Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effect of depletion of GMDS-AS1 on gene expression of HCT116 colorectel cancer cells

ABSTRACT: To detect the biological function of LncRNA GMDS-AS1 in colorectal cancer tumorigenesis, we constructed lentivirus-infected stable GMDS-AS1-knockdown (KD) HCT116 cell lines using shRNA (GMDS-AS1 shRNA2) and a nontarget control shRNA Next we performed gene expression profiling analysis using data obtained from RNA-seq of control and GMDS-AS1 KD cells, three biological replicates were applied.

ORGANISM(S): Homo sapiens

PROVIDER: GSE205630 | GEO | 2022/06/10

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Gene expression profiling by RNA-seq of control and METTL14-knockdown HCT116 human colon cancer cells

Project description:In order to define the cohort of genes whose expression is regulated by METTL14 in p53 wild-type colorectal cancer, we constructed HCT116 cells stably infected with lentivirus carrying control shRNA (sh_NC) or METTL14 shRNA (sh_MET). Subsequently, total RNA was isolated and then performed transcriptome RNA sequence.

2023-03-27 | GSE186791 | GEO

Effect of Sprouty2 Downregulation on MicroRNA Expression Profile in HCT116 Colon Cancer Cells

Project description:Sprouty proteins are evolutionarily conserved modulators of mitogen-activated protein kinase pathway. Sprouty2 appears to function as a tumor suppressor in cancers, whereas we reported earlier that Sprouty2 functions as an oncogene in colorectal cancer. To further understand the oncogenic potential of Sprouty2 in the colon, microRNA expression profile of colon cancer cells was investigated. Sprouty2 suppression in HCT116 colon cancer cells significantly increased MicroRNA 194-5p. Sprouty2 dependent regulation of microRNA194-5p and its biological targets were studied further for their tumor suppressive actions in reducing epithelial-mesenchymal transition in colorectal cancer. Sprouty2 knockdown was performed by infecting HCT116 cells with three different lentivirus expressing shRNAs against human Sprouty2 mRNA and a control non targeted non-silencing shRNA (Sprouty2 MISSION shRNA Lentiviral Transduction Particles; TRCN 0000007522, TRCN 0000231589, TRCN 0000231588 and a non-targeted shRNA control from Sigma) following lentiviral transduction protocols provided by Sigma. Due to the random integration of the lentivirus into the host genome, varying levels of Sprouty2 gene knockdown was expected in puromycin resistant colonies. Three colonies in triplicate that demonstrated highest to lowest level of Sprouty2 suppression, as assessed by western blotting, were selected. RNA samples from these colonies and one from non-targeted shRNA expressing colony were prepared for microRNA expression profile analysis. Pooled RNA samples from each group were shipped to Exiqon for microRNA profiling based on miRCURY LNATM array technology.

2015-06-09 | E-GEOD-69665 | biostudies-arrayexpress

RNA-seq analysis of differentially expressed genes between WT and shTRIM21 HCT116 cells.

Project description:To investigate the biological function TRIM21 in the colorectal cancer, we established HCT116 cell lines in which the TRIM21 gene has been knocked down by shRNA. We used a lentiviral shRNA technique to knockdown TRIM21 expression in HCT116 cells. A scrambled shRNA (shRNA/Control) was used as a control. We then performed RNA-Seq with Cloud-seq Biotech Inc. (Shanghai, China) to analyze gene expression changes in HCT116 cells. For each sample, three independent biological replicates were performed.

2023-05-23 | GSE211267 | GEO

Expression data from HCT116 cell transduced with lentivirus encoding PNO1 shRNA (sh-PNO1) or Control shRNA (sh-Ctrl)

Project description:To further explore the underlying mechanism of PNO1 knockdown on suppression of CRC cell growth in vivo and in vitro, Affymetrix human GeneChip primeview arrays were performed to determine the global gene expression in HCT116 cells after transduction lentivirus encoding PNO1 shRNA (n=3) or control shRNA (n=3).

2019-04-23 | GSE113514 | GEO

Expression data from HCT116 cell transduced with lentivirus encoding HAUS6 shRNA (sh-HAUS6) or Control shRNA (sh-Ctrl)

Project description:To further explore the underlying mechanism of HAUS6 knockdown on suppression of CRC cell growth in vivo and in vitro, Affymetrix human GeneChip primeview arrays were performed to determine the global gene expression in HCT116 cells after transduction lentivirus encoding HAUS6 shRNA (n=3) or control shRNA (n=3).

2020-10-01 | GSE140326 | GEO

Effect of depletion of GMDS-AS1 on gene expression of HCT116 colorectel cancer cells

Project description:Effect of depletion of GMDS-AS1 on gene expression of HCT116 colorectel cancer cells

| PRJNA846740 | ENA

Expression data from human colon cancer cell line HCT116 with NFX1-91 knockdown and control cells

Project description:NFX1-91, a novel E6 cellular downstream target, functions as a transcriptional regulator and is involved in repressing hTERT expression. Other functions and downstream targets regulated by NFX1-91 were not well understood. We used microarrays to determine gene expression deregulated when NFX1-91 was knocked down. HCT116 cells was infected with lentivirus carrying NFX1-91 shRNA or control β-Galactosidase shRNA to stably knock down target gene expression. Total RNAs were extracted and hybridized on Affymetrix microarrays.

2010-08-18 | E-GEOD-23674 | biostudies-arrayexpress

Expression profiling of HCT116 cells transfected with shCTRL or shKSR1

Project description:We engineered HCT116 cells by transfecting a non targeting control hairpin or 2 different short hairpin against KSR1 to knockdown KSR1 and microarrays were performed on non-transfected controls, non-targeting shRNA controls, shRNA #1 targeting KSR1, and shRNA #2 targeting KSR1. We used microarray for molecular profiling of colon cancer cells in presence or in absence of KSR1, an important scaffold of Raf/MEK/ERK pathway and identify genes which are regulated by KSR1 Cell lines were measured in as single biological replicates 1. HCT116 untransfected 2 HCT116 + shCTRL 3.HCT116 + shKSR1#1 4. 3.HCT116 + shKSR1#2

2015-01-28 | E-GEOD-65351 | biostudies-arrayexpress

USP7 shRNA knock-down in T-ALL cells [Jurkat_HSB2_shRNA_RNA-seq]

Project description:RNAseq analysis of USP7 shRNA KD in T-ALL cell lines. USP7 shRNAs lentivirus was generated by co-transfecting 293T cells with shRNA vectors (OriGene or Sigma). T-ALL cells were transduced with USP7 shRNA lentivirus and sorted for GFP positive cells five days after transduction or selected by puromycin.

2021-03-09 | GSE148522 | GEO

Effect of depletion of NUDT21 on gene expression in HCT116

Project description:To investigate the function of NUDT21 in the regulation of progression of colorectal cancer, we established HCT116 cell line in which each target gene has been knocked down by shRNA. We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells at two time points.

2024-01-01 | GSE223415 | 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