Wt expression changes in deletion strain-conditioned media
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
SUBMITTER: Philip Lijnzaad
PROVIDER: E-MTAB-2218 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
Cell cycle population effects in perturbation studies.
O'Duibhir Eoghan E Lijnzaad Philip P Benschop Joris J JJ Lenstra Tineke L TL van Leenen Dik D Groot Koerkamp Marian J A MJ Margaritis Thanasis T Brok Mariel O MO Kemmeren Patrick P Holstege Frank C P FC
Molecular systems biology 20140621
Growth condition perturbation or gene function disruption are commonly used strategies to study cellular systems. Although it is widely appreciated that such experiments may involve indirect effects, these frequently remain uncharacterized. Here, analysis of functionally unrelated Saccharyomyces cerevisiae deletion strains reveals a common gene expression signature. One property shared by these strains is slower growth, with increased presence of the signature in more slowly growing strains. The ...[more]
Similar Datasets
Project description:Alteration of growth condition or disruption of gene function are commonly used strategies to study cellular systems. Although widely appreciated that such experiments may result in indirect effects, these frequently remain uncharacterized. Here, genome-wide expression reanalysis of functionally unrelated Saccharyomyces cerevisiae deletion strains reveals a common expression signature. One property shared by these strains is slower growth, with increased presence of the signature in more slowly growing strains. The slow growth signature is highly similar to the environmental stress response, an expression response common to diverse environmental perturbations. Both environmental and genetic perturbations result in growth rate changes. These are accompanied by a change in the distribution of cells over different cell cycle phases. Rather than representing a direct expression response, the slow growth signature is a consequence of the redistribution of cells over different cell cycle phases, primarily characterized by an increase in the G1 population. The findings have implications for any study of perturbation that is accompanied by growth rate changes. Strategies to counter these effects are presented and discussed. This series shows the absence of media effects by growing wt strains in filtered medium in which slow-growing strains were grown previously. Two channel microarrays were used. RNA isolated from a large amount of wt yeast from a single culture was used as a common reference. Two independent cultures were hybridized on two separate microarrays. For the first hybridization the Cy5 (red) labeled cRNA from the deletion mutant is hybridized together with the Cy3 (green) labeled cRNA from the common reference. For the replicate hybridization, the labels are swapped.
2014-05-14 | E-GEOD-54539 | biostudies-arrayexpress
Project description:Heatshock (30 to 37 deg C) and Coldshock (37 to 30 deg C) experiment looking at 5, 15, 30, 45 and 60 mins after the temp change in each condition.
2014-05-14 | E-MTAB-2219 | biostudies-arrayexpress
Project description:Alteration of growth condition or disruption of gene function are commonly used strategies to study cellular systems. Although widely appreciated that such experiments may result in indirect effects, these frequently remain uncharacterized. Here, genome-wide expression reanalysis of functionally unrelated Saccharyomyces cerevisiae deletion strains reveals a common expression signature. One property shared by these strains is slower growth, with increased presence of the signature in more slowly growing strains. The slow growth signature is highly similar to the environmental stress response, an expression response common to diverse environmental perturbations. Both environmental and genetic perturbations result in growth rate changes. These are accompanied by a change in the distribution of cells over different cell cycle phases. Rather than representing a direct expression response, the slow growth signature is a consequence of the redistribution of cells over different cell cycle phases, primarily characterized by an increase in the G1 population. The findings have implications for any study of perturbation that is accompanied by growth rate changes. Strategies to counter these effects are presented and discussed. In this series, the effects, over time, of heatshock (shifting cells from 30 to 37 C) or the reverse (cold 'shock') are studied. Two channel microarrays were used. RNA isolated from a large amount of wt yeast from a single culture was used as a common reference. Two independent cultures were hybridized on two separate microarrays. For the first hybridization the Cy5 (red) labeled cRNA from the test sample is hybridized together with the Cy3 (green) labeled cRNA from the common reference. For the replicate hybridization, the labels are swapped. In the statistical analysis, factor levels are compared using the common reference as an intermediate.
2014-05-14 | E-GEOD-54528 | biostudies-arrayexpress
Project description:expression changes of 75 uM phosphate vs. 10000 uM phosphate
2014-05-14 | E-MTAB-2217 | biostudies-arrayexpress
Project description:The transcription profile of Candida glabrata grown under two different Niacin limitation conditions were determined. Condition 1 is comparing log phase C. glabrata cells (O.D. 0.5-0.6) grown in synthetic medium containing 0.016 uM versus 3.25 uM nicotinic acid (NA), a common form of Niacin. The NA concentration of 3.25 uM is the standard concentration in synthetic complete (SC) medium. Condition 2 is comparing log phase C. glabrata cells (O.D. 0.4-0.6) grown in 3 individual human urine samples (supplemented with 2% glucose) versus in SC medium. Keywords: transcriptional profiling by microarray GSM151863, GSM151869 are dye-swap experiment #1 and GSM151880, GSM151881 are dye-swap experiment #2 for Niacin limitation condition 1. GSM151934, GSM152116 are dye-swap experiment #1, GSM152118, GSM152119 are dye-swap experiment #2 and GSM152130, GSM152131 are dye-swap experiment #3 for Niacin limitation condition 2.
2010-06-05 | E-GEOD-6582 | biostudies-arrayexpress
Project description:A universal feature of the response to stress and nutrient limitation is transcriptional upregulation of genes encoding proteins important for survival. Interestingly, under many of these conditions overall protein synthesis levels are reduced, thereby dampening the stress response at the level of protein expression. For example, during glucose starvation in yeast, translation is rapidly and reversibly repressed, yet transcription of many stress- and glucose-repressed genes is increased. Using ribosome profiling and microscopy, we found that this transcriptionally upregulated gene set consists of two classes: (1) one producing mRNAs that are preferentially translated during glucose limitation and are diffusely localized in the cytoplasm – this class includes many heat shock protein mRNAs; and (2) another producing mRNAs that are poorly translated during glucose limitation, have high rates of translation initiation, and are concentrated in foci that co-localize with P bodies and stress granules – this class is enriched for glucose metabolism mRNAs. Remarkably, the information specifying differential localization and translation of these two classes of mRNAs is encoded in the promoter sequence – promoter responsiveness to heat shock factor (Hsf1) specifies diffuse cytoplasmic localization and preferential translation upon glucose starvation, whereas different promoter elements upstream of genes encoding poorly translated glucose metabolism mRNAs direct these mRNAs to RNA granules under glucose starvation. Thus, promoter sequences and transcription factor binding can influence not only mRNA levels, but also subcellular localization of mRNAs and the efficiency with which they are translated, enabling cells to tailor protein production to environmental conditions. Examination of mRNA translation in S. cerevisiae upon glucose starvation.
2014-07-28 | E-GEOD-56622 | biostudies-arrayexpress
Project description:In this study we probe how prototrophic yeast from different environmental backgrounds respond to perturbing agents presented in the context of a conflicting signal, repletion of glucose after transient deprivation. To assess the contribution of genetic v
2013-03-03 | E-MTAB-1463 | biostudies-arrayexpress
Project description:Microarray timecourses followed the gene expression response of Saccharomyces cereviciae to osmotic shock, over 4 hours. Data was compared to timecourses of quantitative proteomic data to understand the dynamic relationship between RNA and protein The dynamic genomic expression response to osmotic shock (0.7M NaCl) was measured in Saccharomyces cereviciae, over the course of 4 hours in biological triplicate. Six timepoints were taken for each time course, for a total of 18 tiled-genomic Nimblegen arrays against the S288c yeast genome.
2011-08-17 | E-GEOD-23798 | biostudies-arrayexpress
Project description:To explore putative connections between genetic methionine restriction and the retrograde response, we asked whether the altered transcriptional program of methionine-restricted cells required RTG3 (which is indispensible for retrograde signaling in yeast). Towards this end, we used Affymetrix GeneChip Yeast Genome 2.0 arrays to perform expression profiling of aged (Day 3) wild-type, met15Δ and rtg3Δ met15Δ yeast.
2014-04-10 | E-GEOD-56641 | biostudies-arrayexpress
Project description:The C-terminal domain (CTD) of RNA polymerase II (RNAPII) is composed of heptapeptide repeats, which play a key regulatory role in gene expression. Using genetic interaction and mRNA expression analysis we found that truncating the CTD resulted in distinct changes to cellular function. Truncating the CTD altered RNAPII occupancy to not only cause decreases, but also increases in mRNA levels. The latter were largely mediated by promoter elements, and in part were linked to the transcription factor Rpn4. The mediator subunit Cdk8 was enriched at promoters of these genes, and its removal not only restored normal mRNA and RNAPII occupancy levels, but also reduced the abnormally high cellular amounts of Rpn4. This suggested a positive role of Cdk8 in relationship to RNAPII, which contrasted with the negative role at the activated INO1 gene. Here, loss of CDK8 suppressed the reduced mRNA expression and RNAPII occupancy levels of CTD truncation mutants. Two channel microarrays were used. RNA isolated from a large amount of wt yeast from a single culture was used as a common reference. This common reference was used in one of the channels for each hybridization and used in the statistical analysis to obtain an average expression-profile for each deletion mutant relative to the wt. Two independent cultures were hybridized on two separate microarrays. For the first hybridization the Cy5 (red) labeled cRNA from the deletion mutant is hybridized together with the Cy3 (green) labeled cRNA from the common reference. For the replicate hybridization, the labels are swapped. Each gene is represented twice on the microarray, resulting in four measurements per mutant. Using the Erlenmeyer growth protocol up to five deletion strains were grown on a single day. In the tecan platereader, up to eleven deletion strains could be grown on a single day. Wt cultures were grown parallel to the deletion mutants to assess day-to-day variance.
2013-09-13 | E-GEOD-43120 | biostudies-arrayexpress