Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

X-QTL performed on wild-type and sup35 (C653R) BY x RM segregants in various growth conditions

ABSTRACT: Genotyping pools of wildtype(wt) or sup35-C653R(sup35) BYxRM segregants after growth on YPD (control) or YPD+drug-of-interest(selection) 10 Growth conditions tested are control (YPD alone), and YPD plus the following drugs: Chlorpromazine, CoCl2, Cycloheximide, Diamide, E6berbamine, Ethanol, H2O2, Neomucin, and Tunicamycin. Two-condition experiment, control vs selection. 6 biological replicates for control and two biological replicates for each selection included.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Noorossadat Torabi

PROVIDER: E-GEOD-33817 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

X-QTL performed on wild-type and sup35 (C653R) BY x RM segregants in various growth conditions

Project description:Genotyping pools of wildtype(wt) or sup35-C653R(sup35) BYxRM segregants after growth on YPD (control) or YPD+drug-of-interest(selection) 10 Growth conditions tested are control (YPD alone), and YPD plus the following drugs: Chlorpromazine, CoCl2, Cycloheximide, Diamide, E6berbamine, Ethanol, H2O2, Neomucin, and Tunicamycin.

2011-12-01 | GSE33817 | GEO

Transcription profiling by tiling array of Saccharomyces cerevisiae segregants spores obtained from a cross of the yeast strains S96 and YJM789.

Project description:Transcription profile in YPD media of 48 segregants spores obtained from a cross of the yeast strains S96 and YJM789. These spores are a subset of those published by Mancera et al, Nature, 2008. Two CEL files were mislabelled: eQTL_080822_spore_38B.CEL and eQTL_080826_spore_21C.CEL, actually spores 24A and 8D respectively. The correct spore IDs are in the sample annotation (under StrainOrLine).

2010-10-06 | E-TABM-845 | biostudies-arrayexpress

Methylated RNA immunoprecipitation sequencing in the Kasumi-1 cell line treated with CoCl2 and echinomycin

Project description:To evaluate the role of HIF1α in modulating the m6A abundance, we conducted m6A sequencing in the Kasumi-1 cell line treated with CoCl2 and echinomycin. CoCl2 can mediate the stabilization of HIF1α protein. Echinomycin is a small-molecule inhibitor of HIF1α, which functions through sequence-specific binding to HRE to competitively inhibit HIF1α binding to its target genes. The m6A sequencing results of the Kasumi-1 cell line treated with CoCl2 and non-treated control were uploaded previously (GSE168778). The differential m6A peaks analysis between CoCl2 + echinomycin group and CoCl2 group was performed.

2022-07-01 | GSE200605 | GEO

Long-term exposure of Candida glabrata to human monocyte-derived macrophages, with long-term medium growth controls

Project description:Candida glabrata were kept within human moncoyte-derived macrophages (MDM) for up to seven days to investigate the transcriptome of long-term residence within phagosomes. Samples were taken after 6h and 1, 2, 4, and 7 days. To control for general starvation, long-term exposure data for the growth media YPD, SD, and RPMI (with serum) were included. Experiments were performed as a common reference design, with log-phase YPD growth as Cy3-labeled reference for all arrays.

2023-05-31 | E-MTAB-11801 | biostudies-arrayexpress

RNA-Seq of Saccharomyces cerevisiae cells carrying different YRR1 alleles in response to 4-nitroquinoline-N-oxide (4NQO) and to glycerol as the sole carbon source

Project description:In this study, we constructed three isogenic strains of S96 yrr1Î? background (its native YRR1 gene was knocked out) carrying three different YRR1 alleles, YRR1_S96, YRR1_YJM789 and YRR1_S96-I775E, respectively. We then conducted RNA deep sequencing (RNA-Seq) on the three strains grown in Yeast Peptone Dextrose medium (YPD), YPD + 4NQO and Yeast Peptone glycerol medium (YPglycerol). RNA-Seq was performed in biological duplicates on S96 cells carrying three different YRR1 alleles grown in YPD, YPD + 4NQO, YPglycerol

2016-03-01 | E-GEOD-74642 | biostudies-arrayexpress

Expression data from Saccharomyces cerevisiae strains deleted for the THSC/TREX-2 subunits Thp1, Sac3 and Sus1

Project description:Transcription is a major obstacle for replication fork progression and a cause of genome instability. Such instability increases in mutants with a suboptimal assembly of the nascent messenger ribonucleo-protein particle (mRNP), as THO/TREX and the NPC-associated THSC/TREX-2 complex. We used microarrays to analyze the global impact of THSC/TREX-2 in gene expression and found that Thp1 and Sac3 depletion has a functional impact in highly-expressed, long and G+C-rich genes regardless of their function S. cerevisiae strains were grown in YPD liquid culture, total RNA was isolated and hybridized on Affymetrix microarrays

2014-10-08 | E-GEOD-56702 | biostudies-arrayexpress

Comparison of the transcriptome of the ethanol adapted yeast and control at 10% ethanol

Project description:In this study, using DNA microarray analysis, we compared the comprehensive expression profiles of two yeast trains, i.e, the previously obtained ethanol-adapted yeast strain and the parental strain as control (FY834), under the ethanol stress condition (YPD medium contained 10% ethanol). As a result, we identified certain genes and functional categories of the genes that are possible involved in growth under the ethanol stress condition. The ethanol adapted and FY834 yeasts were cultivated in YPD medium containing 10% ethanol. For the control, FY834 strain was cultivated in YPD medium. Cells were harvested in the logarithmic growth phase and then immediately frozen in liquid nitrogen. Total RNA was extracted by the hot phenol method and purified into mRNA using an Oligo dT30<Super> mRNA purification kit. Cy3-labelled cDNA targets were prepared from 1.5 Âµg of mRNA samples of yeasts grown in the ethanol stress condition. Cy5-labelled cDNA targets were prepared from 1.5 Âµg of mRNA samples of yeast grown in YPD. Cy3-and Cy5-labelled cDNA targets were mixed and then hybridized with probes on the DNA microarray, Yeast gene chip ver.2. (DNA Chip Research Inc.,Japan). The preparation of fluorescent-dye-labeled cDNA targets, hybridization, and washing were carried out as described in instruction manuals supplied by the manufacturer of the DNA microarray.

2010-05-15 | E-GEOD-13757 | biostudies-arrayexpress

RNA sequencing of pheromone stimulated and unstimulated MATa and MATM-NM-1 Saccharomyces cerevisiae

Project description:Haploid budding yeast has two mating types, defined by the alleles of the MAT locus, MATa and MATM-NM-1. Mating occurs when two haploid cells of opposite mating types signal to each other using reciprocal pheromones and receptors, polarize and grow towards each other, and eventually fuse to form a single diploid cell. The pheromones and receptors are necessary and sufficient to define a mating type, but other mating type-specific proteins make mating more efficient. We examined the role of these proteins by genetically engineering M-bM-^@M-^\transvestiteM-bM-^@M-^] cells that swap the pheromone, pheromone receptor, and pheromone processing factors of one mating type for another. These cells can mate with each other, but their mating is inefficient. By characterizing their mating defects and examining their transcriptomes, we found Afb1 (a-factor barrier), a novel MATM-NM-1-specific protein that interferes with a-factor, the pheromone secreted by MATa cells. We show that strong pheromone secretion is essential for efficient mating and that the weak mating of transvestites can be improved by boosting their pheromone production. Using synthetic biology, it is possible to characterize the factors that control efficiency in biological processes. In the case of budding yeast mating, selection for increased mating efficiency is likely to have continually boosted pheromone levels and the ability to discriminate between partners who make more (potentially fitter) and less (potentially less fit) pheromones. This sensitivity to which partner makes more pheromone comes at a cost: it means mating is not robust in situations where all potential partners make less pheromone. 4 conditions were analysed, each with 3 biological replicates. The conditions were unstimulated MATa cells in YPD. Stimulated MATa cells in YPD+10nM M-NM-1-factor. Unstimulated MATM-NM-1 cells in YPD. Stimulated MATM-NM-1 cells in YPD+10nM M-NM-1-factor.

2014-01-07 | E-GEOD-49372 | biostudies-arrayexpress

A Comparative Analysis of the Transcriptome of Hypoxia and Inflammation in Swan 71 Human Trophophoblast Cells: Its Implications in Preeclampsia

Project description:Chemical hypoxia by CoCl2 treatment and pro-inflammatory cytokines induced distinct changes in the transcriptome of Swan 71 human trophoblasts. Not Paired. Samples were treated with control treatments (PBS) as well as with CoCl2, IL-1β, and TNFα.

2011-11-15 | E-GEOD-31679 | biostudies-arrayexpress

Zebrafish fins: normoxic Controls vs. hypoxic fins

Project description:Transcriptional profiling of zebrafish fins comparing control fins and hypoxic fins (cobalt chloride (CoCl2, 1 mM)

2017-02-09 | GSE58568 | GEO