Deletions_TETs_WTs
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
SUBMITTER: Timothy Hughes
PROVIDER: E-GEOD-457 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
A panoramic view of yeast noncoding RNA processing.
Peng Wen Tao WT Robinson Mark D MD Mnaimneh Sanie S Krogan Nevan J NJ Cagney Gerard G Morris Quaid Q Davierwala Armaity P AP Grigull Jörg J Yang Xueqi X Zhang Wen W Mitsakakis Nicholas N Ryan Owen W OW Datta Nira N Jojic Vladimir V Pal Chris C Canadien Veronica V Richards Dawn D Beattie Bryan B Wu Lani F LF Altschuler Steven J SJ Roweis Sam S Frey Brendan J BJ Emili Andrew A Greenblatt Jack F JF Hughes Timothy R TR
Cell 20030601 7
Predictive analysis using publicly available yeast functional genomics and proteomics data suggests that many more proteins may be involved in biogenesis of ribonucleoproteins than are currently known. Using a microarray that monitors abundance and processing of noncoding RNAs, we analyzed 468 yeast strains carrying mutations in protein-coding genes, most of which have not previously been associated with RNA or RNP synthesis. Many strains mutated in uncharacterized genes displayed aberrant nonco ...[more]
Similar Datasets
Project description:These series of experiments compares the expression profile of the motility variants of E.coli MG1655 ( Motile and NonMotile isolates) to an isogenic E.coli MG1655 strain in which the IS5 upstream of flhDC has been deleted. The expression profiles of genes in the E.coli MG1655 motile isolate and E.coli MG1655 Non_Motile isolate also compared.
2010-06-09 | E-GEOD-2694 | biostudies-arrayexpress
Project description:The Saccharomyces cerevisiae gene PIF1 encodes a conserved eukaryotic DNA helicase required for both mitochondrial and nuclear DNA integrity. Our previous work revealed that a pif1D strain is tolerant to zinc overload. We demonstrate here that this effect is independent of the Pif1 helicase activity and is only observed when the protein is absent from the mitochondria. pif1 cells accumulate abnormal amounts of mitochondrial zinc and iron. Transcriptional profiling reveals that pif1 cells under standard growth conditions overexpress aconitase-related genes. When exposed to zinc, pif1 cells show lower induction of genes encoding iron (siderophores) transporters and higher expression of genes related to oxidative stress responses than wild type cells. Coincidently, pif1 mutants are less prone to zinc-induced oxidative stress and display a higher reduced/oxidized glutathione ratio. Strikingly, although pif1 cells contain normal amounts of the Aco1 protein, they completely lack aconitase activity. Loss of Aco1 activity is also observed when the cell expresses a non-mitochondrially targeted form of Pif1. We postulate that lack of Pif1 forces aconitase to play its DNA protective role as nucleoid protein and that this would trigger a domino effect on iron homeostasis resulting in increased zinc tolerance. Four samples were analyzed: WT and pif1 mutant both, in the presence and in the absence of 5 mM ZnCl2 for 1 h. We compared the expression profile of: 1) WT+Zn vs WT-Zn, 2) pif1 mutant+Zn vs pif1 mutant-Zn, 3) pif1 mutant vs WT, and 4) pif1 mutant+Zn vs WT+Zn. A Dye-swap was carried out for each comparison of samples. Total number of chips analyzed: 8.
2010-05-31 | E-GEOD-18411 | biostudies-arrayexpress
Project description:We measured steady-state mRNA levels by microarray hybridization, comparing WT, (delta)ire1, (delta)gcn4, and (delta)gcn2 cells treated with 2 mM DTT for 30 min (by which time the UPR is qualitatively complete) to untreated samples of the same genotype. WT cells were taken as a positive control for UPR induction, and (delta)ire1 cells as a negative control. Fold change in expression of a given gene was computed as the ratio of mRNA level in the treated sample to the level in an untreated sample of the same genotype. Values reported here are the log2 fold change. Keywords = unfolded protein response Keywords = UPR Keywords = ire1 Keywords = gcn4 Keywords = gcn2
2010-06-06 | E-GEOD-1688 | biostudies-arrayexpress
Project description:Potassium is the major intracellular cation in S. cerevisiae, which can be concentrated up to 200-300 mM even from relatively low potassium (< 1 mM) environments. This is achieved by mean of a high affinity K+-transport system encoded by the genes TRK1 and TRK2. Recently, our group became interested in the effects of sudden shortage of extracellular potassium. Transcriptomic analysis indicates that lack of potassium drastically alters sulfur metabolism (mainly Met and Cys metabolism), triggers an oxidative stress response and activates the mitochondrial retrograde pathway. We also observe a dramatic halt in the expression of genes required for ribosome biogenesis and translation, as well as decrease in expression of diverse genes (cyclins, protein kinases) required for progression through the cell cycle. Only subsets of these changes were observed in a strain deleted for the TRK1 and TRK2 genes growing in the presence of sufficient potassium (50 mM). Research involving molecular genetics and metabolomic approaches aiming to clarify the primary targets for potassium requirements is currently ongoing. The effect of a sudden shortage of extracellular potassium was studied using a wt yeast strain. Samples of cell cultures grown in either, in the presence or in the absence of potassium, were taken after 10, 20, 40, 60 and 120 min of potassium shortage. We compared the expression profile of: 1) WT w/o K vs WT w/ KCl at 10 min: 2) WT w/o K vs WT w/ KCl at 20 min. 3) WT w/o K vs WT w/ KCl at 40 min. 4) WT w/o K vs WT w/ KCl at 60 min. 5) WT w/o K vs WT w/ KCl at 120 min. Two independent experiments were performed, except for the timepoint of 10 min. For each experiment a dye-swap was carried out. Chips analyzed: 2 for 10 min 4 for 20 min 4 for 40 min 4 for 60 min 4 for 120 min Total number of chips: 18
2012-10-13 | E-GEOD-24712 | biostudies-arrayexpress
Project description:The two-component system CBO0366/CBO0365 was recently demonstrated to have a role in cold tolerance of Group I Clostridium botulinum ATCC 3502. The mechanisms under its control, ultimately resulting in increased sensitivity to low temperature, are unknown. A transcriptomic analysis with DNA microarrays was performed to identify the differences in global gene expression patterns of the wild-type ATCC 3502 and a derivative mutant with insertionally inactivated cbo0365 at 37 M-BM-0C and 15 M-BM-0C. Altogether 150 or 141 chromosomal CDSs were found to be differently expressed in the cbo0365 mutant at 37 M-BM-0C or 15 M-BM-0C, respectively, and thus considered to be under direct or indirect transcriptional control of the response regulator CBO0365. Of the differentially-expressed CDSs, expression of 141 CDSs was similarly affected at both temperatures investigated, suggesting that the putative CBO0365 regulon was practically not affected by temperature. The regulon involved genes related to acetone-butanol-ethanol (ABE) fermentation, motility, to arsenic resistance, and phosphate uptake and transport. Deteriorated growth at 17 M-BM-0C was observed for mutants with disrupted ABE fermentation pathway components (crt, bdh and ctfA), arsenic detoxifying machinery components (arsC and arsR), or phosphate uptake mechanism components (phoT), suggesting roles for these mechanisms in cold tolerance of Group I C. botulinum. Electrophoretic mobility shift assays showed recombinant CBO0365 to bind to the promoter regions of crt, arsR, and phoT, as well as to the promoter region of its own operon, suggesting direct DNA-binding transcriptional activation or repression as means for CBO0365 in regulating these operons. The results provide insight to the mechanisms Group I C. botulinum utilize in coping with cold. C. botulinum ATCC 3502 cbo0365 mutant vs. wild type; 3 replicates of each strain; growth at 37C in TPGY broth batch culture and subjected to cold shock to 15C; sampling at mid-log growth phase before cold shock, and 1 h after temperature downshift to 15C (= 2 time points). Dye-swapped hybridization.
2013-10-29 | E-GEOD-26587 | biostudies-arrayexpress
Project description:Tumor-associated breast stroma was laser-capture microdissected from IDC breast cancer cases. The goal of the study was to characterize the heterogeneity of breast tumor-assocaited stroma and identify gene expression signatures predictive of clinical outcome. Experiment Overall Design: Common reference design, 53 samples, with dye-swap replicates. Some samples replicated three or four times, a total of 111 arrays.
2008-06-16 | E-GEOD-9014 | biostudies-arrayexpress
Project description:We are interested in the study of the already reported sensitivity of yeast cells lacking the type 1 protein phosphatase Ptc1 to the drug rapamycin. In order to carry out our studies, we analyzed the changes in the transcription profile that a short-term incubation with rapamycin (200 ng/mL) has in both, wild type and ptc1 cells. It has been shown that inhibition of the TOR pathway by treatment with rapamycin has profound effects on the global transcriptional profile. We confirmed the previously described transcription changes induced by the drug in wild type cells. Under our working conditions rapamycin increased, in wild type cells, at least 2-fold the expression of 667 genes, whereas it decreased the mRNA level of 721 genes (13.8% and 14.9% of genes with measurable expression level, respectively). Gene ontology analysis shows that, as previously documented, many induced genes falls into the NCR, Msn2/Msn4 regulated stress response or Retrograde response categories, whereas genes encoding cytoplasmic, but not mitochondrial, ribosomal proteins and the so called RIBI regulon where largely repressed. Deletion of PTC1 decreases the number of genes induced or repressed at least 2-fold by rapamycin treatment. Remarkably, lack of Ptc1 seems to lead to a general attenuation of changes triggered by rapamycin. The wt and the ptc1 mutant strains were analyzed in this series. We compared the expression profile of each strain treated with Rapamycin (200 ng/ml for 1h) with that of the same strain mock-treated (90% ethanol, 10% Tween-20). A Dye-swap was carried out for each RNA sample. Total number of chips analyzed: 4
2008-12-31 | E-GEOD-11530 | biostudies-arrayexpress
Project description:Array-based comparative genome hybridization. The aneuploid progeny could return to euploid state. We determined genome-wide gene copy number in the genomes of aneuploid progeny after 14, 24 and 34 days vegetative propagation in dextrose-containing rich medim.
2015-01-07 | E-GEOD-42359 | biostudies-arrayexpress
Project description:Comparison of gene expression profiles of wild-type and fl-mutant upland cotton ovules Data for six replicate experiments performed with biologically independent samples. Cy3 and Cy5 dyes were used as follows: Set 1: wt+5-Cy5 wt+3-Cy3 Set 1 (dye swap): wt+5-Cy3 wt+3-Cy5 Set 2: wt+5-Cy5 wt+3-Cy3 Set 2 (dye swap): wt+5-Cy3 wt+3-Cy5 Set 3: wt+5-Cy5 wt+3-Cy3 Set 3 (dye swap): wt+5-Cy3 wt+3-Cy5 GSM63341, GSM63342, GSM63343, GSM63344, GSM63345, GSM63346 Data for 3 replicate experiments performed with biologically independent samples. Cy3 and Cy5 dyes were used as follows: Set 1: wt+3-Cy5 vs wt+3-Cy3 Set 2: wt+3-Cy3 vs wt+3-Cy5 Set 3: wt+3-Cy5 vs wt+3-Cy3 GSM63365, GSM63366, GSM63367 Data for six replicate experiments performed with biologically independent samples. Cy3 and Cy5 dyes were used as follows: Set 1: wt+3-Cy5 wt-3-Cy3 Set 1 (dye swap): wt+3-Cy3 wt-3-Cy5 Set 2: wt+3-Cy5 wt-3-Cy3 Set 2 (dye swap): wt+3-Cy3 wt-3-Cy5 Set 3: wt+3-Cy5 wt-3-Cy3 Set 3 (dye swap): wt+3-Cy3 wt-3-Cy5 GSM63368, GSM63369, GSM63370, GSM63371, GSM63372, GSM63373 Data for six replicate experiments performed with biologically independent samples. Cy3 and Cy5 dyes were used as follows: Set 1: 0wt-Cy5 wt+3-Cy3 Set 1 (dye swap): 0wt-Cy3 wt+3-Cy5 Set 2: 0wt-Cy5 wt+3-Cy3 Set 2 (dye swap): 0wt-Cy3 wt+3-Cy5 Set 3: 0wt-Cy5 wt+3-Cy3 Set 3 (dye swap): 0wt-Cy3 wt+3-Cy5 GSM63374, GSM63375, GSM63376, GSM63377, GSM63378, GSM63379 Data for six replicate experiments performed with biologically independent samples. Cy3 and Cy5 dyes were used as follows: Set 1: wt+3-Cy5 fl+3-Cy3 Set 1 (dye swap): wt+3-Cy3 fl+3-Cy5 Set 2: wt+3-Cy5 fl+3-Cy3 Set 2 (dye swap): wt+3-Cy3 fl+3-Cy5 Set 3: wt+3-Cy5 fl+3-Cy3 Set 3 (dye swap): wt+3-Cy3 fl+3-Cy5 GSM63391, GSM63392, GSM63393, GSM63394, GSM63395, GSM63396 Data for six replicate experiments performed with biologically independent samples. Cy3 and Cy5 dyes were used as follows: Set 1: wt+10-Cy5 fl+10-Cy3 Set 1 (dye swap): wt+10-Cy3 fl+10-Cy5 Set 2: wt+10-Cy5 fl+10-Cy3 Set 2 (dye swap): wt+10-Cy3 fl+10-Cy5 Set 3: wt+10-Cy5 fl+10-Cy3 Set 3 (dye swap): wt+10-Cy3 fl+10-Cy5 GSM63397, GSM63398, GSM63399, GSM63400, GSM63401, GSM63402 Data for six replicate experiments performed with biologically independent samples. Cy3 and Cy5 dyes were used as follows: Set 1: wt+10-Cy5 wt+3-Cy3 Set 1 (dye swap): wt+10-Cy3 wt+3-Cy5 Set 2: wt+10-Cy5 wt+3-Cy3 Set 2 (dye swap): wt+10-Cy3 wt+3-Cy5 Set 3: wt+10-Cy5 wt+3-Cy3 Set 3 (dye swap): wt+10-Cy3 wt+3-Cy5 GSM63403, GSM63404, GSM63405, GSM63406, GSM63407, GSM63408 Data for six replicate experiments performed with biologically independent samples. Cy3 and Cy5 dyes were used as follows: Set 1: wt+15-Cy5 wt+3-Cy3 Set 1 (dye swap): wt+15-Cy3 wt+3-Cy5 Set 2: wt+15-Cy5 wt+3-Cy3 Set 2 (dye swap): wt+15-Cy3 wt+3-Cy5 Set 3: wt+15-Cy5 wt+3-Cy3 Set 3 (dye swap): wt+15-Cy3 wt+3-Cy5 GSM63409, GSM63410, GSM63411, GSM63412, GSM63413, GSM63414 Data for six replicate experiments performed with biologically independent samples. Cy3 and Cy5 dyes were used as follows: Set 1: wt+20-Cy5 wt+3-Cy3 Set 1 (dye swap): wt+20-Cy3 wt+3-Cy5 Set 2: wt+20-Cy5 wt+3-Cy3 Set 2 (dye swap): wt+20-Cy3 wt+3-Cy5 Set 3: wt+20-Cy5 wt+3-Cy3 Set 3 (dye swap): wt+20-Cy3 wt+3-Cy5 GSM63415, GSM63416, GSM63417, GSM63418, GSM63419, GSM63420
2010-07-01 | E-GEOD-2901 | biostudies-arrayexpress
Project description:Chromosome segregation depends on proper attachment of sister kinetochores to microtubules. Merotelic kinetochore orientation is an error which occurs when a single kinetochore is attached to microtubules emanating form opposite poles. Mechanisms preventing or correcting the merotelic attachment must operate to avoid chromosome missegregation. Pcs1 has been implicated in preventing merotelic attachment in mitosis and meiosis II. We describe here the identification of Mde4 protein which forms a complex with the Pcs1. Both Mde4 and Pcs1 localize to the central core of the centromere. Similarly to the pcs1 mutant, in the absence of mde4 lagging chromosomes are frequently observed during mitosis and meiosis II . We provide the first evidence that the lagging chromosomes in pcs1 and mde4 mutants are due to merotelic kinetochore orientation. Keywords: ChIP-chip analysis ChIP-chip analysis: In all cases, hybridization data for ChIP fraction was compared with that of SUP (supernatant) fraction. Pombe whole chromosome array was used.
2010-06-10 | E-GEOD-5257 | biostudies-arrayexpress