GEO DataSets

(Submitter supplied) While the core splicing machinery is highly conserved between budding yeast and mammals, the absence of alternative splicing in Saccharomyces cerevisiae raises the fundamental question of why introns have been retained in ~5% of the 6,000 genes. Because Ribosomal Protein-encoding Genes (RPGs) are highly over-represented in the set of intron-containing genes, we tested the hypothesis that splicing of these transcripts would be regulated under conditions where translation is impaired. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platforms:

GPL5756 GPL5052

72 Samples

Download data: GPR

(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

Download data

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

Download data

(Submitter supplied) Introns in pre-mRNAs must be spliced out prior to their translation. During splicing, introns are removed in the form of a lariat, in which the 5' end is linked to the 2' hydroxyl of an internal adenosine. Lariat degradation is initiated by an 2'-5' phosphodiester-specific RNA endonuclease which debranches these lariat RNAs to linear form. Deletion of the debranching enzyme is yeast results in the accumulation of lariat introns. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by genome tiling array

Platform:

GPL4065

6 Samples

Download data: CEL

(Submitter supplied) To address co-transcriptional pre-mRNA processing events, Saccharomyces nascent RNA was isolated by chromatin fractionation and analyzed on a genome-wide high density tiling microarray. Co-transcriptional splicing efficiencies were derived by determination of intronic relative to exonic sequence concentrations.

Organism:

Saccharomyces; Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL7250

10 Samples

Download data: CEL, TXT

(Submitter supplied) Set of experiments done on yeast deletion strains of various non-essential mRNA processing factors. Keywords = splicing Keywords: repeat sample

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL105

36 Samples

Download data

(Submitter supplied) Prp4-1 and wt strains were grown at 26°C to A600 of 1.0, then an equal volume of 48°C media was added to bring the temperature to 37°C. Both strains were allowed to grow at 37°C and samples were taken at 0 (before shift), 5, 15, 30, 60, and 120 mins after shift to restrictive temperature. Keywords = splicing Keywords: time-course

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL108

12 Samples

Download data

(Submitter supplied) During meiosis in yeast, global splicing efficiency increases. The mechanism for this is relief of competition for the splicing machinery by repression of intron-containing ribosomal protein genes (RPGs). Repression of RPGs with rapamycin also increases splicing efficiency in vegetative cells. Reducing levels of an RPG-dedicated transcription factor globally improves splicing and suppresses the temperature-sensitive growth defect of a spliceosome mutation. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

8 Samples

Download data: GTF, TXT

(Submitter supplied) Appropriate expression of most eukaryotic genes requires the removal of introns from their pre-messenger RNAs (pre-mRNAs), a process catalyzed by the spliceosome. In higher eukaryotes a large family of auxiliary factors known as SR proteins can improve the splicing efficiency of transcripts containing suboptimal splice sites by interacting with distinct sequences present in those pre-mRNAs. The yeast Saccharomyces cerevisiae lacks functional equivalents of most of these factors; thus, it has been unclear whether the spliceosome could effectively distinguish among transcripts. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL5052

297 Samples

Download data: GPR

(Submitter supplied) The Saccharomyces cerevisiae MYO1 gene encodes the myosin type II heavy chain (Myo1p), a protein required for normal cytokinesis in budding yeast. Deletion of the MYO1 gene prevents actomyosin-driven cytokinesis thereby activating an alternative mechanism that involves the synthesis of a remedial septum. Myo1p deficiency in yeast (myo1) also causes the formation of attached cells, abnormal budding patterns, formation of enlarged and elongated cells, increased osmotic sensitivity, delocalized chitin deposition, and increased chitin synthesis. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL884

6 Samples

Download data: TXT

(Submitter supplied) The splicing machinery associates with genes to facilitate efficient co-transcriptional mRNA processing. We have mapped these associations by genome localization analysis to ascertain how splicing is achieved and regulated on a system-wide scale. Our data show that factors important for intron recognition sample nascent mRNAs and are retained specifically at intron-containing genes via RNA-dependent interactions. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by array

Platform:

GPL4641

24 Samples

Download data: GPR

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

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array; Other

Platforms:

GPL7662 GPL8546

60 Samples

Download data

(Submitter supplied) In this study, we systematically identified RNAs associated with ribosomes. To identify ribosome associated RNAs, C-terminal ZZ-tagged Rpl16a or Rpl16b, expressed under control of thier native promoter, were affinity purified from whole cell extracts of cultures grown to mid-log phase in minimal medium. Extracts were incubated with immunoglobulin G (IgG) coupled microbeads, washed, and ribosomes were eluted by tobacco etch virus (TEV) protease treatment. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL8546

8 Samples

Download data

(Submitter supplied) In this study, we systematically identified ribosome associated RNAs. To identify ribosome associated RNAs, C-terminal ZZ-tagged Rpl16a, expressed under control of its native promoter, was affinity purified from whole cell extracts of cultures grown to mid-log phase. Extracts were incubated with immunoglobulin G (IgG) coupled microbeads, washed, and ribosomes were eluted by tobacco etch virus (TEV) protease treatment. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array; Other

Platform:

GPL7662

52 Samples

Download data

(Submitter supplied) The coding portions of most eukaryotic genes are interrupted by non-coding regions termed introns that must be excised prior to their translation. The excision of introns from precursor messenger RNA (pre-mRNA), is catalyzed by the spliceosome, a large macromolecule composed of both RNA and protein components. Several studies have uncovered connections between pre-mRNA splicing and other RNA processing pathways such as the remodeling of chromatin structure, transcription and processing events which take place at the 3’ end of the transcript. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array; Expression profiling by RT-PCR

Platforms:

GPL8154 GPL14990

64 Samples

Download data: GPR, TXT

(Submitter supplied) Gene expression in Eukaryotic cells is profoundly shaped by the post-transcriptional processing of mRNAs, including the splicing of introns in the nucleus and both nuclear and cytoplasmic degradation pathways. Here we report the use of a splicing isoform specific microarray platform to investigate the effects of a host of diverse stress conditions on both splicing pre-mRNA fate. Interestingly, We find that diverse stresses cause distinct patterns of changes at the level of pre- mRNA processing. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL5052

593 Samples

Download data: GPR

(Submitter supplied) Deleting the introns from either the chromatin remodeling MMS2 gene or the splicing regulator gene YSF3 modified the expression of a common set of genes in the stationary phase of growth.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17342

12 Samples

Download data: CSV