Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-Seq of human colorectal cancer (CRC) cell lines with or without METTL17 knockdown

ABSTRACT: To investigate the mRNA profiling in RKO and SW620 cells with or without shRNA-mediated METTL17 knockdown, we performed RNA-seq with the total RNA extracted from the CRC cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE239325 | GEO | 2023/08/08

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Expression profiles of piRNAs in Colorectal Cancer (CRC) cell lines

Project description:To investigate the presence and abundance of piRNAs in Colorectal Cancer (CRC), we performed deep-sequencing of the small RNA transcriptome of eight human CRC cell lines (HT-115, Caco-2, SW-1417, SW 403, COLO 205, HT-29, HCT 116 and RKO).

2020-08-06 | E-MTAB-8117 | biostudies-arrayexpress

Identification of super-enhancers in colorectal cancer cell lines

Project description:H3K27 acetylation statuses were analyzed in four colon cancer cell lines (RKO, Caco2, SW48, and SW620), and colorectal cancer-specific super-enhancers were identified.

2017-05-31 | GSE96069 | GEO

Tumor-derived exosomal miR-181a-5p activates hepatic stellate cells to promote liver metastasis of colorectal cancer

Project description:A previous study suggested that the expression of miR181a-5p was higher in CRC tissues, but whether CRC cell-derived exosomes regulate the activation of HSCs through secreting miR181a-5p and promoting CRLM warrants further investigation. We compared the miRNA expression profiles between exosomes from highly metastatic CRC cells (RKO and SW620) and those from weakly-metastatic CRC cells (HT29 and SW480).

2021-12-05 | GSE141997 | GEO

Epigenomic analysis reveals a unique DNA methylation program of metastasis-competent circulating tumor cells in colorectal cancer

Project description:Metastasis is the main cause of cancer-related deaths in patients with solid tumors, including colorectal cancer (CRC). Circulating tumor cells (CTCs) and epigenetic alterations are involved in the development of metastasis. It is important to characterize the DNA methylation pattern of metastasis-competent CTCs to better understand the metastatic process and obtain new clinical applications for cancer patients. Therefore, the aim of this study was to investigate the DNA methylation landscape of metastasis-competent CTCs in CRC. The DNA methylome of the human colorectal cancer-derived cell line CTC-MCC-41 was compared with primary (HT29, Caco2, HCT116, RKO) and metastatic (SW620 and COLO205) CRC cells using a genome-wide methylation analysis.

2023-09-20 | GSE220096 | GEO

microRNA expression signatures in colorectal cancer cell lines with demethylating treatment

Project description:To screen for epigenetically silenced miRNAs, wecarried out miRNA microarray analysis in three colorectal cancer (CRC) cell lines (HCT116, DLD-1 and RKO) treated with or without 5-aza-2'-deoxycytidine (aza). HCT116 and RKO cells were also treated with aza plus 4-phenylbutyric acid (PBA). In addition, we analyzed HCT116 cells in which the DNA methyltransferase genes DNMT1 and DNMT3B were genetically disrupted (double knockout; DKO cells), thereby abrogating DNA methylation. Expression of a majority of miRNAs was downregulated in all three CRC cell lines tested, as compared to normal colonic mucosa. DAC treatment upregulated expression of a large number of miRNAs in all three CRC cell lines, and combination treatment with DAC plus PBA induced even greater numbers of miRNAs in CRC cells. The most profound effect on the miRNA expression profile was induced by genetic disruption of DNMT1 and DNMT3B in HCT116 cells. CRC cells were treated with 5-aza-2’-deoxycytidine (aza) or aza plus 4-phenylbutyrate (PBA). Nomal colon RNA was purchased from BioChain. Expression of 470 miRNAs was analyzed using Human miRNA Microarray V1 (G4470A; Agilent technologies, Santa Clara, CA, USA).

2011-07-01 | E-GEOD-29900 | biostudies-arrayexpress

IGF2 shRNA knockdown in the colorectal cancer (CRC) cell line SW480

Project description:In order to identify gene expression changes associated with the deregulated of IGF2, Doxycylin inducible empty vector and IGF2 shRNA permanent cell lines were generated by lentivral transduction in the colorectal cancer (CRC) cell line SW480 and selected with puromycin. For microarray analysis, both cell lines were plated at 3 x 105 cells in 6 well plates using RPMI plus 10% FCS and penicillin/ streptomycin, either without/ with 50 ng/ ml doxycycline at the time of plating. The respective cell lines were harvested at day 1, 3, and 5. Three experiments were performed for each time point and condition and were separately analyzed. The samples were analyzed on Illumina human HT-12 v 4 expression bead chips. The microarray data was processed and normalized using the lumi pipline.

2016-04-30 | E-MTAB-3786 | biostudies-arrayexpress

Gene expression profiling of RKO cells with or without SQLE knockdown.

Project description:RKO cells (WT or SQLE knockdown) were harvested and mRNA were extracted for high-throughput sequencing.

2024-05-20 | GSE232678 | GEO

microRNA expression signatures in colorectal cancer cell lines with demethylating treatment

2011-07-01 | GSE29900 | GEO

RNA-Seq of human colorectal cancer (CRC) cell lines with or without METTL17 knockdown

Project description:RNA-Seq of human colorectal cancer (CRC) cell lines with or without METTL17 knockdown

| PRJNA998811 | ENA

Differentially expressed miRNAs in TGF-M-NM-21-knock down human colorectal cancer cell lines vs controls

Project description:To investigate the role of TGF-M-NM-21-regulated miRNAs in the progression of colorectal cancer,we performed comprehensive miRMA microarray analysis on RNA derived from typical human colorectal cancer cell lines and TGF-M-NM-21 knock-down human colorectal cancer cell lines. We identified a novel set of TGF-M-NM-21-related miRNAs. Total RNA was isolated from TGF-M-NM-21-knock down colorecatl cancer cell lines and controls.Three-condition experiment: shRNA-TGF-M-NM-21/Lovo cells vs. shRNA-Control/Lovo cells, shRNA-TGF-M-NM-21/SW620 cells vs. shRNA-Control/ SW620 cells, and shRNA-TGF-M-NM-21/HT29 cells vs. shRNA-Control/HT29 cells. Biological replicates: 1 Lovo cells stably transfected with shRNA-TGF-M-NM-21- pSUPER gfp-neo, 1SW620 cells stably transfected with shRNA-TGF-M-NM-21- pSUPER gfp-neo, 1HT29 cells stably transfected with shRNA-TGF-M-NM-21- pSUPER gfp-neo, 1Love cells stably transfected with shRNA-Control- pSUPER gfp-neo, 1SW620 cells stably transfected with shRNA-Control- pSUPER gfp-neo, and 1HT29 cells stably transfected with shRNA-Control- pSUPER gfp-neo, independently grown and harvested. One replicate per array.

2013-12-16 | E-GEOD-53338 | biostudies-arrayexpress

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