Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

To identify the deficient enzyme(s) in the glycosylation pathway that yield incomplete maturation of (uPAR) protein

ABSTRACT: We previously demonstrated plasticity in urokinase receptor (u-PAR) display in clonal colon cancer cells (Cancer Research 66: 7957-7967 (2006)). Thus, u-PAR display oscillates 10 fold between high and low density at the cell surface. We have determined that this oscillation in u-PAR display is posttranslational in nature. Thus, while clonal cell populations with high and low u-PAR density synthesize u-PAR at the same rate, the protein is inefficiently glycosylated in cells down-shifted for u-PAR display and subsequently degraded. The objective of this study is to identify the deficient enzyme(s) in the glycosylation pathway that yield incomplete maturation of the u-PAR protein and hence its premature degradation. We will compare a clonal population of the RKO colon cancer cell line (designated RKO C2) with a population derived (by FACS sorting for low u-PAR) from RKO C2 (designated RKO C2 F3).

ORGANISM(S): Homo sapiens

SUBMITTER: Steven Head

PROVIDER: E-GEOD-31929 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

To identify the deficient enzyme(s) in the glycosylation pathway that yield incomplete maturation of (uPAR) protein

Project description:We previously demonstrated plasticity in urokinase receptor (u-PAR) display in clonal colon cancer cells (Cancer Research 66: 7957-7967 (2006)). Thus, u-PAR display oscillates 10 fold between high and low density at the cell surface. We have determined that this oscillation in u-PAR display is posttranslational in nature. Thus, while clonal cell populations with high and low u-PAR density synthesize u-PAR at the same rate, the protein is inefficiently glycosylated in cells down-shifted for u-PAR display and subsequently degraded.

2011-09-06 | GSE31929 | GEO

Expression data from RKO cells transfected with SPARCL1 and vector control

2011-09-30 | GSE31440 | GEO

Effect of coculture with normal colonic epithelial cells on gene expression of RKO colon cancer cells

Project description:To investigate the effect of extracellular vesicle-treated normal colonic epithelial cells (FHC) on the activities of oncogenic signaling pathways in colon cancer cells (RKO), RKO cells were cocultured with FHC cells prestimulated with extracellular vesicles (EVs) or PBS.

2023-05-24 | GSE233326 | GEO

Expression data from RKO cells transfected with SPARCL1 and vector control

Project description:Colon cancer cell line RKO grown on Matrigel form a luminal-like structure after the transfection of SPARCL1 gene, which may imply the differentiation of the cells. To indentify genes regulated by SPARCL1, we built two stable cell lines: RKO with pLXSN-SPARCL1 plasmid (RKO-SPARCL1) and RKO with pLXSN plasmid (RKO-pLXSN). Then we cultured these two cell lines on both plastic dish and dish cover with a layer of Matrigel. We used microarrays to undentify global gene expression change in RKO cells after the tranfection of SPARCL1. Four samples including RKO-pLXSN cells cultured on plastic, RKO-pLXSN cells cultured on Matrigel, RKO-SPARCL1 cells cultured on plastic and RKO-SPARCL1 cells cultured on Matrigel were trypsinized and collected for RNA extraction and hybridization on Affymetrix microarray U133plus2.0. Supplementary files: * RLvsRP: up and down regulated genes comparing with RKO-SPARCL1(RL) and RKO-pLXSN(RP) cells cultured on plastic * RLMvsRPM: up and down regulated genes comparing with RKO-SPARCL1(RL) and RKO-pLXSN(RP) cells cultured on Matrigel

2011-09-29 | E-GEOD-31440 | biostudies-arrayexpress

A20 regulates canonical wnt-signaling through an interaction with RIPK4

Project description:The role of A20 in regulating canonical wnt signaling was investigated in colon cancer cell lines (RKO) by RNAseq

2018-04-04 | GSE111084 | GEO

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

RNAi knock down of SIM2s in human RKO colon carcinoma cells in a timecourse

Project description:RKO Colon Carcinoma Cells were treated with 100nM of either SIM2s Control or Antisense oligos in a timecourse (10, 14, 18, 24hr) dependent manner.

2004-11-01 | E-MEXP-101 | biostudies-arrayexpress

Anti-cancer agent ONC201 activates early ATF4/DR5 upregulation, and cell death associated with XIAP inhibition

Project description:Two experiments were performed with ONC201/TIC10 in human colon cancer cell lines. The first experiment is TIC10-induced transcriptional changes at 48hrs in HCT116 p53-null cells (10uM). The second experiment is RKO cells, with and without acquired resistance to ONC201, treated with with ONC201 (10uM) for 48 hrs. For the first experiment, six samples of HCT116 p53-null cells with TIC10 (10uM) or DMSO treatment. Three replicates each. For the second experiment, six samples of wild-type RKO cells with ONC201 (10uM) or DMSO treatment and the same treatments for RKO cells with acquired resistance to ONC201.

2016-06-01 | E-GEOD-72865 | biostudies-arrayexpress

DNMT3B targets in RKO cells by ChIP-on-chip

Project description:Chromatin immunoprecipitation with DNMT3B specific antibody followed by CGI microarray identified genes with or without CGIs, repeat elements and genomic contigs in RKO cells. ChIP-Chop analysis showed that majority of the target genes including P16, DCC, DISC1, SLIT1, CAVEOLIN1, TBX5, TBX18, HOXB13 and some histone variants, that harbor CGI in their promoters, were methylated in multiple colon cancer cell lines but not in normal colon epithelial cells. Further, these genes were reactivated in RKO cells after treatment with 5-aza-2â-deoxycytidine, a DNA hypomethylating agent. COBRA and bisulfite genomic sequencing showed that the CGIs encompassing the transcription start sites (TSS) of DCC, TBX5, TBX18, SLIT1 were also methylated in primary colorectal tumors compared to matching normal tissues whereas GNA11 was methylated in both. MassARRAY analysis demonstrated that the CGI located ~4.5 kb upstream of HOXB13 +1 site was tumor-specifically hypermethylated in primary colorectal cancers and cancer cell lines. Analysis of tumor suppressor properties of two aberrantly methylated transcription factors, HOXB13 and TBX18, revealed that both inhibited growth and clonogenic survival of colon cancer cells in vitro, but only HOXB13 abolished tumor growth in nude mice. Chromatin immunoprecipitation with DNMT3B specific antibody in RKO cells was compared to control antibody.

2010-05-06 | E-GEOD-18929 | biostudies-arrayexpress

Thermal stability variation during transtion to pluripotency

Project description:To investigate functional differences between pluripotent stem cells and somatic cells, we measured protein thermal stability and expression after transitions between cell types using allogenic cell lines. To this purpose, we reprogrammed hFF into human iPSCs and initiated undirected differentiation through formation of EBs during 21 days. We also included human embryonic stem cells (ESC) in order to validate our approach and colon cancer cell line RKO.

2021-10-05 | PXD018453 | Pride

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