GEO DataSets

(Submitter supplied) The nuclear matrix associated hnRNP U/SAF-A protein has been implicated in diverse pathways from transcriptional regulation to telomere length control to X inactivation, but the precise mechanism underlying each of these processes has remained elusive. Here, we report hnRNP U as a regulator of SMN2 splicing from a custom RNAi screen. Genome-wide analysis by CLIP-seq reveals that hnRNP U binds virtually to all classes of regulatory non-coding RNAs, including all snRNAs required for splicing of both major and minor classes of introns, leading to the discovery that hnRNP U regulates U2 snRNP maturation and Cajal body morphology in the nucleus. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL9115 GPL11154

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:

GPL10999 GPL5188

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) We profiled the gene expression/splicing program of normal and hnRNP U-deficient mouse hearts by RNA-seq.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

4 Samples

Download data: TXT

(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) We report the high-throughput sequencing for differential alternative splicing analyzation in hnRNP DL knockdown and control mice

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

6 Samples

Download data: TXT

(Submitter supplied) HnRNP K is a heterogeneous nuclear ribonucleoprotein and has been identified as an oncogene in most solid tumors via regulating gene expression or alternative splicing of genes by binding both DNA and pre-mRNA. However, how hnRNP K affects tumorigenesis and regulates the gene expression in cervical cancer (CESC) remains to be elucidated. In these data, higher expression of hnRNP K was observed in CESC and was negatively correlated with the patient survival time. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

4 Samples

Download data: TXT

(Submitter supplied) Transcription by RNA polymerase II (Pol II) is coupled to pre-mRNA splicing, but the underlying mechanisms remain poorly understood. Co-transcriptional splicing requires assembly of a functional spliceosome on nascent pre-mRNA, but whether and how this influences Pol II transcription remains unclear. Here we show that inhibition of pre-mRNA branch site recognition by the spliceosome component U2 snRNP leads to a widespread and strong decrease in new RNA synthesis in human cells. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL18573 GPL21697

48 Samples

Download data: BW, GTF

(Submitter supplied) Analysis of the alternative pre-mRNA procesing after SF3b155 siRNA knock-down in HeLa cells employing a custom microarray platform sensitive to splicing.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10635

12 Samples

Download data: GPR

(Submitter supplied) HeLa cell line treated with Spliceostatin or methanol

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10635

8 Samples

Download data: GPR

(Submitter supplied) Alternative splicing comprises a robust generator of mammalian transcriptome complexity. Splice site specification and activity are controlled by interactions of cis-acting determinants on a transcript with specific RNA binding proteins. A major subset of these interactions comprises interactions localized to the intronic U-rich polypyrimidine tract located immediately 5’ to the majority of splice acceptors. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

6 Samples

Download data: TXT, XLSX

(Submitter supplied) Much remains unknown concerning the mechanism by which the splicing machinery pinpoints short exons within intronic sequences and how splicing factors are directed to their pre-mRNA targets. Part of the explanation probably lies in differences in chromatin organization between exons and introns. Proteomic, co-immunoprecipitation, and sedimentation analyses described here indicated that SF3B1, an essential splicing component of the U2 snRNP complex, is strongly associated with nucleosomes. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL11154

6 Samples

Download data: TXT, WIG

(Submitter supplied) Analysis of gene expression by RNA-seq upon siRNA mediated knockdown of scaffold attachment factor A (SAF-A) versus control siRNA in RPE1 cells at 24 hour and 48 hour time points post transfection reveals SAF-A loss does not impact on gene transcription

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

4 Samples

Download data: GTF, TXT, XLSX

(Submitter supplied) To study Hnrnpu function during cortical development we preformed single-cell RNA sequencing (scRNA-seq) on mouse neutrosphere cultures derived from E13 ICR cortices, 24 hours following treatment with CRISPR/CAS9 and two sgRNA sequences targeting mouse Hnrnpu. In parallel, we analyzed bulk RNA-seq from dissected cortices of E13 embryos in which Hnrnpu conditional truncation in the telencephalon was driven by Emx1::Cre. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24247 GPL21626

33 Samples

Download data: MTX, TSV, TXT