GEO DataSets

(Submitter supplied) Background: Alternative splicing (AS), which generates multiple mRNA isoforms from single genes, is crucial for the regulation of eukaryotic gene expression. The flux through competing AS pathways cannot be determined by traditional RNA-Seq, however, because different mRNA isoforms can have widely differing decay rates. Indeed, some mRNA isoforms with extremely short half-lives, such as those subject to translation-dependent nonsense-mediated decay (AS-NMD), may be completely overlooked in even the most extensive RNA-Seq analyses. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21697

12 Samples

Download data: BW

(Submitter supplied) We demonstrates that pre-translational mammalian mRNPs fold as linear rod-like structures with no strong propensity for 5' and 3' end interaction.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

6 Samples

Download data: TXT

(Submitter supplied) A major task in analyzing alternative splicing (AS) by RNA-Seq is to explore and quantify the differential representation of various splice classes and the protein-coding potential of the mapped reads. To this end, we have generated a streamlined bioinformatic pipeline available to the scientific community, which maps RNA-Seq reads to a complex combinatorial database of exon-exon junctions for the unique junction discovery, PTC detection and identification of splice isoforms. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9250

4 Samples

Download data: BEDGRAPH, SAM

(Submitter supplied) This study aims at confidently identifying endogenous nonsense mediated decay (NMD) targets. To achieve this purpose, we performed KD of a few NMD factors in HeLa cells. Additionally, we performed rescue experiments for each factor, expressing an RNAi-resistant version of the gene from a plasmid. To determine transcripts bound by UPF1 in HeLa cells, A construct with a C-terminally flag tagged version of UPF1 was expressed. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

35 Samples

Download data: CSV

(Submitter supplied) The exon junction complex (EJC) deposited upstream of mRNA exon junctions shapes structure, composition and fate of spliced mRNA ribonucleoprotein particles (mRNPs). To achieve this, the EJC core nucleates assembly of a dynamic shell of peripheral proteins that function in diverse post-transcriptional processes. In this study we show that EJC exists in two mutually exclusive compositions characterized by peripheral proteins RNPS1 and CASC3. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

15 Samples

Download data: XLSX

(Submitter supplied) Purpose: We present a genome-wide investigation to distinguish mRNA substrates directly regulated by nonsense-mediated mRNA decay (NMD) from indirect secondary effects using true NMD null alleles Methods: mRNA profiles of wild type (N2), smg-1(r910), and smg-1(r910) smg-2(r915) animals were generated by deep sequencing, in triplicate, using Illumina HiSeq2000. We further performed deep sequencing in triplicate on RNAs that co-immunoprecipitate with the central effector of NMD, SMG-2, in both smg-1(r910) and smg-1(r910) smg-2(r915) mutant animals. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL13657

15 Samples

Download data: GTF, TXT

(Submitter supplied) Two core factors of the NMD machinery in D. melanogaster, Upf1 and Upf2, were knocked down using RNAi, as described in Rehwinkel et al. (2005) RNA, PMID: 16199763. Each of the two knockdowns were compared to mock RNAi knockdowns as described in Blanchette et al. (2005) Genes Dev, PMID: 15937219 in a dual channel experiment, using a custom splice-junction microarray design, see Blanchette et al. (2005), PMID: 15937219. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL7508

6 Samples

Download data: TXT

(Submitter supplied) Divergence of alternative splicing in duplicated genes is investigated

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13222

3 Samples

Download data: TSV

(Submitter supplied) Nonsense-mediated mRNA decay (NMD) is a eukaryotic surveillance pathway that recognizes aberrant transcripts arising from mutations and transcriptional mistakes. Moreover, differential transcript processing such as alternative precursor mRNA splicing (AS) can generate NMD substrates, however, the extent of coupled AS and NMD remained unclear. To investigate NMD targeting of AS variants, we performed transcriptome-wide splicing studies using Arabidopsis thaliana single and double mutants in the NMD factor homologues UPF1 and UPF3, as well as samples treated with the translation inhibitor cycloheximide (CHX). more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9302

12 Samples

Download data: TXT

(Submitter supplied) Purpose: This study is to more comprehensively understand the genome-wide host response to avian pathogen E. coli (APEC). Methods: Four-week-old male broiler chickens were infected with APEC O1 or given saline as a control. Bursas were collected at 1 and 5 days post-infection (dpi). Infected birds were classified based upon lesions in liver, pericardium and air sacs as having mild or severe pathology, representing resistant and susceptible phenotypes, respectively. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16133

22 Samples

Download data: TXT

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

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16133

48 Samples

Download data: TXT

(Submitter supplied) Purpose: This study is to more comprehensively understand the genome-wide host response to avian pathogen E. coli (APEC). Methods: Male broiler chicks were challenged with APEC (or mock-challenged as controls), and bone marrow was harvested at 1 and 5 days post-infection (dpi). Based upon necropsy-scored lesions on liver, pericardium, and air sacs, the challenged birds were assigned to mild or severe pathology categories, representing resistant and susceptible phenotypes, respectively. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16133

24 Samples

Download data: TXT

(Submitter supplied) Rapamycin is a naturally occurring macrolide whose target is at the core of nutrient and stress regulation in a wide range of species. Despite well-established roles as an inhibitor of cap-dependent mRNA translation, relatively little is known about its effects on other modes of RNA processing. Here, we characterize the landscape of rapamycin-induced post-transcriptional gene regulation. Transcriptome analysis of rapamycin-treated cells revealed genome-wide changes in alternative mRNA splicing and pronounced changes in NMD-sensitive isoforms. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

9 Samples

Download data: GFF3, GTF, XLSX

(Submitter supplied) Identification of RNAs differentially expressed during depletion of ICE1, UPF1 or a non-targeting control (NS) in HEK-293TO cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

18 Samples

Download data: CSV

(Submitter supplied) Sub-thalamic deep brain stimulation (DBS) reversibly modulates Parkinson’s disease (PD) motor symptoms, providing an unusual opportunity to compare leukocyte transcripts in the same subjects before and after neurosurgery and after disconnecting the stimulus (ON-and OFF-stimulus). Here, we report rapid stimulus-induced and largely reversible changes in PD leukocyte transcripts, which were larger in scope than the disease-induced changes. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

27 Samples

Download data: CEL

(Submitter supplied) Mammalian body temperature oscillates with the time of the day and is altered in diverse pathological conditions. We recently identified a body temperature-sensitive thermometer-like kinase, which alters SR protein phosphorylation and thereby globally controls alternative splicing (AS). AS can generate unproductive variants which are recognized and degraded by diverse mRNA decay pathways – including nonsense-mediated decay (NMD). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

12 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

Platforms:

GPL24676 GPL20301 GPL18573

24 Samples

Download data: TSV

(Submitter supplied) To investigate the effect of DHX34 and UPF1 depletion on transcription and splicing, DHX34 and UPF1 were knocked down in K562 cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

9 Samples

Download data: CSV, TSV

(Submitter supplied) To investigate the effect of DHX34 depletion on transcription and splicing, DHX34 was knocked down in HeLa cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

6 Samples

Download data: CSV, TSV

(Submitter supplied) To investigate binding of DHX34 protein to RNA, RNA IP was performed in HEK293T cells using the seCLIP protocol.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

9 Samples

Download data: BED, XLSX