Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seqs of SRSF3 and hnRNPK depleted C2C12 cells

ABSTRACT: RNA-seqs of SRSF3 and hnRNPK depleted C2C12 cells

PROVIDER: PRJNA678879 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR13071982_1.fastq.gz	Fastqsanger.gz
	SRR13071982_2.fastq.gz	Fastqsanger.gz
	SRR13071983_1.fastq.gz	Fastqsanger.gz
	SRR13071983_2.fastq.gz	Fastqsanger.gz
	SRR13071984_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

RNA-seqs of SRSF3 and hnRNPK depleted C2C12 cells

Project description:Total RNA was extracted from C2C12 cells transfected with the indicated siRNA using TRIZOL (Thermo Fisher Scientific), and was further purified with Quick-RNA Miniprep Kit (Zymo research) according to the manufacturer’s instructions. The extracted RNA was subjected to RNA-seq at Macrogen, Japan. Briefly, a sequencing library was prepared using the TruSeq Stranded mRNA kit (Illumina), and the library was read on Illumina NovaSeq 6000 (150 bp paired-end reads).

2021-07-20 | GSE161601 | GEO

RNA sequencing of SRSF3 depleted pluripotent cells

Project description:RNA sequencing of SRSF3 depleted pluripotent cells

| PRJNA454002 | ENA

Genome-wide maps of RNA-protein interactions of SRSF3, hnRNPK and CPSF6

Project description:Genome-wide maps of RNA-protein interactions of SRSF3, hnRNPK and CPSF6

| PRJNA678880 | ENA

RNA sequencing of SRSF3 depleted pluripotent cells

Project description:RNA seqeuncing was performed to identifiy changes in genes expression and alternative splicing following SRSF3 depletion in pluripotent stem cells.

2018-05-10 | GSE113794 | GEO

hnRNPK knock down in Ewing cell line

Project description:Ewing sarcoma is a highly aggressive tumor characterized by a translocation between members of the FET family of RNA binding proteins and one of several ETS transcription factors, with the most common translocation being EWS-FLI1. EWS-FLI1 leads to changes in gene expression through mechanisms that are not completely understood. We performed RNA sequencing analysis on primary pediatric human mesenchymal progenitor cells (pMPCs) expressing EWS-FLI1 in order to identify novel target genes. This analysis identified lnc277 as a previously uncharacterized long non-coding RNA upregulated by EWS-FLI1 in pMPCs. Inhibiting the expression of lnc277 diminished the ability of Ewing sarcoma cell lines to proliferate and form colonies in soft agar whereas inhibiting lnc277 had no effect on other cell types tested. By analyzing gene expression after shRNA knockdown, we found that both EWS-FLI1 and lnc277 repressed many more genes that they induced and that a significant fraction of EWS-FLI1 repressed targets were also repressed by lnc277. Analysis of primary human Ewing sarcoma RNA sequencing data further supports a role for lnc277 in mediating gene repression. We identified hnRNPK as an RNA binding protein that interacts directly with lnc277. We found a significant overlap in the genes repressed by hnRNPK and those repressed by both EWS-FLI1 and lnc277, suggesting that hnRNPK participates in lnc277 mediated gene repression. Thus, lnc277 is a previously uncharacterized long non-coding RNA downstream of EWS-FLI1 that facilitates the development of Ewing sarcoma via the repression of target genes. Our studies identify a novel mechanism of oncogenesis downstream of a chromosomal translocation and underscore the importance of lncRNA-mediated gene repression as a mechanism of EWS-FLI1 transcriptional regulation. A673 Ewing cells expressing an shRNA targeting hnRNPK or control were subjected to paired end RNA sequencing and compared to shGFP control.

2014-11-01 | E-GEOD-60890 | biostudies-arrayexpress

The differentially expressed genes in SRSF3 siRNA-treated HCT116 cells

Project description:Several members of SRSF family play wide-ranging roles in the regulation of transcription and post-splicing processes as well as splice sites selection. Although the expression of SRSF3 was reported to be overexpressed in several cancers, the roles of SRSF3 in the cancer cells are almost unknown. We analyzed differentially expressed genes in SRSF3 siRNA-treated HCT116 cells and identified the specific pathways regulated by SRSF3. After treatment of HCT116 cells with SRSF3 (sample 02) or control (sample 01) siRNA, total RNA was extracted using RNeasy Mini Kit (Qiagen, Valencia, CA). The quality of the purified RNA and its applicability for microarray analysis were assessed by the Agilent 2100 Bioanalyzer using a RNA 6000 Nano Labchip kit (Agilent Technologies, Palo Alto, CA, USA). Total RNA (400 ng) was used for amplification, labeling and hybridization to a whole human genome oligoDNA microarray (4x44k; Agilent) according to the manufacture’s instructions.

2013-08-04 | E-GEOD-31876 | biostudies-arrayexpress

Symbiodinium ITS seqs

Project description:Symbiodinium ITS seqs from Orbicella annularis in The Bahamas

| PRJEB31000 | ENA

RNA-Seq analysis of SRSF3 KO hearts compared to controls and iCLIP analysis of SRSF3 binding profile in neonatal cardiomyocytes

Project description:The goal of this study is to analyse the transcriptome of control hearts vs hearts lacking SRSF3 expression and to analyse binding preferences of SRSF3 in cardiac myocytes.

2019-05-27 | GSE123002 | GEO

Effect of overexpressing HNRNPK in glioblastoma stem cell

Project description:The mechanisms underlys GBM cellular transitions remain unclear.In our study, we overexpressed HNRNPK in three different types of GSCs. HNRNPK (WT) leads to high expression of core markers in GSCs, and its characteristics are similar to those of the MES subtype, exhibiting stronger invasive abilities and tumorigenic potential. We mutated 422 site from lysine(K) to argnine(R) to study the function of SUMOylation in HNRNPK. Sequencing of GSCs with overexpression of HNRNPK (K422R) mutation confirmed the upregulation of infiltrating markers within the GSCs. The changes in GSC subtypes driven by overexpression of HNRNPK (WT or K422R) were not restricted by GSC mutation features.

2024-12-13 | GSE262681 | GEO

The differentially expressed genes in SRSF3 siRNA-treated HCT116 cells

2013-08-04 | GSE31876 | GEO