GEO DataSets

(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) 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) Intron-containing gene expression in eukaryotes proceeds through the process of RNA splicing to generate protein-coding messenger RNAs (mRNAs). Herein a large and dynamic ribonucleoprotein complex — the spliceosome — removes non-coding introns from pre-mRNAs and joins exons. Spliceosomes must also ensure accurate and timely removal of diverse and highly prevalent introns. Here we show that Sde2 is a conserved splicing regulator, contains a ubiquitin fold, and supports splicing of a subset of pre-mRNAs in an intron-specific manner in Schizosaccharomyces pombe. more...

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by array

Platform:

GPL21065

4 Samples

Download data: GPR

(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) The role of many splicing factors in pre-mRNA splicing and the involvement of these factors in the processing of specific transcripts have often been defined through the analysis of loss of function mutants in vivo. Here we show that inactivating the nonsense mediated mRNA decay (NMD) results in an enhancement of splicing phenotypes associated with several splicing factors mutations. Tiling microarrays showed that inactivation of the NMD factor Upf1p in the prp17Δ and prp18Δ mutant strains reveals a larger spectrum of splicing defects than what is observed in the single mutants, including new transcripts previously shown unaffected by Prp17p or Prp18p inactivation. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL9286

12 Samples

Download data: CEL

(Submitter supplied) Analysis of splicing defects in Schizosaccharomyces pombe upon chemical genetic inhibition of splicing kinases dsk1, lkh1, and prp4, as well as alanine-mutation of phosphorylated residues in the splicing factors bpb1, prp2, rsd1, srp1, srp2, usp101, usp103, sum3, prp22, cdc5, and cwf22. This study shows the splicing kinase dsk1 modulates splicing efficiency of introns with non-consensus splice sites, likely through phosphorylation of bpb1. more...

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by array

Platform:

GPL19357

39 Samples

Download data: GPR

(Submitter supplied) In eukaryotic cells, inefficient splicing is surprisingly common and leads to degradation of transcripts with retained introns. How pre-mRNAs are committed to nuclear decay is unknown. Here we uncover a mechanism by which intronic transcripts are targeted for nuclear degradation in fission yeast. Surprisingly, sequence elements within “suicidal” introns co-transcriptionally recruit the exosome adaptor Mmi1 not only to degrade unspliced precursor, but also to downregulate levels of the resulting mRNA. more...

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Other

Platforms:

GPL17225 GPL16192

10 Samples

Download data: GTF

(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) Tools to understand how the spliceosome functions in vivo have lagged behind advances in its structural biology. We describe methods to globally profile spliceosome-bound precursor, intermediates and products at nucleotide resolution. We apply these tools to three divergent yeast species that span 600 million years of evolution. The sensitivity of the approach enables detection of novel cases of non- canonical catalysis including interrupted, recursive and nested splicing. more...

Organism:

Saccharomyces cerevisiae; Schizosaccharomyces pombe; Cryptococcus neoformans

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL21656 GPL21073 GPL22682

56 Samples

Download data: BED, BEDGRAPH, CSV

(Submitter supplied) Cold senstive alleles of prp43, S249A and G429A were assayed for splicing and RNA processing defects. Keywords: splicing, pre-mRNA processing

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL2985

4 Samples

Download data

(Submitter supplied) Splicing and expression profiling of nascent and mRNA by RNA sequencing This SuperSeries is composed of the SubSeries listed below.

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL17225 GPL21481

18 Samples

Download data: BED, BEDGRAPH

(Submitter supplied) Recent data from several organisms indicate that the transcribed portions of genomes are larger and more complex than expected, and many functional properties of transcripts are not based on coding sequences but on regulatory sequences in untranslated regions or non-coding RNAs. Alternative start and polyadenylation sites and regulation of intron splicing add additional dimensions to the rich transcriptional output. more...

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9854

31 Samples

Download data: TXT

(Submitter supplied) Recent ChIP experiments indicate that spliceosome assembly and splicing can occur cotranscriptionally in S. cerevisiae. However, only a few genes have been examined, and all have long second exons. To extend these studies, we analyzed intron-containing genes with different second exon lengths, by ChIP as well as by whole-genome tiling arrays (ChIP-CHIP). The data indicate that U1 snRNP recruitment is independent of exon length. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL4613

3 Samples

Download data: TXT

(Submitter supplied) Prp2 (U2AF65) is an essential splicing factor, that recognizes the poly-Py track near the 3' SS. We have previously observed that when Prp2 is inactivated using a prp2 temperature-sensitive allele, while most of the pre-mRNA is not processed, some are normally spliced. This observation even more noticeable during meiosis, since pre-mRNA regulation is executed at different levels (splicing, polyadenylation and stability). more...

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13988

2 Samples

Download data: XLSX

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

Organism:

Schizosaccharomyces pombe

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other; Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL20584 GPL16192

11 Samples

Download data: BEDGRAPH, FPKM_TRACKING, SGR

(Submitter supplied) Long non-coding RNAs (lncRNAs) dynamically regulate gene expression during development and in response to environmental conditions. In S. pombe, lncRNAs repress the expression of nearby genes via a mechanism involving silencing effector proteins. In this study, we find that invasion of a lncRNA into the neighboring gene results in inclusion of a cryptic intron that is required for its repressive activity. more...

Organism:

Schizosaccharomyces pombe

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16192

6 Samples

Download data: SGR

(Submitter supplied) Long non-coding RNAs (lncRNAs) dynamically regulate gene expression during development and in response to environmental conditions. In S. pombe, lncRNAs repress the expression of nearby genes via a mechanism involving silencing effector proteins. In this study, we find that invasion of a lncRNA into the neighboring gene results in inclusion of a cryptic intron that is required for its repressive activity. more...

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16192

2 Samples

Download data: FPKM_TRACKING

(Submitter supplied) Long non-coding RNAs (lncRNAs) dynamically regulate gene expression during development and in response to environmental conditions. In S. pombe, lncRNAs repress the expression of nearby genes via a mechanism involving silencing effector proteins. In this study, we find that invasion of a lncRNA into the neighboring gene results in inclusion of a cryptic intron that is required for its repressive activity. more...

Organism:

Schizosaccharomyces pombe

Type:

Other

Platform:

GPL20584

2 Samples

Download data: BEDGRAPH