GEO DataSets

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

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array; Other; Expression profiling by high throughput sequencing

Platforms:

GPL13821 GPL9825 GPL17846

16 Samples

Download data: TXT

(Submitter supplied) Whi3 associated mRNAs were identified by immunoprecipitation of TAP-tagged Whi3 followed by microarray analysis

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL17846

4 Samples

Download data: TXT

(Submitter supplied) Measurement of the change in steady state mRNA level in cells with whi3 deletion or WHI3 overexpression relative to wildtype cells. In the overexpression experiment, WHI3 is moderately overexpressed by integrating four copies of WHI3 at its endogenous locus. This was performed in YEP glucose medium and YEP ethanol medium. Goal was to measure the effects of WHI3 on global gene expression at RNA level.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL9825

8 Samples

Download data: TXT

(Submitter supplied) In general, RNA-binding proteins act to modulate gene expression at transcript level through degradation or at protein level through translation. To elucidate the effect of Whi3, a yeast RNA binding protein, on gene expression, we performed ribosome profiling experiment on whi3 mutant and wildtype cells.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL13821

4 Samples

Download data: TXT

(Submitter supplied) The Ccr4-Not complex is a major regulator of stress responses that controls gene expression at multiple levels, from transcription to mRNA decay. Ccr4, a core subunit of the complex, is the main cytoplasmic deadenylase in Saccharomyces cerevisiae, however its mRNA targets have not been mapped on a genome-wide scale. Here we describe a genome-wide approach, RNA immunoprecipitation-high throughput sequencing (RIP-seq), to identify the RNAs bound to Ccr4, and two proteins that associate with it, Dhh1 and Puf5. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL15263

14 Samples

Download data: TXT

(Submitter supplied) We have identified mRNAs whose abundance or translational efficiency is regulated in nutrient-rich medium by the Scd6 or Dhh1 protein in either wild-type cells or dcp2∆ cells lacking the decapping enzyme

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17342

28 Samples

Download data: CSV

(Submitter supplied) To assess the role of the decapping activator Scd6 in mRNA decay, we used RNA-Seq to analyze the expression profile of yeast cells harboring a deletion of the SCD6 gene. Consistent with our recent model for decapping regulation, we found that Scd6 targets a small number of specific mRNAs in yeast cells. Interestingly, degradation of Scd6-targeted transcripts also requires the functions of the decapping activators Pat1, Lsm1, and Dhh1, suggesting that Scd6 functions together with Pat1, Lsm1, and Dhh1 in promoting mRNA decapping.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21656

6 Samples

Download data: TXT

(Submitter supplied) To assess the roles of the Dcp2 C-terminal domain and the decapping activators Pat1, Lsm1, and Dhh1 in mRNA decapping, we used RNA-Seq to analyze the expression profiles of yeast cells harboring a truncation of the Dcp2 C-terminal domain, mutations that render Dcp2 catalytically inactive, or deletions of the PAT1, LSM1, and DHH1 genes. Consistent with our recent model for decapping regulation, we found that: i) the Dcp2 C-terminal domain is an effector of both negative and positive regulation and that loss of these control functions causes significant deregulation of mRNA decapping; ii) rather than being global activators of decapping, Pat1, Lsm1, and Dhh1 directly target specific subsets of yeast mRNAs and loss of the functions of each of these factors has substantial indirect consequences for genome-wide mRNA expression; and iii) transcripts targeted by Pat1, Lsm1, and Dhh1 exhibit only partial overlap and, as expected, are targeted to decapping-dependent decay.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21656

24 Samples

Download data: TXT

(Submitter supplied) The Ydr374c is the only protein that has the YTH domain in Saccharomyces cerevisiae. The YTH domain was identified by comparing all known protein sequences with the YT521-B splicing factor, and it is found only in eukaryotes. Recently, it has been reported that the YTH domain conveys RNA-binding ability to a new class of proteins. However, the roles of most YTH family members lacking common sequence motifs outside the YTH domain are unknown. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL7293

2 Samples

Download data: TXT

(Submitter supplied) The eukaryotic translation factor eIF5A, originally identified as an initiation factor, was later shown to promote translation elongation of iterated proline sequences. Using a combination of ribosome profiling and in vitro biochemistry, we report a much broader role for eIF5A in elongation and uncover a substantial function for eIF5A in termination. Ribosome profiling of an eIF5A-depleted strain reveals a global elongation defect, with abundant ribosomes stalling at many sequences, not limited to proline stretches. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL17342

8 Samples

Download data: WIG

(Submitter supplied) RNA-coimmunopurifications with TAP-tagged Khd1 protein from Saccharomyces cereviseae. Untagged strain (BY4741) served as a control (Gerber et al., 2004). Cells were grown to midlog phase in rich media and harvested by centrifugation. TAP-tagged Khd1 was affinity purified from cell-free extracts with IgG sepharose and eluted with TEV protease. RNA was isolated from extract (=input) and from purified protein samples by phenol-chloroform extraction. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platforms:

GPL6419 GPL6420 GPL6421

7 Samples

Download data: PDF

(Submitter supplied) To identify RNAs specifically associated with potential RBPs, yeast cells expressing TAP-tagged RBP or the wild-type strain BY4741 (mock control) were grown to mid-log phase in rich medium and harvested by centrifugation. RNA affinity isolations were essentially performed as described (Gerber et al. 2004 PLoS Biol.; see protocol). In brief, TAP-tagged protein were captured from cell extracts with IgG coupled agarose beads (Sigma) and released by incubation with a site-specific protease (AcTEV, Sigma). more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platforms:

GPL10418 GPL8306

44 Samples

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(Submitter supplied) BY4741 cells bearing plasmid pBG1805-Map1 (MAP1 with a galactose inducible promotor) or the empty plasmid pBG1805 (=control).

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL8546

3 Samples

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(Submitter supplied) The FAR1 gene encodes a large protein, whose major function is inhibition of cyclin-dependent kinase complexes involved in the G1/S transition. It has been proposed that Far1, together with the G1 cyclin Cln3, may be part of a cell sizer mechanism that controls the entry into S phase. A genome-wide transcriptional analysis of FAR1-overexpressing and far1 deleted cells grown in ethanol- or glucose-supplemented minimal media indicates that FAR1 overexpression induces strong transcriptional remodelling, metabolism being the most affected cellular property. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL90

18 Samples

Download data: CEL

(Submitter supplied) Measurement of expression levels as a time course after shifting temperature-sensitive splicing factor mutant cells from 23C to 37C. Analysis of WT SS330, prp17 null, prp17-1 and prp22-1 cells. Samples were analyzed at 0, 5, 15, 30, 60 and 120 min. Keywords = pre-mRNA splicing Keywords = time course Keywords = intron Keywords: time-course

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Dataset:

GDS759

Platform:

GPL1458

24 Samples

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Analysis of gene expression in temperature sensitive pre-mRNA splicing factor mutants prp17 null, prp17-1, and prp22-1 at various time points following a shift from the permissive temperature of 23°C to the restrictive temperature of 37°C. Results identify substrates of Prp17p and Prp22p.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, log ratio, 4 genotype/variation, 2 temperature, 6 time sets

Platform:

GPL1458

Series:

GSE1784

24 Samples

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(Submitter supplied) APA mechanisms in S. pombe and S. cerevisiae are largely different, distinctly impacting gene expression, antisense transcripts and 3’UTR evolution, and core processing factors regulate APA in a PAS-dependent manner.

Organism:

Saccharomyces cerevisiae; Schizosaccharomyces pombe

Type:

Other

Platforms:

GPL17225 GPL17342

8 Samples

Download data: TXT

(Submitter supplied) We report here the transcriptome-wide distribution of yeast Rpb2, Sen1, Nrd1 and Nab3 binding sites. These data sets provide highresolution definition of non-poly(A) terminators, identify novel genes regulated by attenuation of nascent transcripts close to the promoter, and demonstrate the widespread occurrence of Nrd1-bound 3'-antisense transcripts on genes that are poorly expressed. In addition, we show that Sen1 does not cross-link to many expected ncRNAs but surprisingly binds to pre-mRNA transcripts suggesting a role in 3' end formation and/or termination.

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL13272

6 Samples

Download data: WIG

(Submitter supplied) We measured half-lives of 21,248 mRNA 3’ isoforms in yeast by rapidly depleting RNA polymerase II from the nucleus and performing direct RNA sequencing throughout the decay process. Interestingly, the half-lives of mRNA isoforms from the same gene, including nearly identical isoforms, often vary widely. Based on clusters of isoforms with different half-lives, we identify hundreds of sequences conferring stabilization or destabilization upon mRNAs terminating downstream. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL17245

16 Samples

Download data: TXT

(Submitter supplied) Glycolytic (G) bodies were purified from hypoxic yeast using differential centrifugation and immunoprecipitation by Pfk2-GFP-Flag in order to determine the RNAs that localize to G bodies by determining the enrichment of RNAs copurified with G bodies over both the flow through and total RNA fractions. We find significant overlap between enriched RNAs and RNAs bound by glycolysis enzymes in normoxic conditions. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL17342

6 Samples

Download data: TXT