GEO DataSets

(Submitter supplied) Time course after the addition of the transcriptional inhibitor thiolutin at 3µg/mL to an exponential growing culture of S. cerevisiae in YPD. Keywords: time course, mRNA stability analysis

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL3763

5 Samples

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(Submitter supplied) Time course after the addition of the transcriptional inhibitor thiolutin at 3 and 10 µg/mL to an exponential growing culture of S. cerevisiae in YPD. Keywords: time course, mRNA stability analysis

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL3763

6 Samples

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(Submitter supplied) This study involves the role of yeast mRNA decay factors in transcription. The experiment included here are the ChIP-exo results of three decay factors: Xrn1, Dcp2 & Lsm1.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13821

4 Samples

Download data: BEDGRAPH, TAB, WIG

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array; Genome binding/occupancy profiling by array

Platform:

GPL16503

22 Samples

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(Submitter supplied) Determination of 3' or 5' intragenic RNA pol II occupancy. Maintaining the proper mRNA levels is a key aspect in the regulation of gene expression. The balance between mRNA synthesis and decay determines these levels. Using a whole-genome analysis, we demonstrate that most yeast mRNAs are degraded by the 5'-to-3' pathway (the "decaysome"), as proposed previously. Unexpectedly, the level of these mRNAs is highly robust to perturbations in this major pathway, as defects in various decaysome components lead to transcription down-regulation. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by array

Platform:

GPL16503

10 Samples

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(Submitter supplied) Determination of the 3' or 5' intragenic nascent transcriptional rate. Maintaining the proper mRNA levels is a key aspect in the regulation of gene expression. The balance between mRNA synthesis and decay determines these levels. Using a whole-genome analysis, we demonstrate that most yeast mRNAs are degraded by the 5'-to-3' pathway (the "decaysome"), as proposed previously. Unexpectedly, the level of these mRNAs is highly robust to perturbations in this major pathway, as defects in various decaysome components lead to transcription down-regulation. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL16503

12 Samples

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(Submitter supplied) Maintaining the proper mRNA levels is a key aspect in the regulation of gene expression. The balance between mRNA synthesis and decay determines these levels. Using a whole-genome analysis, we demonstrate that most yeast mRNAs are degraded by the 5'-to-3' pathway (the "decaysome"), as proposed previously. Unexpectedly, the level of these mRNAs is highly robust to perturbations in this major pathway, as defects in various decaysome components lead to transcription down-regulation. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL13620

9 Samples

Download data: TXT

(Submitter supplied) Isogenic UPF1+ or upf1- yeast strains were treated with 10 ug/ml thiolutin to inhibit global transcription. Targets were obtained from 16 time points: 0, 2, 4, 6, 8, 10, 12, 15, 20, 25, 30, 35, 40, 45, 50, 60 minutes after transcription inhibition. Three biological replicates of each were generated and the expression profiles were determined using Affymetrix YG-S98 arrays. Comparisons between the sample groups allow the identification of genes with differential expression over time between UPF1+ and upf1-. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Dataset:

GDS1611

Platform:

GPL90

96 Samples

Download data: CEL, CHP, EXP

Analysis of wild type and mutant upf1 strains up to 60 minutes after treatment with 10 ug/ml thiolutin, a global transcription inhibitor. Upf1 is an RNA helicase required for nonsense-mediated mRNA decay (NMD). Results identify genes with differential expression over time between the two strains.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, transformed count, 2 genotype/variation, 16 time sets

Platform:

GPL90

Series:

GSE3076

96 Samples

Download data: CEL, CHP, EXP

(Submitter supplied) Strain background is BMA64 with RNT1 gene deleted with the TRP marker Media is SD -Trp (synthetic dextrose minimal media missing tryptophan) Cells were grown until midlog and harvested at OD600=0.4; MAS5 (Statistical Algorithm) Scaling:All Probe Sets Target Signal 500;Normalization:All Probe Sets; Alpha1=0.04; Alpha2=0.06; Tau=0.015 Strain background is BMA64 with plasmid expressing TRP marker Media is SD -Trp (synthetic dextrose minimal media missing tryptophan) Cells were grown until midlog and harvested at OD600=0.4 ; MAS5 (Statistical Algorithm) Scaling:All Probe Sets Target Signal 500;Normalization:All Probe Sets; Alpha1=0.04; Alpha2=0.06; Tau=0.015 Keywords: repeat sample

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Dataset:

GDS1214

Platform:

GPL90

9 Samples

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Expression profiling of isogenic strains lacking Rnt1p, a member of the RNase III family of double-stranded RNA endonucleases. Results identify potential Rnt1p mRNA targets.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, count, 2 genotype/variation sets

Platform:

GPL90

Series:

GSE2683

9 Samples

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(Submitter supplied) We have taken five different time points of a Yeast culture in exponential grow in rich medium, each one elapsed ten minutes from de previous one (from OD600 0.36 to 0.47). Then, for each time point we have measured the transcription rates (TR) and mRNA amounts (RA) for all the genes using the Genomic run-on (GRO) technique .

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL6727

39 Samples

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(Submitter supplied) Series containes 4 independent experiments and high and low power scanns for each independent experiment. Genome-wide mRNA expression profiles of Saccharomyces cerevisiae growing under hydrostatic pressure were characterized. We selected a hydrostatic pressure of 30 MPa at 25°C because yeast cells were able to grow under these conditions, while cell size and complexity were increased after decompression. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL1951

8 Samples

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(Submitter supplied) We analyzed the effect of the elimination of the cap-binding protein Cbc1 on transcription rate and mRNA amount during the response to osmotic stress using the Genomic Run-on assay

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array; Other

Platform:

GPL13620

20 Samples

Download data: TXT

(Submitter supplied) We study the transcriptional response of wt S. cerevisiae cells to alkaline pH by using a genome-wide method (Genomic run-on) that allows for the determination of transcription rates (TR) and mRNA amounts (RA) for each gene. The stabilities of the mRNAs can be calculated from the TR and RA data.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL13620

42 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL4566

42 Samples

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(Submitter supplied) Within a GRO experiment, samples for mRNA amount (RA) were taken at 0, 4, 11, 16, 26 and 40 minutes after heat stress (from 25ºC to 37ºC). Analysis was done in filters also used for Transcription rate (TR) analysis of aliquots from the same cultures.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL4566

24 Samples

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(Submitter supplied) Within a GRO experiment, samples for Transcription rate (TR) analysis were taken at 0, 4, 11, 16, 26 and 40 minutes after heat stress (from 25ºC to 37ºC) and subjected to run-on. Analysis was done in filters also used for RA analysis of aliquots from the same cultures.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL4566

24 Samples

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(Submitter supplied) Transcription rate (TR) analysis of W303-1a yeast strain growing in exponential phase in YPD subjected to terbutyl stress Keywords: time course

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL4565

24 Samples

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(Submitter supplied) mRNA amount analysis of W303-1a yeast strain growing in exponential phase in YPD subjected to terbutyl stress Keywords: time course

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL4565

24 Samples

Download data