GEO DataSets

(Submitter supplied) Alternative splicing generates distinct mRNA isoforms and is crucial for proteome diversity in eukaryotes. The RNA-binding protein (RBP) U2AF65 is central to splicing decisions, as it recognizes 3' splice sites and recruits the spliceosome. We established 'in vitro iCLIP' experiments, in which recombinant RBPs are incubated with long transcripts, to study how U2AF65 recognizes RNA sequences and how this is modulated by trans-acting RBPs. more...

Organism:

synthetic gene

Type:

Other

Platform:

GPL23545

37 Samples

Download data: BEDGRAPH, BW

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

Organism:

synthetic gene; Homo sapiens

Type:

Other

Platforms:

GPL16791 GPL23545

79 Samples

Download data: BEDGRAPH, BW

(Submitter supplied) Alternative splicing generates distinct mRNA isoforms and is crucial for proteome diversity in eukaryotes. The RNA-binding protein (RBP) U2AF65 is central to splicing decisions, as it recognizes 3' splice sites and recruits the spliceosome. We established 'in vitro iCLIP' experiments, in which recombinant RBPs are incubated with long transcripts, to study how U2AF65 recognizes RNA sequences and how this is modulated by trans-acting RBPs. more...

Organism:

synthetic gene

Type:

Other

Platform:

GPL23545

31 Samples

Download data: BED, BW

(Submitter supplied) Alternative splicing generates distinct mRNA isoforms and is crucial for proteome diversity in eukaryotes. The RNA-binding protein (RBP) U2AF65 is central to splicing decisions, as it recognizes 3' splice sites and recruits the spliceosome. We established 'in vitro iCLIP' experiments, in which recombinant RBPs are incubated with long transcripts, to study how U2AF65 recognizes RNA sequences and how this is modulated by trans-acting RBPs. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

11 Samples

Download data: BW

(Submitter supplied) Alternative splicing drives transcriptome and proteome diversification. While splicing regulatory proteins govern this process, their global mechanisms remain enigmatic. We generated high resolution transcriptome-wide protein-RNA interaction maps to determine how the splicing repressor hnRNPA1 influences the global association of spliceosome assembly factor U2AF2 and SRSF1 with pre-mRNA. We observed changes in the distribution of U2AF2 crosslinking sites relative to the 3’ splice sites of cassette exons but not constitutive exons upon hnRNPA1 overexpression. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

20 Samples

Download data: BED, TXT

(Submitter supplied) Examination of transcriptome of SPF45 knockdown cells by Ribosomal RNA depleted RNA-Seq

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

6 Samples

Download data: BW

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL18573

15 Samples

Download data: BEDGRAPH

(Submitter supplied) L1TD1 is a cytoplasmic RNA-binding protein that is specifically expressed in pluripotent stem cells and, unlike its mouse paralogue, is essential for the maintenance of stemness in human cells. Although L1TD1 is the only known domesticated gene from a LINE-1 (L1) retroelement, the functional legacy from its ancestral protein, ORF1p of L1, and the novelty are so far unknown. Here, we determined RNAs associated with L1TD1 and found that, like ORF1p, L1TD1 binds L1 RNAs, localizes to high-density ribonucleoprotein (RNP) condensates, and increases L1 retrotransposition. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

7 Samples

Download data: BEDGRAPH

(Submitter supplied) Eukaryotic nuclear introns have been dichotomously classified into common U2-type introns and rare U12-type introns. Because the highly conserved consensus sequences for the 5’ splice site and the branch point are found within all U12-type introns, weighted matrices for these motifs are used for prediction of U12-type introns. However, the U12-type consensus sequences per se are also recognized by the U2-type spliceosome. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

11 Samples

Download data: BEDGRAPH

(Submitter supplied) The essential pre-mRNA splicing factor U2AF2 (also called U2AF65) identifies polypyrimidine (Py) tract signals of nascent transcripts, despite length and sequence variations. Previous studies have shown that the U2AF2 RNA recognition motifs (RRM1 and RRM2) preferentially bind uridine-rich RNAs. Nonetheless, the specificity of the RRM1/RRM2 interface for the central Py tract nucleotide has yet to be investigated. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

2 Samples

Download data: TXT

(Submitter supplied) Splicing factor mutations are common among cancers, recently emerging as drivers of myeloid malignancies. U2AF1 carries hotspot mutations in its RNA binding motifs; yet how they affect splicing and promote cancer remains unclear. The U2AF1/U2AF2 heterodimer is critical for 3’ splice site (3’SS) definition. To specifically unmask changes in U2AF1 function in vivo, we developed a crosslinking and immunoprecipitation procedure detecting contacts between U2AF1 and the 3’SS AG at single-nucleotide resolution (fractionated eCLIP-seq or freCLIP-seq). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL20301 GPL16791

43 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) Examination of transcriptome of SAP30BP knockdown cells by Ribosomal RNA depleted RNA-Seq

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

6 Samples

Download data: BEDGRAPH

(Submitter supplied) To investigate DHX15's functions in splicing QC in human cells, we induced rapid proteolysis-mediated depletion of endogenous DHX15 and DHX38 and performed high-throughput sequencing of totalRNA and chRNA.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24676

48 Samples

Download data: TSV

(Submitter supplied) The maize Rough endosperm3 (Rgh3) gene encodes an ortholog of the human essential splicing factor, ZRSR2. To test whether a mutation in Rgh3 affects mRNA splicing, we compared rgh3 mutants and wild-type sibling transcriptomes in an RNA-seq experiment. Twelve libraries were constructed with mRNA extracted from the roots and shoots of three seedlings of each genotype. The libraries were multiplexed and sequenced on one lane of the HiSeq 2000 platform. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15463

12 Samples

Download data: GTF

(Submitter supplied) OThe N6-methyladenosine (m6A) RNA modification is widely used to alter the fate of mRNAs. Here we demonstrate that the C. elegans writer METT-10 (orthologue of mouse METTL16) deposits an m6A mark on the 3′ splice site (AG) of the SAM synthetase pre-mRNA which inhibits its proper splicing and protein production. The mechanism is triggered by a rich diet, and acts as an m6A-mediated switch to stop SAM production and regulate its homeostasis. more...

Organism:

Caenorhabditis elegans; Bombyx mori; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19757 GPL22765 GPL28266

42 Samples

Download data: BW, CSV, XLSX

(Submitter supplied) Internal modification of RNAs with N6-methyladenosine (m6A) is a highly conserved and widely used means of gene expression control. METTL16 is an m6A writer but how it recognizes its RNA targets and its physiological roles remain unknown. Here we describe the crystal structure of human METTL16 to reveal a classical methyltransferase domain but with an extra N-terminal module that is essential for catalysis. more...

Organism:

synthetic RNA; Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL19057 GPL24911

74 Samples

Download data: CSV