Gene expression analysis for Oregon R embryos at different developmental stages.
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila melanogaster
SUBMITTER: Bing He
PROVIDER: E-GEOD-36265 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Mapping the Drosophila melanogaster centromeric heterochromatin by CGH analysis of embryos lacking specific chromosomes or chromosome arms. Nine chromosome or chromosome arm deletions were tested: embryos lacking the entire second chromosome (2En-), 2L (2L-), 2R (2R-), the entire third chromosome (3En-), 3L (3L-), 3R (3R-), the entire fourth chromosome (4En-), the X chromosome (X-), or both X and Y chromosomes (XY-). Control: Blastoderm stage wild type Oregon R embryos. For each experiment 100-150 embryos of the appropriate genotype were collected. DNA from randomly staged 0-8 hr wild type Oregon R embryos was used as reference for all experiments. Embryos with no X chromosome were obtained by crossing attached-X/Y females (C(1)DX, y f) to X/Y males. Embryos with no X and Y chromosomes were obtained by crossing attached-X/Y females (C(1)RM, y2suwawa) to attached-XY males (YSX YL, In(1)EN, y B). The compound II chromosomes RM(2L); RM(2R)=C(2)v and the compound III chromosomes RM(3L); RM(3R)=C(3)se were used to generate 2L- and 2R-, and 3L- and 3R- embryos, respectively. The compound II C(2)EN and compound III C(3)EN st1 cu1es stocks were used to generate embryos deficient for the entire second and third chromosome, respectively. The compound IV C(4)RM, ci1eyR/0 were used to generate embryos deficient for the fourth chromosome. Embryos deficient for chromosome 4 were identified by their defects in denticle belt patterning during late embryogenesis, whereas embryos deficient for other chromosome/chromosome arm were recognized based on their specific phenotypic defects during early embryonic development. All embryos were collected at room temperature.
2012-03-06 | E-GEOD-36260 | biostudies-arrayexpress
Project description:Aneuploidy is a condition frequently found in tumor cells but how it affects cellular physiology is not known. We have characterized one aspect of aneuploidy, the gain of extra chromosomes. We created a collection of haploid yeast strains that each bear an extra copy of one or more of almost all of the yeast chromosomes. Their characterization revealed that aneuploid strains share a number of phenotypes, including defects in cell cycle progression, increased glucose uptake and increased sensitivity to conditions interfering with protein synthesis and protein folding. These phenotypes were observed only in strains carrying additional yeast genes indicating that they reflect the consequences of additional transcription and translation as well as the resulting imbalances in cellular protein composition. We conclude that aneuploidy causes not only a proliferative disadvantage but also a set of phenotypes that is independent of the identity of the individual extra chromosomes. Keywords: CGH, gene expression This series of microarrays compares yeast strains carrying extra chromosomes to wt yeast with normal chromosome content. Both DNA/CGH and gene expression comparisons were done, as noted. In some experiments, biological replicates were performed as noted. Reference wt nucleic acid was most commonly labeled with Cy3. Experiments labeled as "swap" have the wt reference nucleic acid labeled with Cy5, and ratio values for these experiments are reported as Cy3/Cy5.
2007-05-17 | E-GEOD-7812 | biostudies-arrayexpress
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2010-05-18 | E-GEOD-13435 | biostudies-arrayexpress
Project description:A major goal of biology is the construction of networks that predict complex system behavior. We combine multiple types of molecular data, including genotypic, expression, transcription factor binding site (TFBS), and protein-protein interaction (PPI) data previously generated from a number of yeast experiments in order to reconstruct causal gene networks. Networks based on different types of data are compared using metrics devised to assess the predictive power of a network. A network reconstructed by integrating genotypic, TFBS and PPI data is shown to be the most predictive. This network is used to predict causal regulators responsible for hot spots of gene expression activity in a segregating yeast population. The network is also shown to elucidate the mechanisms by which causal regulators give rise to larger-scale changes in gene expression activity. Predictions are prospectively validated to provide direct experimental evidence that predictive networks can be constructed by integrating multiple, appropriate data types. Keywords: allele replacement Allele replacement strains were created in two backgrounds: BY (BY4724 and BY4742), and RM11-1a, and compared to the parental type (BY4716 and RM11-1a). BY7g, BY9g, BY11g are BY4716, while RM7g, RM9g, and RM11g are RM11-1a. YAD350 is a MKT1 D30G replacement strain in BY4742 background. YLK804 is a SAL1-RM allele in BY4724 and YLK806 is a SAL1-BY allele in RM11-1a. All strains were grown in YNB + 2% glucose, with leucine, lysine, and uracil. YAD350 was also grown with histidine.
2008-06-15 | E-GEOD-11111 | biostudies-arrayexpress
Project description:Technological advances now make gene expression analysis feasible in any sequenced organism, and new sequencing methods have greatly accelerated genome sequencing. Here we show that important insights into gene function are possible by comparing gene expression response to genetic and environmental perturbations between related species. We present a gene expression compendium designed for maximal gene expression variation in the sensu stricto yeast Saccharomyces bayanus. While many aspects of gene expression are conserved over the 20 million years of evolution separating S. bayanus from the model yeast S. cerevisiae, we observe regulatory changes, including in galactose metabolism and sporulation. The expression data also allows us to predict the biological roles of genes unique to S. bayanus, leading us to propose a role in oxidative stress response for a group of genes, and also to identify a regulatory network specific to this yeast. This dataset contains 53 experiments as follows: (experiment: number of datasets (number of arrays)) growth at different temperatures: 1 (3) heat shock: 4 (18) ammonium: 1 (6) cadmium: 1 (4) copper: 1 (6) lead: 1 (6) nickel: 1 (5) sulfite toxicity: 1 (6) zinc: 1 (6) ethanol toxicity: 1 (6) sorbitol: 1 (6) bleach: 1 (6) hydrogen peroxide: 3 (17) 2-deoxyglucose: 1 (6) hydroxyurea: 1 (6) lovastatin: 1 (4) MG-132: 1 (5) MMS: 1 (6) rapamycin: 1 (6) tunicamycin: 1 (6) zeocin: 1 (6) chronological aging: 3 (13) diauxic shift: 1 (6) galactose: 5 (38) glycerol: 1 (4) sucrose: 1 (4) auxotroph starvation: 1 (11) nutrient limited chemostat growth: 3 (7) mating type and ploidy: 1 (3) alpha factor: 1 (8) cell cycle: 1 (30) sporulation: 3 (18) strain backgrounds: 1 (4) cross progeny: 1 (22) Tn7 insertions: 1 (27) 555.11 and 670.20 knockout tetrads: 2 (8) Timecourse datasets: heat shock, ammonium, cadmium, copper, lead, nickel, sulfite toxicity, zinc, ethanol toxicity, sorbitol, bleach, hydrogen peroxide, 2-deoxyglucose, hydroxyurea, lovastatin, MG-132, MMS, rapamycin, tunicamycin, zeocin, chronological aging, diauxic shift, galactose, glycerol, sucrose, auxotroph starvation, alpha factor, cell cycle, sporulation Single timepoint datasets: growth at different temperatures, strain backgrounds, cross progeny, Tn7 insertions, nutrient limited chemostat growth, mating type and ploidy, 555.11 and 670.20 knockout tetrads Almost all samples were hybridized versus a common reference prepared from a mixture of RNA from Mat a, Matx, and Mata/x cells sampled in both exponential and stationary phase. Additionally, RNA from stress conditions was included: hydrogen peroxide treatment sampled at 10, 30 and 45 minutes, and heat shock from 25 to 37 degrees sampled at 10 and 30 minutes. Samples from the following datasets were not hybridized versus the common reference (reference used in parenthesis and in array annotations): cell cycle (asynchronous culture), constant temperatures (log phase culture), mating type and ploidy (log phase culture), diauxic shift (log phase culture), and strain backgrounds (log phase culture). Replicates and dye swaps were not used.
2010-05-16 | E-GEOD-16544 | biostudies-arrayexpress
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2008-04-15 | E-GEOD-9376 | biostudies-arrayexpress
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2012-03-06 | E-GEOD-36262 | biostudies-arrayexpress
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2012-03-06 | E-GEOD-36263 | biostudies-arrayexpress
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2010-02-24 | E-GEOD-20464 | biostudies-arrayexpress
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2007-08-18 | E-GEOD-8805 | biostudies-arrayexpress