Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq (CAFs stimulated with control or HNRNPK knockdown supernatants)

ABSTRACT: Purpose: The goals of this study are to invsetigate the primary signaling pathway enriched in CAFs after stimulation of LUAD supernatants. Methods: Briefly, the supernatants (HNRNPK knockdown and control) of H1299 cells were incubated with CAFs for 24h. Then the CAFs were used to extract total RNAs for quality control and RNA-seq loading samples. RNA-seq was performed as DGE on an Illumia HiSeq platform and 50 bp paired-end reads were generated (BGI Co. Ltd.). Results: Gene Ontology (GO) analysis revealed that cell proliferation and migration were identified as the biological functions of HNRNPK Conclusions: In CAFs, we confirmed that the PI3K-AKT signaling pathway was significantly enriched after stimulation of H1299 supernatants.

ORGANISM(S): Homo sapiens

PROVIDER: GSE197540 | GEO | 2022/03/02

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

RNA-seq (CAFs stimulated with control or HNRNPK knockdown supernatants)

Project description:RNA-seq (CAFs stimulated with control or HNRNPK knockdown supernatants)

| PRJNA810860 | ENA

RNA-seq in H1299 cell lines.

Project description:Purpose: The goals of this study are to invsetigate the primary biological process of HNRNPK. Methods: Briefly, samples (H1299 cells transfected with control or HNRNPK shRNA) were used to extract total RNAs for quality control and RNA-seq loading samples. RNA-seq was performed as DGE on an Illumia HiSeq platform and 50 bp paired-end reads were generated (BGI Co. Ltd.). Results: Gene Ontology (GO) analysis revealed that cell proliferation and migration were identified as the biological functions of HNRNPK Conclusions: RNA-seq in H1299 cell lines revealed that HNRNPK mainly regulated cell proliferation and migration.

2022-03-09 | GSE197946 | GEO

RNA-seq in FHC cell lines.

Project description:Purpose: The goals of this study are to invsetigate the primary biological process of hnRNPK. Methods: Samples (FHC cells transfected with control or hnRNPK shRNA) were used to extract total RNAs for quality control and RNA-seq loading samples. RNA-seq was performed as DGE on an Illumia HiSeq platform and 50 bp paired-end reads were generated. Results: In FHC, metabolism was regulated hnRNPK. Conclusions: RNA-seq in FHC cell lines revealed that hnRNPK mainly regulated metabolism.

2022-03-18 | GSE198445 | GEO

RNA-seq in H1299 cell lines.

Project description:Purpose: The goals of this study are to invsetigate the primary biological process of CLCN3. Methods: Briefly, samples (H1299 cells transfected with control or CLCN3 shRNA) were used to extract total RNAs for quality control and RNA-seq loading samples. RNA-seq was performed as DGE on an Illumia HiSeq platform and 50 bp paired-end reads were generated (BGI Co. Ltd.). Results: Locomotion and growth were identified as the biological functions of CLCN3 Conclusions: RNA-seq in H1299 cell lines revealed that CLCN3 mainly regulated locomotion and growth.

2022-03-06 | GSE197845 | GEO

RNA-seq in HCT116 cell lines

Project description:Purpose: The goals of this study are to invsetigate the primary biological process of hnRNPK. Methods: Briefly, samples (HCT116 cells transfected with control or hnRNPK shRNA) were used to extract total RNAs for quality control and RNA-seq loading samples. RNA-seq was performed as DGE on an Illumia HiSeq platform and 50 bp paired-end reads were generated (BGI Co. Ltd.). Results: Regulation of transcription by RNA polymerase II was identified as the primary biological process according to the gene ontology (GO) analysis. Regulation of transcription by RNA polymerase II and translation by ribosome were identified as the primary biological processes according to the gene set enrichment analysis (GSEA). Conclusions: RNA-seq in HCT116 cell lines revealed that hnRNPK mainly regulated cellular transcription and translation.

2021-10-24 | GSE186371 | 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

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

Expression data from gemcitabine treated pancreatic CAFs

Project description:Pancreatic ductal adenocarcinoma (PDAC) has a characteristically dense stroma comprised predominantly of cancer associated fibroblasts (CAFs). CAFs promote tumor growth, metastasis and treatment resistance. We aimed to investigate the molecular changes and functional consequences associated with chemotherapy treatment of PDAC CAFs. Chemoresistant immortalized CAFs (R-CAFs) were generated by continuous incubation in 100nM gemcitabine. Gene expression differences between treatment naÃ¯ve CAFs (N-CAFs) and R-CAFs were compared by array analysis. Immortalized human pancreatic CAFs were grown for 30 days in either control media or media containing 100nM gemcitabine. RNA was then isolated and hybidized on U133 Plus 2.0 Affymetrix arrays.

2016-03-09 | E-GEOD-78982 | biostudies-arrayexpress

Next Generation Sequencing Analysis of control and hnRNPK-/- RKO cells Transcriptomes

Project description:We generated the hnRNPK-/- RKO cells,and collected the cells at 2 days after transfectd with siRNA. Then,we extracted RNAs and performed next generation sequencing. By comparing sequcing data from control and hnRNPK -/- samples, we profiled the alternative splicing events and gene expression regulated by hnRNPK in CRC.

2018-10-26 | GSE85522 | GEO

Hnrnpk orchestrates embryonic growth plate development via regulating glycolysis

Project description:Here we show a multifunctional protein, Hnrnpk, is essential for preventing excessive apoptosis and premature differentiation of growth plate chondrocytes. These datas were the RNA-seq of E18.5 growth plate chondrocytes with or without Hnrnpk.

2022-09-28 | GSE197283 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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