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

BRAF paradox breakers PLX8394 and PLX7904 comparison to BRAF inhibitor PLX4720 effect on BRAF V600Ε mutant colorectal adenocarcinoma cells

ABSTRACT: Genomic analysis on RKO cells treated with PLX7904, PLX8394 and PLX4720 to reveal gene expression patterns. The goal is to investigate the potential of the novel BRAF inhibitors-paradox breakers to impede colorectal cancer cells proliferation, using human cell lines bearing the BRAFV600E mutation.

INSTRUMENT(S): BGISEQ-500

ORGANISM(S): Homo sapiens

SUBMITTER: Georgia Kontogianni

PROVIDER: E-MTAB-9014 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq of Colo-205 and RKO colon adenocarcinoma cell lines treated with Novel 2-Acetamido, 6-Carboxamide Substituted Benzothiazole Derivatives as Potential BRAFV600E Inhibitors and PLX4720

Project description:Two human colorectal adenocarcinoma cell lines (Colo-205 and RKO) were treated with PLX4720 and newly synthesized 2-Acetamido, 6-Carboxamide Substituted Benzothiazole Derivatives, as potential BRAF V600E inhibitors; IDK142, IDK145, IDK133 and DMSO as control.

2023-12-19 | E-MTAB-13097 | biostudies-arrayexpress

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

Coordinated Chromatin Remodeling induced by Demethylation requires SRCAP mediated H2A.Z exchange [expression]

Project description:Genome wide gene expression profiling of RKO cells with combination treatments of non-target siRNA or SRCAP siRNA and PBS or 1uM 5-Aza-CdR treatment. The sample treated with non target siRNA and PBS serves as control sample. Total RNA obtained from isolated RKO cells.

2013-01-01 | E-GEOD-26684 | biostudies-arrayexpress

Coordinated Chromatin Remodeling induced by Demethylation requires SRCAP mediated H2A.Z exchange [Methylation]

Project description:Genome wide DNA methylation profiling of RKO cells with combination treatments of non-target siRNA or SRCAP siRNA and PBS or 1uM 5-Aza-CdR treatment. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across 27,578 CpGs in treated RKO cells. Samples included cells under 4 different treatments. The sample treated with non target siRNA and PBS serves as control sample. Bisulphite converted DNA from the 4 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2

2013-01-01 | E-GEOD-26433 | 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

BRAF paradox breakers PLX8394 and PLX7904 comparison to BRAF inhibitor PLX4720 effect on BRAF V600Ε mutant colorectal adenocarcinoma cells

Project description:BRAF paradox breakers PLX8394 and PLX7904 comparison to BRAF inhibitor PLX4720 effect on BRAF V600Ε mutant colorectal adenocarcinoma cells

| PRJEB38086 | ENA

Expression array of RKO colorectal cancer cells resistant to irinotecan (CPT-11)

Project description:RKO cells and irinotecan resistant derivatives (316 and 526) were compared for expression profile.

2017-06-17 | E-MTAB-5184 | biostudies-arrayexpress

Transcriptional profile of mouse macrophage RAW 264.7 cells upon treatment with dexamethasone or the glucocorticoid receptor modulator AZD9567 in the presence or absence of inflammatory response.

Project description:The aim of the experiment was to gain insight into the selective anti-inflammatory action of the glucocorticoid receptor modulator AZD9567 in comparison with the classical synthetic glucocorticoid dexamethasone. To this end, the transcriptional profile of macrophage RAW 264.7 cells treated with dexamethasone or AZD9567 in the presence or absence of inflammatory response (elicited by lipopolysaccharide treatment) was identified.

2023-06-30 | E-MTAB-12816 | biostudies-arrayexpress

Assessing the ceRNA hypothesis with quantitative measurements of miRNA and target abundance

Project description:Recent studies have reported that competitive endogenous RNAs (ceRNAs) can act as sponges for a miRNA through their binding sites and that changes in ceRNA abundances from individual genes can modulate the miRNA’s activity. Consideration of this hypothesis would benefit from knowing the quantitative relationship between a miRNA and its endogenous target sites. Here, we altered intracellular target-site abundance through expression of a miR-122 target in hepatocytes and livers, and analyzed the effects on miR-122 target genes. Target repression was released in a threshold-like manner at high target-site abundance (≥1.5x10^5 added target sites per cell), and this threshold was insensitive to the effective levels of the miRNA. Furthermore, in response to extreme metabolic liver disease models, global target-site abundance of hepatocytes did not change sufficiently to affect miRNA-mediated repression. Thus, modulation of miRNA target abundance is unlikely to cause significant effects on gene expression and metabolism through a ceRNA effect. Seventeen mRNA profiles were generated of 1) primary hepatocytes of mice expressing variable levels of a recombinant Adenovirus expressing the transcript of AldolaseA (Ad-AldoA), containing either 1 or 3 sites matching miR-122 or a mutated miR-122 site (no site), 2) primary hepatocytes derived from mice treated with Antagomir-122 (treatment group) or Antagomir-122mm (control group), 3) livers originating of a genetic model (Ldlr deficient mice) causing severe pathological changes in cholesterol metabolism, 4) livers of mice perfused with Insulin or PBS, and 5) livers of mice fed a high-fat or chow diet; most samples were sequenced in duplicate or triplicate by an Illumina HiSeq 2000. One small RNA profile was also generated from livers of mice fed a chow diet by Solexa sequencing.

2014-05-01 | E-GEOD-52801 | biostudies-arrayexpress

Expression data after BCLAF1-L knockdown in human RKO cells

Project description:Bcl-2-accociated transcription factor 1(BCLAF1) has been reported to be involved in diverse biological processes. Alternative splicing leads to mutiple transcript virants in human cells and we are interested in functions of its full length isoform(BCLAF1-L) in human colon cancer cells, thus to understanding its role in colon cancer progression. We used microarray to detail the global programme of gene expression after BCLAF1-L knockdown(sh-BCLAF1-L#1) in RKO cells and identified distinct classes of up-regulated or down-regulated genes impaired by its inhibition, when comparing with the control group(sh-Luci). RKO cells were infected with retroviruses either expressing control (sh-Luci) or BCLAF1-L knockdown (sh-BCLAF1-L#1). Medium was replaced 24h after infection, and infected cells were selected by the addition of puromycin (2ug/ml) for 72-96h. Then cells were havested for RNA extraction and hybridization on Affymetrix microarrays.

2013-12-05 | E-GEOD-52990 | 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