Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effect of CLK2 overexpression on alternative splicing

ABSTRACT: To investigate the function CLK2 in the regulation of alternative splicing, we established HeLa cells overexpressing GFP, CLK2 (WT), or (T343A). We then performed alternative splicing analysis using data obtained from RNA-seq of the three cell lines.

ORGANISM(S): Homo sapiens

PROVIDER: GSE227673 | GEO | 2023/11/09

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Effect of CLK2 expression in the regulation of intron retention during heat shock

Project description:We established the HeLa cells expressing the GFP (control) or CLK2 (WT) and subjected them to heat shock. These cells were subjected to RNA-seq for the alternative splicing analysis.

2023-11-09 | GSE247417 | GEO

Effect of the intrinsically disordered region (IDR) within the CLK2 (T343A) mutant in the regulation of intron retention

Project description:We established the HeLa cells expressing the GFP (control) or CLK2 (T343A) with deletion of the IDR [T343A (dIDR)]. These cells were subjected to RNA-seq for the alternative splicing analysis.

2023-11-09 | GSE247419 | GEO

Genomewide analysis of U1C-dependent alternative splicing

Project description:To investigate whether U1C plays a role in splicing regulation in human system, we performed siRNA-mediated knockdown of U1C in HeLa cells and analyzed alternative splicing patterns by high-throughput RNA sequencing (RNAseq) RNAseq performed with poly(A)+ selected total RNA from U1C-knockdown and control-treated HeLa cells

2013-09-30 | E-GEOD-42485 | biostudies-arrayexpress

Coupling between alternative polyadenylation and alternative splicing is limited to terminal introns

Project description:Alternative polyadenylation has been implicated as an important regulator of gene expression. In some cases, alternative polyadenylation is known to couple with alternative splicing to influence last intron removal. However, it is unknown whether alternative polyadenylation events influence alternative splicing decisions at upstream exons. Knockdown of the polyadenylation factors CFIm25 or CstF64 was used as an approach in identifying alternative polyadenylation and alternative splicing events on a genome-wide scale. Although hundreds of alternative splicing events were found to be differentially spliced in the knockdown of CstF64, genes associated with alternative polyadenylation did not exhibit an increased incidence of alternative splicing. These results demonstrate that the coupling between alternative polyadenylation and alternative splicing is usually limited to defining the last exon. The striking influence of CstF64 knockdown on alternative splicing can be explained through its effects on UTR selection of known splicing regulators such as hnRNP A2/B1, thereby indirectly influencing splice site selection. We conclude that changes in the expression of the polyadenylation factor CstF64 influences alternative splicing through indirect effects. HeLa cell line was stably transfected with shRNA plasmids targeting CstF64. Total RNA was isolated from CstF64 KD cells and wild-type control cells using Trizol according to manufacturerâs protocols. Samples were deep sequenced in duplicate using the Illumina GAIIx system.

2016-03-14 | E-GEOD-79157 | biostudies-arrayexpress

Genomewide analysis of EGF-induced alternative splicing

Project description:We performed EGF treatment and hnRNP A1 knockdown in HeLa cells and analyzed alternative splicing patterns by high-throughput RNA sequencing.

2017-03-01 | GSE92939 | GEO

Genomewide analysis of U1C-dependent alternative splicing

2013-09-30 | GSE42485 | GEO

Alternative splicing regulation by homologous Muscleblind proteins

Project description:We provide data showing alternative splicing regulation by Muscleblind proteins in MEFs. MEFs lacking functional Muscleblind (DKO MEFs) were stably reconstituted with Muscleblind proteins from Homo sapiens, Ciona intestinalis, Drosophila melanogaster, Caenorhabditis elegans or Trichoplax adhaerens and splicing regulation was explored using RNA-seq analysis followed by MISO (Mixture of Isoforms). Alternative splicing was accessed using RNA-sequencing data from five DKO MEF lines reconstituted with different GFP-tagged Muscleblind homologs or GFP alone and compared to RNA-seq data from three WT MEF lines and three control DKO MEFs (no Muscleblind reconstitution). A total of 12 samples were used for high-throughput sequencing.

2016-06-01 | E-GEOD-79095 | biostudies-arrayexpress

Identification of RBM39-dependent alternative splicing events in HeLa cells

Project description:We report a comprehensive analysis of alterations in gene expression and alternative splicing upon RBM39 depletion and rescue in HeLa cells.

2023-06-19 | GSE202134 | GEO

CRKL regulates alternative splicing of genes that function in tumorigenesis and cancer progression

Project description:CRKL adaptor protein was demonstrated to have important effects in various types of human cancer and contributes to malignant cell growth and chemoresistance as an overexpressed oncoprotein in cervical carcinoma. But the special molecular mechanisms of CRKL in cervical cancer remain unknown. Here we reported that CRKL regulates genes in cervical cancer related pathways via targeting alternative splicing. We analyzed the expression level of CRKL in 300 cervical cancer tissue samples available in TCGA database, showing a significant increase expression in Stage I cancer samples. From these tumor samples, we selected 40 cancer samples with 20 showing high CRKL expression and 20 showing low, which were analyzed for the potential impact of CRKL on alternative splicing regulation of cancer transcriptome. We further explored the potential function of CRKL in promoting cell proliferation and regulating alternative splicing in HeLa cells using shRNA to knock-down CRKL expression. More importantly, we showed that 34 (94%) of CRKL-regulated alternative splicing events detected in HeLa cells could be validated by qPCR approach and more than a half of these validated events detected in HeLa cells were also correlated with the CRKL expression level in cervical cancers. These results together support a conclusion that CRKL adaptor protein extensively regulates alternative splicing of many genes which are important in tumorigenesis and cancer progression, which expands the functional importance of signaling adaptors in coordinating the dynamic activation of signaling pathways with cellular responses at the alternative splicing level.

2019-06-10 | GSE120631 | GEO

RBM6 promotes tumor cell apoptosis and disrupts the alternative splicing of related genes in HeLa cells

Project description:RNA binding proteins have important functions in tumorigenesis; therefore, their regulatory mechanisms should be further explored. The present study aimed to determine the regulatory roles of RNA binding motif protein 6 (RBM6) in transcription and alternative splicing in Hela cells. RBM6 expression levels and its effect on the prognosis of different tumors in The Cancer Genome Atlas database were analyzed using TIMER2.0. Short hairpin RNA was used to ablate RBM6 expression in HeLa cells. Differentially expressed genes and alternative splicing events in Hela cells were assessed using RNA sequencing and quantitative real-time reverse transcription polymerase chain reaction. RBM6 was identified as a prognostic marker for bladder urothelial carcinoma, kidney renal clear cell carcinoma, mesothelioma, and pancreatic adenocarcinoma. Knockdown of RBM6 promoted cell proliferation. In Hela cells, RMB6 regulated the expression and alternative splicing of many genes involved in tumorigenesis_x001E_related pathways, including ‘apoptotic process’, ‘mitotic cell cycle’, and ‘RNA splicing’. RBM6-regulated alternatively spliced genes (DIABLO (Diablo IAP-binding mitochondrial protein), PAK4 (P21 (RAC1) activated kinase 4) and ERCC2 (ERCC excision repair 2, TFIIH core complex helicase subunit)) were subjected to quantitative real-time reverse transcription polymerase chain reaction validation, which demonstrated the same expression trends as the RNA sequencing results. Our findings showed that RBM6 affects tumorigenesis and cancer progression by disrupting alternative splicing in HeLa cells.

2023-10-17 | GSE196600 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data