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 NUDT21 on gene expression in HCT116

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE223415 | GEO | 2024/01/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Effect of depletion of NUDT21 on gene expression in HCT116

Project description:Effect of depletion of NUDT21 on gene expression in HCT116

| PRJNA926109 | ENA

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

DNA methylation analysis of HCT116 after knockdown of LIG1, UHRF1, or luciferase (control)

Project description:In HCT116 colorectal cancer cells, UHRF1, LIG1, or luciferase was knocked down by shRNA followed by selection with puromycin for 2 days. DNA was analyzed 12 days after viral transduction.

2020-03-26 | GSE147518 | GEO

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

Project description: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.

2022-06-10 | GSE205630 | GEO

DNA methylation analysis of HCT116 after knockdown and rescue of UHRF1

Project description:In HCT116 colorectal cancer cells, UHRF1 was knocked down by shRNA (puromycin) while simultaneously transduced with wildtype or mutant UHRF1 (blasticidin) or NDI1 (- control) followed by dual antibiotic selection. DNA was analyzed 11 days after viral transduction.

2019-08-14 | GSE135802 | GEO

The global transcriptome analysis of HCT116 cells transfected with scrambled or CBX4 shRNA

Project description:To investigate the molecular mechanism of CBX4 in CRC, the global transcriptomes were analyzed in HCT116 cells in which CBX4 was knocked down with shRNA, and these transcriptomes were compared to those of HCT116 cells transfected with scrambled shRNA.

2017-02-10 | GSE87778 | GEO

NUDT21 Negatively Regulates PSMB2 and CXXC5 by Alternative Polyadenylation and Contributes to Hepatocellular Carcinoma Suppression

Project description:HCC is the third leading cause of cancer-related deaths worldwide. However, the molecular mechanisms underlying the progression of HCC is still largely elusive. NUDT21 (CFIm25) is an important mediator of 3′ UTR APA and demonstrates a causal relationship between alternative polyadenylation and cancer cell proliferation. Although the function of NUDT21 has been explored in glioblastoma tumor, the functional significance of NUDT21 in solid tumors is not well understood. In this study, we observed that NUDT21 is suppressed in human HCC tissues, compared to adjacent noncancerous tissues. In addition we found that the HCC patients with suppressed NUDT21 are statistically associated with poor outcomes. These observations suggest NUDT21 possibly functions as tumor suppressor in hepatocellular carcinoma (HCC).

2018-01-25 | E-MTAB-6368 | biostudies-arrayexpress

NUDT21 regulates intron detention of the SAM synthetase MAT2A RNA

Project description:NUDT21 encodes the CFIm25 protein, a component of the CFIm complex that regulates alternative polyadenylation (APA). Our data suggest that the CFIm complex also induces splicing of a detained intron in the the S-adenosylmethionine (SAM) synthetase MAT2A to control intracellular levels of SAM. To genetically separate these functions, we used poly(A) Click-seq (PAC-seq) to determine the changes in poly(A) site selection in two cell lines. The parental cell line is the colorectal cell line HCT116 and a derivative line that has the detained intron of MAT2A deleted in both alleles of MAT2A (116-DDI). We found few differences in alternative polyadenylation after CFIm25 depletion were similar supporting teh conclusion that CFIm's role in APA is mechanistically distinct from its role in regulation of MATA splicing.

2021-05-04 | GSE158591 | 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

Effect of depletion of MIB1 in HCT116 cells

Project description:To investigate gene regulation by MIB1 in HCT116 cells, we established stable knockdown HCT116 cell lines.

2022-11-22 | GSE218399 | GEO