Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Two groups of control and RANBP1-knockdown HCT116 cells

ABSTRACT: Two groups of control and RANBP1-knockdown HCT116 cells

PROVIDER: PRJNA748887 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Two groups of control and RANBP1-knockdown HCT116 cells

Project description:Colorectal cancer (CRC) is among the top five most common malignant tumors worldwide and has a high mortality rate. Identification of the mechanism of CRC and potential therapeutic targets is critical for improving survival. In the present study, we observed high expression of RAN binding protein 1 (RANBP1) in CRC tissues. Upregulated RANBP1 expression was strongly associated with TNM stages and was an independent risk factor for poor prognosis. In vitro and in vivo functional experiments demonstrated that RANBP1 promoted the proliferation and invasion of CRC cells, affected the cell cycle, and inhibited the apoptosis of CRC cells. Low RANBP1 expression reduced the expression levels of hsa-miR-18a, hsa-miR-183, and hsa-miR-106 microRNAs (miRNAs) by inhibiting the nucleoplasmic transport of precursor miRNAs (pre-miRNAs), thereby promoting the accumulation of the latter in the nucleus and reducing the expression of mature miRNAs. Further experiments and bioinformatic analyses demonstrated that RANBP1 promoted the expression of YAP by regulating miRNAs and the Hippo pathway. We also found that YAP acted as a transcriptional cofactor to activate RANBP1 transcription in combination with TEAD4 transcription factor. Thus, RANBP1 further promoted the progression of CRC by forming a positive feedback loop with YAP. Our results revealed the biological role and mechanism of RANBP1 in CRC for the first time, suggesting that RANBP1 can be used as a diagnostic molecule and a potential therapeutic target in CRC.

2021-07-27 | GSE180613 | GEO

Gene expression analysis of HCT116 colorectal cancer cells with shRNA mediated control (GFP) or ZEB1 knockdown

Project description:Epithelial-to-mesenchymal transition (EMT) is a fundamental process in development and disease. If aberrantly activated it is a trigger for tumour progression and metastasis (Thiery et al 2009 Cell). It is now known that EMT activation is also associated with the maintenance of stem-cell properties (Mani et al. 2008 Cell). Since Zinc-finger enhancer binding transcription factor 1 (ZEB1) is a crucial EMT activator, we analyzed the changes in the gene expression profile that accompany shRNA mediated loss of ZEB1 in HCT116 colorectal cancer cells. HCT116 is a cell line that exhibits mesenchymal characteristics, but reverts to an epithelial phenotype upon ZEB1 knock down (Spaderna et al. 2008 Cancer Research). HCT116 cells were stably transfected with control (GFP) or ZEB1 shRNA. Upon puromycin selection, single cell clones were picked and characterized. Cells from two control versus two ZEB1 knockdown clones were harvested, total RNA was isolated and processed to hybridization.

2016-06-15 | E-MTAB-3480 | biostudies-arrayexpress

RNA-seq of HCT116 KRAS G13D and HCT116 KRAS WT cell lines with control or CFIm25 knockdown

Project description:RNA-seq of HCT116 KRAS G13D and HCT116 KRAS WT cell lines with control or CFIm25 knockdown

| PRJEB38811 | ENA

Transcriptome analysis of Control and FBXO38 knockdown in HCT116 and Hela cell lines

Project description:F-box only protein 38 (FBXO38), which belongs to SKP1-CUL1-F-box protein (SCF) family, exhibits the ability to mediate Lys48-linked poly-ubiquitination and subsequent proteasome degradations of PD-1.To investigate the effect of FBXO38 knockdown on transcription in tumor, we constructed control and FBXO38 knockdown by shRNA in Hela and HCT116 cell lines. We found that FBXO38 may interact with the immune pathway in the tumor.

2024-02-07 | GSE220879 | GEO

Expression data from HCT116 cells following H19 knockdown

Project description:Knockdown of H19 leads to cell cycle arrest, reduced cell proliferation, and reduced cell migration in HCT116 cells. We used microarrays to detail the global programme of gene expression following H19 knockdown in HCT116 cells

2016-09-29 | GSE87430 | GEO

mRNA-seq of HCT116 USP22 knockdown cells

Project description:This analysis identifies genes which are affected in HCT116 cells upon USP22 knockdown

2019-10-26 | E-MTAB-7393 | biostudies-arrayexpress

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

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

| PRJNA615136 | ENA

HCT116 (CRC): control siRNA vs. ZNF746 siRNA Transfected

Project description:Transcriptional profiling of HCT116 cells compared to untreated control with HCT116 cells transfected with ZNF746 siRNA plasmid. Goal was to determine the effects of ZNF746 gene transfection on CRC progression. Two-condition experiment, HCT116 vs. ZNF746 siRNA.

2019-12-01 | GSE90832 | GEO

mRNA-seq of HCT116 USP22 knockdown cells

Project description:mRNA-seq of HCT116 USP22 knockdown cells

| PRJEB29794 | ENA

Next Generation Sequencing Profiles Transcriptomes of Control and shDANCR HCT116 Cell Lines

Project description:Purpose: The goal of this study is to compare Next Generation Sequencing-derived transcriptome profiling (RNA-seq) of a negative control cell line to two independent shDANCR cell lines. Methods: mRNA profiles of HCT116 colorectal cancer cell lines transfected with lentiviruses containing a negative control vector and two independent shRNA vectors for DANCR knockdown were generated by deep sequencing using Illumina HiSeq2000. The sequence reads that passed quality filters were analyzed at the transcript level with the method of HISAT2, and StringTie followed by FPKM calculation. Results: Using the described data analysis workflow, we mapped about 40 million sequence reads per sample to the human genome (GRCh38) and identified about 130,000 transcripts (transcribed from about 40,000 genes) per sample with StringTie. Approximately 2.5% of the genes showed differential expression between the Control and shDANCR cell lines, with a fold change ≥1.5 and p value <0.05. Conclusions: Our study represents a detailed analysis of gene expression changes affected by DANCR knockdown in colorectal cancer cell line HCT116.

2021-01-13 | GSE145407 | 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