GEO DataSets

(Submitter supplied) Spliced messages constitute one-fourth of expressed mRNAs in the yeast Saccharomyces cerevisiae, and most mRNAs in metazoans. Splicing requires 5' splice site (5'SS), branch point (BP), and 3' splice site (3'SS) elements, but the role of the BP in splicing control is poorly understood because BP identification remains difficult. We developed a high-throughput method, Branch-seq, to map BP and 5'SS of isolated RNA lariats. more...

Organism:

Saccharomyces cerevisiae; Saccharomyces cerevisiae S288C

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL20072 GPL19756 GPL20073

30 Samples

Download data: FPKM_TRACKING, XLSX

(Submitter supplied) We used CRISPR in HEK293T cells to create two DBR1 knockout cell lines (C19 and C22). After high-throughput sequencing of total RNA extracted from these cells, we performed lariat read mapping using the method described in "Large-scale mapping of branchpoints in human pre-mRNA transcripts in vivo" (Taggart et al, 2012). We found lariats in the two DBR1- cell lines to be ~20-fold enriched relative to the levels observed in the HEK293T control samples.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

5 Samples

Download data: BED

(Submitter supplied) Fidelity of 3´-splice site (3´SS) selection by the spliceosome is critical for proper gene expression but is a daunting task considering the low complexity of the 3´SS consensus YAG. Here we show that loss of the splicing factor Prp18p in budding yeast activates a diverse array of alternative 3´SS at more than half of all introns. Some alternative sites highly diverge from the YAG consensus, demonstrating a critical role for Prp18p in promoting spliceosome fidelity. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL13821

6 Samples

Download data: TXT

(Submitter supplied) Both canonical and alternative splicing of RNAs is governed by intronic sequence elements and produces transient lariat structures fastened by branch-points within introns. To map precisely the location of branch-points on a genomic scale, we developed LaSSO (Lariat Sequence Site Origin), a data-driven algorithm which utilizes RNA-seq data. Using fission yeast cells lacking the debranching enzyme Dbr1, LaSSO not only accurately identified canonical splicing events, but also pinpointed novel, but rare, exon-skipping events, which may reflect aberrantly spliced transcripts. more...

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13988

4 Samples

Download data: TXT

(Submitter supplied) Knockdown and overexpression of C* proteins in Hela and HEK293 cells was investigated by RNA-Seq.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

74 Samples

Download data: TXT

(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) 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) The differentiation of cells into distinct cell types, each of which is heritable for many generations, underlies many biological phenomena. White and opaque cells of the fungal pathogen Candida albicans are two such heritable cell types, each thought to be adapted to unique niches within their human host. To systematically investigate the differences between the two cell types, we performed strand-specific massively-parallel sequencing of RNA from C. more...

Organism:

Candida albicans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10314

7 Samples

Download data: PDF, TXT, WIG

(Submitter supplied) Mitochondria fulfil many essential roles in eukaryotic cells, yet some of their molecular mechanisms are still unexplored. Although 99% of the mitochondrial proteins are imported from the cytosol, mitochondria have their own DNA, transcription and translation machinery. The Saccharomyces cerevisiae mitochondrial DNA contains 11 polycistronic transcripts that encode 2 ribosomal subunits, 24 tRNAs and 9 genes, which can be spliced in alternative ways to yield different proteins. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25739

6 Samples

Download data: CSV

(Submitter supplied) We address define differential usage of branchpoint (BP) in by wild-type SF3B1 SF3B1-K700E using a synthetic mini-gene synthetic library with variable 3' spice sites (3'SS). Minigene-specific libraries were prepared and sequenced on the illumina platform to determine differnces in splice-site usage.

Organism:

Homo sapiens; Mus musculus; synthetic construct

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL11154 GPL15228 GPL19057

7 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; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL11154

12 Samples

Download data

(Submitter supplied) We used GFP-tagged SR proteins expressed at endogenous levels and iCLIP to compare the extent and pattern of SR protein binding to expression-matched lincRNAs and protein-coding RNAs

Organism:

Homo sapiens

Type:

Other

Platform:

GPL11154

10 Samples

Download data: BED

(Submitter supplied) We sequenced total RNA from HeLa WT cells to quantify the expression of protein-coding mRNAs and lincRNAs. RPKM values were used to normalize iCLIP binding to RNA abundance.

Organism:

Homo sapiens

Type:

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

Platform:

GPL11154

2 Samples

Download data: BED

(Submitter supplied) Spliceosomal introns are ubiquitous non-coding RNAs typically destined for rapid debranching and degradation. Here, we describe 34 excised Saccharomyces cerevisiae introns that, although rapidly degraded in log-phase growth, accumulate as linear RNAs under either saturated-growth conditions or other stresses that cause prolonged inhibition of TORC1, a key integrator of growth signaling. Introns that become stabilized remain associated with components of the spliceosome and differ from other spliceosomal introns in having a short distance between their lariat branch point and 3´ splice site, which is necessary and sufficient for their stabilization. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL13821

10 Samples

Download data: TXT