GEO DataSets

(Submitter supplied) Understanding how RNA binding proteins control the splicing code is fundamental to human biology and disease. Here we present a comprehensive study to elucidate how heterogeneous nuclear ribonucleoparticle (hnRNP) proteins, among the most abundant RNA binding proteins, coordinate to regulate alternative pre-mRNA splicing (AS) in human cells. Using splicing-sensitive microarrays, cross-linking and immunoprecipitation coupled with high-throughput sequencing, and cDNA sequencing, we find that more than half of all AS events are regulated by multiple hnRNP proteins, and that some combinations of hnRNP proteins exhibit significant synergy, whereas others act antagonistically. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL9115 GPL11154

31 Samples

Download data: BOWTIE

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

4 related Platforms

67 Samples

Download data: BOWTIE, CEL

(Submitter supplied) Understanding how RNA binding proteins control the splicing code is fundamental to human biology and disease. Here we present a comprehensive study to elucidate how heterogeneous nuclear ribonucleoparticle (hnRNP) proteins, among the most abundant RNA binding proteins, coordinate to regulate alternative pre-mRNA splicing (AS) in human cells. Using splicing-sensitive microarrays, cross-linking and immunoprecipitation coupled with high-throughput sequencing, and cDNA sequencing, we find that more than half of all AS events are regulated by multiple hnRNP proteins, and that some combinations of hnRNP proteins exhibit significant synergy, whereas others act antagonistically. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL9115 GPL9052

15 Samples

Download data: BOWTIE

(Submitter supplied) Understanding how RNA binding proteins control the splicing code is fundamental to human biology and disease. Here we present a comprehensive study to elucidate how heterogeneous nuclear ribonucleoparticle (hnRNP) proteins, among the most abundant RNA binding proteins, coordinate to regulate alternative pre-mRNA splicing (AS) in human cells. Using splicing-sensitive microarrays, cross-linking and immunoprecipitation coupled with high-throughput sequencing, and cDNA sequencing, we find that more than half of all AS events are regulated by multiple hnRNP proteins, and that some combinations of hnRNP proteins exhibit significant synergy, whereas others act antagonistically. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL15106

21 Samples

Download data: CEL

(Submitter supplied) CLIP-seq of hnRNP L in human T cells

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL11154 GPL10999

4 Samples

Download data: BED

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

Platforms:

GPL5188 GPL10999

12 Samples

Download data: BED, CEL

(Submitter supplied) Transient siRNA-mediated knockdown of hnRNP L, followed by cycloheximide treatment to eliminate NMD. Supplementary files GSE37561_activated_exon.txt and GSE37561_repressed_exon.txt list exons predicted to be activated and repressed by hnRNPL, respectively.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

6 Samples

Download data: CEL, TXT

(Submitter supplied) Individual-nucleotide resolution UV-crosslinking and immunoprecipitation (iCLIP) combined with high-throughput sequencing was used to generate a transcriptome-wide binding map of hnRNP L. Supplementary file GSE37560_hnRNPL_crosslink_site.bed includes filtered crosslink sites of hnRNPL: combining data from all 3 experiments.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10999

6 Samples

Download data: BED

(Submitter supplied) UV-crosslinking and immunoprecipitation (CLIP) combined with high-throughput sequencing was previously used to generate transcriptome-wide binding maps of several RNA-binding proteins. However, since identification of binding sites relied on the analysis of overlapping sequence clusters, distances of less than 30 nucleotides were not resolved. An additional disadvantage of CLIP is the requirement of reverse transcription to pass over residual amino acids that remain covalently attached to the RNA at the crosslink site. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL9115

1 Sample

Download data

(Submitter supplied) Deep Sequencing of mRNA from the Drosophila melanogaster S2-DRSC cells that have been RNAi depleted of mRNAs encoding RNA binding proteins. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9061

121 Samples

Download data: BEDGRAPH, GFF, SAM

(Submitter supplied) Alternative splicing of pre-mRNAs significantly contributes to the complexity of gene expression in higher organisms, but the regulation of the splice site selection remains incompletely understood. We have previously demonstrated that a chromatin-associated protein, AKAP95 (AKAP8), has a remarkable activity in enhancing chromatin transcription. In this study, we have shown that AKAP95 physically interacts with many factors involved in transcription and RNA processing, and functionally regulates pre-mRNA splicing. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL17021

15 Samples

Download data: BW

(Submitter supplied) Through alternative splicing, most human genes express multiple isoforms that may have distinct or even antagonistic functions. To infer isoform regulation based on data from high-throughput sequencing of cDNA fragments (RNA-Seq), we have developed MISO, a computational model that estimates the expression level of alternatively spliced exons and mRNA isoforms and provides intuitive measures of confidence in these estimates. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL9185 GPL9052

6 Samples

Download data: SAM

(Submitter supplied) One day before transfection, HeLa cells were seeded in 6-well culture plates (1.5 x 10e5 cells per well) or 10-cm culture dishes (4.3 x 10e5 cells per dish). siRNA duplex (at a final concentration in culture medium of 30 nM) was transfected with Lipofectamine 2000 (Invitrogen) according to the manufacturer's instructions. siRNA duplices specific for human hnRNP L, human hnRNP LL, and luciferase GL2 were from MWG Biotech (Ebersberg, Germany). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

12 Samples

Download data: CEL

(Submitter supplied) In this work, we have studied four closely related members of the five known Drosophila hnRNP A/B family, hrp36, hrp38, hrp40, and hrp48. Using splicing-sensitive microarrays, between 200 and 300 genes were detected as specifically regulated by each individual hrp protein following down regulation of the protein expression level by RNAi-mediated knock-down. Keywords: Genetic modification

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL7508

4 Samples

Download data: TXT

(Submitter supplied) In this work, we have studied four closely related members of the five known Drosophila hnRNP A/B family, hrp36, hrp38, hrp40, and hrp48. Using splicing-sensitive microarrays, between 200 and 300 genes were detected as specifically regulated by each individual hrp protein following down regulation of the protein expression level by RNAi-mediated knock-down. Keywords: Genetic modification

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL7508

12 Samples

Download data: TXT

(Submitter supplied) In this work, we have studied four closely related members of the five known Drosophila hnRNP A/B family, hrp36, hrp38, hrp40, and hrp48. Using splicing-sensitive microarrays, between 200 and 300 genes were detected as specifically regulated by each individual hrp protein following down regulation of the protein expression level by RNAi-mediated knock-down. Keywords: Genetic modification

Organism:

Drosophila melanogaster

Type:

Expression profiling by array

Platform:

GPL1322

2 Samples

Download data: CEL

(Submitter supplied) In this work, we have studied four closely related members of the five known Drosophila hnRNP A/B family, hrp36, hrp38, hrp40, and hrp48. Using splicing-sensitive microarrays, between 200 and 300 genes were detected as specifically regulated by each individual hrp protein following down regulation of the protein expression level by RNAi-mediated knock-down. Keywords: Genetic modification

Organism:

Drosophila melanogaster

Type:

Other

Platform:

GPL5919

6 Samples

Download data: CEL, SGR, TXT

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

Organism:

Drosophila melanogaster

Type:

Other; Expression profiling by array

Platforms:

GPL5919 GPL1322 GPL7508

24 Samples

Download data: CEL, SGR, TXT

(Submitter supplied) Background. Somatic cell reprogramming is the process that allows differentiated cells to revert to a pluripotent state. In contrast to the extensively studied rewiring of epigenetic and transcriptional programs required for reprogramming, the dynamics of post-transcriptional changes and their associated regulatory mechanisms remain poorly understood. Here we study the dynamics of alternative splicing changes occurring during efficient reprogramming of mouse B cells into induced pluripotent stem (iPS) cells and compare them to those occurring during reprogramming of mouse embryonic fibroblasts. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

18 Samples

Download data: TAB, TXT

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL19057 GPL13112

57 Samples

Download data: BEDGRAPH, BW, TSV