GEO DataSets

(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) 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) CryoEM modeling of the human pre-B complex suggests an interaction between SNU66(H734) and SNRP27(M141) at the base of the ACAGAGA box of U6. We had previously shown in C. elegans that SNRP-27(M141T) mutants alter 5'ss usage. Here we generate new alleles by CRISPR in snu-66 at the corresponding H765 location in C. elegans (H765G and H765L) and demonstrate that they have similar effects as SNRP-27(M141T) mutants on 5'ss selection globally.

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26672

12 Samples

Download data: 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) 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) The coupled activities of RNA polymerase and the spliceosome are responsible for the abundance and isoform composition of mRNA in human cells. However, the dynamics of these megadalton enzymatic complexes working in concert on endogenous genes have not been described. Here, we establish a quasi-genome-scale platform for observing synthesis and processing kinetics of single nascent RNA molecules in real time. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL21697

6 Samples

Download data: XLSX

(Submitter supplied) The coupled activities of RNA polymerase and the spliceosome are responsible for the abundance and isoform composition of mRNA in human cells. However, the dynamics of these megadalton enzymatic complexes working in concert on endogenous genes have not been described. Here, we establish a quasi-genome-scale platform for observing synthesis and processing kinetics of single nascent RNA molecules in real time. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL20795

4 Samples

Download data: XLSX

(Submitter supplied) The coupled activities of RNA polymerase and the spliceosome are responsible for the abundance and isoform composition of mRNA in human cells. However, the dynamics of these megadalton enzymatic complexes working in concert on endogenous genes have not been described. Here, we establish a quasi-genome-scale platform for observing synthesis and processing kinetics of single nascent RNA molecules in real time. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28975

2 Samples

Download data: GTF, TXT

(Submitter supplied) The coupled activities of RNA polymerase and the spliceosome are responsible for the abundance and isoform composition of mRNA in human cells. However, the dynamics of these megadalton enzymatic complexes working in concert on endogenous genes have not been described. Here, we establish a quasi-genome-scale platform for observing synthesis and processing kinetics of single nascent RNA molecules in real time. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

2 Samples

Download data: CSV

(Submitter supplied) The coupled activities of RNA polymerase and the spliceosome are responsible for the abundance and isoform composition of mRNA in human cells. However, the dynamics of these megadalton enzymatic complexes working in concert on endogenous genes have not been described. Here, we establish a quasi-genome-scale platform for observing synthesis and processing kinetics of single nascent RNA molecules in real time. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

1 Sample

Download data: BED

(Submitter supplied) The coupled activities of RNA polymerase and the spliceosome are responsible for the abundance and isoform composition of mRNA in human cells. However, the dynamics of these megadalton enzymatic complexes working in concert on endogenous genes have not been described. Here, we establish a quasi-genome-scale platform for observing synthesis and processing kinetics of single nascent RNA molecules in real time. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

8 Samples

Download data: XLSX

(Submitter supplied) The coupled activities of RNA polymerase and the spliceosome are responsible for the abundance and isoform composition of mRNA in human cells. However, the dynamics of these megadalton enzymatic complexes working in concert on endogenous genes have not been described. Here, we establish a quasi-genome-scale platform for observing synthesis and processing kinetics of single nascent RNA molecules in real time. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

4 related Platforms

23 Samples

Download data: BED, CSV

(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:

GPL22765 GPL19757 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:

Mus musculus; synthetic RNA

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL19057 GPL24911

74 Samples

Download data: CSV

(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) Adjacent alternative 3’ splice sites, those separated by ≤18nt, provide a unique problem in the study of alternative splicing regulation; there is overlap of the cis-elements that define the adjacent sites. Identification of the intron's 3' end depends upon sequence elements that define the branchpoint, polypyrimidine tract and terminal AG dinucleotide. Starting with RNA-seq data from germline-enriched and somatic cell-enriched C. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13657

5 Samples

Download data: TXT

(Submitter supplied) Here we examine the role of mRNA splicing in Caenorhabditis elegans RNAi. We find that viable null mutations in U1 and U2-snRNP-specific splicing factor genes cause defects in RNAi. The U1A orthologue rnp-2 is required for normal ERGO-1 Argonaute-class 26G siRNA biogenesis, trans-splicing of the eri-6/7 transcript and targeting of poorly conserved gene transcripts by WAGO Argonaute-class 22G siRNAs. more...

Organism:

Caenorhabditis elegans

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13657

7 Samples

Download data: XLSX

(Submitter supplied) Alleles of C. elegans genes mog-5 and sacy-1 were found to increase usage of proximal 3' splice sites

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL19757

12 Samples

Download data: GTF

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

Organism:

synthetic construct; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19424 GPL11154 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