GEO DataSets

(Submitter supplied) Purpose: Identify alternative splicing events and changes to transcript expression levels

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

6 Samples

Download data: XLSX

(Submitter supplied) DEAD-box proteins, a family of RNA-dependent ATPases, promote the numerous conformational rearrangements required for spliceosome assembly, activation, and disassembly. Previous work showed that a cold-sensitive substitution in DEAD-box protein Prp28 prevents the switch from U1 to U6 snRNA pairing with the 5’ splice site. Little is known about how Prp28 is regulated, although U5 snRNP protein Prp8 is a potential coordinator of Prp28 and other spliceosomal ATPases. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL5052

16 Samples

Download data: GPR

(Submitter supplied) In this study, we analyzed the pre-mRNA splicing status in wild-type Col, atprmt5 mutants, and two atprmt5 suppressors (m90 and s215). RNA-seq analyses revealed that m90 and s215 can partially rescue the pre-mRNA splicing defects in atprmt5 mutants. Further study showed that m90 and s215 were identified in the highly conserved pre-mRNA splicing factor 8 (AtPrp8) and demonstrated that Prp19C/NTC complex failed to be assembled into U5 snRNP to form activated spliceosome in atprmt5 mutants, while restored in the suppressor. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

4 Samples

Download data: BW, TXT

(Submitter supplied) Purpose: Alternative splicing is fundamental for post-transcriptional regulation and proteome diversity. The goals of this study are to compare transcriptome and splicing profiling (RNA-seq) between wild type and prp8a prp8b mutant ovules of the spliceosome subunit and define the molecular signature of prp8a prp8b pollen tube attraction phenotype. Methods: mRNA profiles from mature ovules of 6-weeks-old wild-type (WT) and pre-mRNA processing factor 8 (PRP8Aa prp8bb) Arabidopsis plants were generated by deep sequencing, in triplicates, using Illumina HiSeq4000 100bp paired-end reads. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21785

6 Samples

Download data: CSV, TXT

(Submitter supplied) The spliceosome undergoes extensive rearrangements as it assembles in multiple steps onto the precursor messenger RNA. In the earliest assembly step, U1snRNA identifies the 5' splice site through base-pairing interactions. However, U1snRNA leaves the spliceosome relatively early in the assembly process. The 5' splice site identity is subsequently maintained through interactions with U6snRNA, protein factor PRP8, and other components of the spliceosome during the complex assembly and rearrangements that build the catalytic site. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26672

12 Samples

Download data: TXT

(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) Dominant mutant alleles of prp-8 and snrp-27 were identifed in a forward genetic screen for suppressors of cryptic splice site activation

Organism:

Caenorhabditis elegans

Type:

Other

Platform:

GPL22765

22 Samples

Download data: TRACK

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

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL24676 GPL24247

42 Samples

Download data: BW

(Submitter supplied) Alternative splicing diversifies mRNA transcripts in human cells. While the spliceosome pairs exons with a high degree of accuracy, the rates of rare aberrant and non-canonical pre-mRNA splicing have not been evaluated at the nucleotide level to determine the quantity and identity of these events across splice junctions. Using ultra-deep sequencing the frequency of aberrant and non-canonical splicing events for three splice junctions flanking exon 7 of SMN1 were determined at single nucleotide resolution. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

1 Sample

Download data: TXT

(Submitter supplied) In eukaryotes, a dynamic ribonucleic protein machine known as the spliceosome catalyzes the removal of introns from pre-messenger RNA (pre-mRNA). Recent studies show the process of RNA-synthesis and RNA-processing to be spatio-temporally coordinated, indicating that RNA splicing takes place in the context of chromatin. H2A.Z is a highly conserved histone variant of the canonical histone H2A. In S. cerevisiae, H2A.Z is deposited into chromatin by the SWR1-complex, is found near the 5’ ends of protein-coding genes, and has been implicated in transcription regulation. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

15 Samples

Download data: XLSX

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

Organism:

synthetic construct; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL11154 GPL19424 GPL18573

61 Samples

Download data: BW

(Submitter supplied) Splicing is a central process in metazoans and greatly expands their proteome by alternative splicing of pre-mRNA transcripts. An essential regulatory step during early spliceosome assembly is the recognition of cis-regulatory RNA motifs in pre-mRNAs. Here, we identified the RNA binding protein FUBP1 as a novel core splicing factor with a ubiquitous footprint on pre-mRNAs. FUBP1 binds to a previously unknown cis-regulatory motif upstream of the branch point of human introns. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

27 Samples

Download data: BW

(Submitter supplied) Splicing is a central process in metazoans and greatly expands their proteome by alternative splicing of pre-mRNA transcripts. An essential regulatory step during early spliceosome assembly is the recognition of cis-regulatory RNA motifs in pre-mRNAs. Here, we identified the RNA binding protein FUBP1 as a novel core splicing factor with a ubiquitous footprint on pre-mRNAs. FUBP1 binds to a previously unknown cis-regulatory motif upstream of the branch point of human introns. more...

Organism:

synthetic construct

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19424

18 Samples

Download data: BED, BW

(Submitter supplied) Splicing is a central process in metazoans and greatly expands their proteome by alternative splicing of pre-mRNA transcripts. An essential regulatory step during early spliceosome assembly is the recognition of cis-regulatory RNA motifs in pre-mRNAs. Here, we identified the RNA binding protein FUBP1 as a novel core splicing factor with a ubiquitous footprint on pre-mRNAs. FUBP1 binds to a previously unknown cis-regulatory motif upstream of the branch point of human introns. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

16 Samples

Download data: TXT

(Submitter supplied) Mutant alleles of KIN17 (dxbp-1) and PRCC (prcc-1) were identifed in a forward genetic screen for suppressors of cryptic splice site activation

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26672

15 Samples

Download data: TXT

(Submitter supplied) Purpose: Understand the transcriptional changes and alternative splicing defects associated to the pleiotropic defects observed in mdf-1 mutants. Methods: Total RNA was extracted from 3 different biological replicates containing 12-day-old seedlings of WT and mdf-1 using the innuPREP Plant RNA kit (Analytik Jena Bio solutions). RNA quality assessment, library preparation, sequencing and bioinformatic analyses were performed by Novogene Co. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26208

6 Samples

Download data: TXT

(Submitter supplied) We generated a human EFTUD2 knockdown cell line using a CRISPR cas9 nickase strategy to investigate the effects of decreased expression of core spliceosome components on cell characteristics and global transcriptome expression/splicing patterns

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

12 Samples

Download data: XLS, ZIP

(Submitter supplied) To investigate whether the observed changes in pre-mRNA splicing led to AtCYP18-1 depletion, we conducted RNA-sequencing to analyse the quantitative profiling of alternative splicing

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17639

12 Samples

Download data: XLSX