryos (stage 0-11), and wing imaginal discs and brains from 3rd instar larvae. Df(2R)ED3921 and Df(2R)ED50000 were described in Ragab et al. (2005) Genetics 172:1069-1078 2005. RNA from Df(2R)ED3921 and Df(2R)ED50000 embryos was compared to a pool of RNA extracted from wild-type embryos at the same stage. For each genotype, 4 independent biological replicates were performed (2 of these dyes swapped with respect to the other two). The same experimental protocol and genotypes were used for the analysis in dissected wing imaginal discs and brains from 3rd instar larvae.
2008-07-15 | E-GEOD-11880 | biostudies-arrayexpress
Project description:Cellular responses to signalling pathways are often highly dynamic, however most analyses of developmental signalling pathways focus on a single endpoint. Here we have analyzed the temporal changes in transcription following a short Notch activation treatment and have related these to the recruitment of the Notch pathway transcription factor, CSL [Suppressor of Hairless, Su(H), in Drosophila], and to the state of RNA Polymerase II (Pol II) binding. A total of 154 genes showed significant differential expression over time and their expression profiles stratified into 14 clusters based on temporal and quantitative differences in their responses. These differences were partially reflected in the profiles of Pol II and Su(H) binding. However neither could fully account for the different response profiles. Furthermore, the timing of the different responses was unaffected by more prolonged Notch activation. Instead our data suggest that regulatory relationships between genes that segregate into different response clusters can partially account for the stratification. Thus feed-forward repression, where products of early responding Enhancer of split bHLH genes (E(spl)bHLH) inhibit expression of endogenous repressors, is one mechanism that explains the profile of genes that exhibit delayed up-regulation. E(spl)bHLH genes may therefore be responsible for co-ordinating the Notch response of a wide spectrum of other targets, explaining their critical functions in many developmental and disease contexts. DmD8 cells were cultured in Schneiders medium (Invitrogen) supplemented with 10% FBS (Sigma), 5ug/ml insulin (Sigma) and 5% penicillin / streptomycin (Sigma) according to standard protocols. Notch signalling was initiated by replacing cell media with 2mM EDTA in PBS. The cells were stimulated for 5 minutes before washing out EDTA using normal culture media. The cells were then collected at 18 time points at 0M-bM-^@M-^Y, 5M-bM-^@M-^Y, 10M-bM-^@M-^Y, 15M-bM-^@M-^Y, 20M-bM-^@M-^Y, 25M-bM-^@M-^Y, 30M-bM-^@M-^Y, 35M-bM-^@M-^Y, 40M-bM-^@M-^Y, 50M-bM-^@M-^Y, 60M-bM-^@M-^Y, 70M-bM-^@M-^Y, 80M-bM-^@M-^Y, 90M-bM-^@M-^Y, 100M-bM-^@M-^Y, 110M-bM-^@M-^Y, 120M-bM-^@M-^Y and 150M-bM-^@M-^Y after stimulation in 4 independent time trials. For control samples, for each time trial, media was replaced with fresh media to mimic the addition and removal of EDTA in corresponding experimental samples and then collected at equivalent times. For each trial 50 M-BM-5g of the untreated control RNA sample of each time point was pooled to create a trial specific reference sample. Samples from trials #1 and #3 were labelled with Cy5 and trails #2 and #4 as dye-swap with Cy3.
2012-12-31 | E-GEOD-35557 | biostudies-arrayexpress