Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cooperative blockade of CK2 and ATM kinases drives apoptosis in VHL-deficient renal carcinoma cells / RNA-seq (BRB-seq) of treated 786-O spheroids

ABSTRACT: Multicellular Tumor Spheroids (MCTS) were pre-formed for 3 days with 786-O cell line to better mimic the tumor microenviroenment. These spheroids were treated with either vehicle (DMSO), drugs alone (KU-60019 10 μM; CX-4945 5 μM) or in combination (KU + CX) for 48h before RNA extraction.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Homo sapiens

SUBMITTER: Christophe Battail

PROVIDER: E-MTAB-9977 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Cooperative Blockade of CK2 and ATM Kinases Drives Apoptosis in VHL-Deficient Renal Carcinoma Cells through ROS Overproduction.

Giacosa Sofia S Pillet Catherine C Séraudie Irinka I Guyon Laurent L Wallez Yann Y Roelants Caroline C Battail Christophe C Evrard Bertrand B Chalmel Frédéric F Barette Caroline C Soleilhac Emmanuelle E Fauvarque Marie-Odile MO Franquet Quentin Q Sarrazin Clément C Peilleron Nicolas N Fiard Gaëlle G Long Jean-Alexandre JA Descotes Jean-Luc JL Cochet Claude C Filhol Odile O

Cancers 20210202 3

Kinase-targeted agents demonstrate antitumor activity in advanced metastatic clear cell renal cell carcinoma (ccRCC), which remains largely incurable. Integration of genomic approaches through small-molecules and genetically based high-throughput screening holds the promise of improved discovery of candidate targets for cancer therapy. The 786-O cell line represents a model for most ccRCC that have a loss of functional pVHL (von Hippel-Lindau). A multiplexed assay was used to study the cellular ...[more]

PMID: 33540838

Similar Datasets

BRBseq performed on 786-O cells treated with 2 inhibitors of protein kinase CK2, CX4945 and AB668

Project description:786-O cells (150, 000) were treated for 24h with DMSO, 5 µM of CX4945 or AB668. Total RNA was extracted from treated cells using the MirVana PARIS kit (Thermofisher). The 3′ Bulk RNA Barcoding and sequencing (BRB-seq) experiments were performed at the Research Institute for Environmental and Occupational Health (Irset, Rennes, France) according to the published protocol (Alpern et al., 2019). Sequencing was perfomred by SiLicium.

2023-05-27 | E-MTAB-12776 | biostudies-arrayexpress

BRBseq performed on tumoroids and corresponding renal tumor tissues

Project description:To evaluate genetic similarities between tumoroids and the corresponding tumor tissues, we performed RNA sequencing of cells for each experimental condition. Since we injected human cancer cells into mice, cancer cells in the tumors were human while microenvironmental cells (i.e. Fibroblasts, Immune cells,…) were derived from mice. Thus, the RNA sequencing datasets generated from ACHN or 786-O tumor tissues (AxM and 7xM) and their respective tumoroids (AxTy and 7xTy) were mapped on human and mouse reference genome.

2023-06-30 | E-MTAB-12928 | biostudies-arrayexpress

RNA-seq of human plasma microRNAs in Alzheimer Disease

Project description:MicroRNAs (miRNAs) could play an important role as potential Alzheimer Disease (AD) biomarkers. Plasma samples were collected from participants: Mild cognitive impairment (MCI) due to AD patients (n= 20), preclinical AD patients (n= 8) and healthy controls (n= 20). Then, small RNA sequencing analysis, followed by miRNA differential expression analysis comparing different methods (DESeq2, edgeR, NOISeq) were carried out.

2022-05-08 | E-MTAB-11103 | biostudies-arrayexpress

RNA-SEQ analysis of single cells extracted from E12.5 embryonic kidneys.

Project description:We used micro-dissection and trypsinization techniques to isolate single cells from the E12.5 total kidney. A subset of these single cell populations is analysed individually via Fluidigm single cell analysis. This analysis will determine the transcriptional profile of each cell type, identify compartment specific transcripts, compartment specific transcript isoforms and cell-type specific long-noncoding RNAs. In addition the unbiased nature of RNA-SEQ will potentially identify novel transcripts that have not been annotated in the database. E12.5 kidneys are dissected; the kidneys are made into a single cell suspension via trypsinization. A subset of these cells is analysed individually via Fluidigm C1 single cell analysis. The long term goal is to generate a single cell resolution transcriptional atlas of the developing kidney.

2014-08-01 | E-GEOD-59127 | biostudies-arrayexpress

Single-molecule, full-length transcript isoform sequencing reveals disease-associated RNA isoforms

Project description:Alternative splicing generates differing RNA isoforms that govern phenotypic complexity of eukaryotes. Its malfunction underlies many diseases, including cancer and cardiovascular diseases. Comparative analysis of RNA isoforms at the genome-wide scale has been difficult. Here, we established an experimental and computational pipeline that accurately quantifies transcript isoforms in their entire length from cDNA sequences with a full-length isoform detection accuracy of 97.6%. We generated a searchable, quantitative human transcriptome annotation with 31,025 known and 5,740 novel transcript isoforms (http://steinmetzlab.embl.de/iBrowser/). By analyzing the isoforms in the presence of RNA Binding Motif Protein 20 (RBM20) mutations associated with aggressive dilated cardiomyopathy (DCM), we identified 121 differentially expressed transcript isoforms in 107 cardiac genes. By establishing an isoform-differential expression test, our approach revealed that 11 of these genes displayed no detectable change in overall RNA expression. However, significant differences in the expression of specific isoforms in these genes was observed. These isoform specific effects demonstrate the need of analyzing RNA isoform expression levels rather than total gene expression levels.

2021-06-16 | E-MTAB-7334 | biostudies-arrayexpress

Wing disc transcriptomic variation from 32 Drosophila genetic reference panel (DGRP) lines selected for a broad range of wing sizes

Project description:We performed RNA sequencing of wing discs at the wandering L3 larval stage from 32 inbred lines of Drosophila genetic reference panel (DGRP) that consists of 16 big and 16 small wing lines. We aimed to understand system-wide gene regulatory mechanisms that attain the observed natural variation in wing size including the sexual size dimorphism.

2019-02-18 | E-MTAB-7662 | biostudies-arrayexpress

Chromatin immunoprecipitation of the MSL-1 and MSL-3 vs a mock IP in Drosophila and transcription profiling of X linked genes in WT male or female III instar larvae to provide X chromosome wide profiling of MSL-1 distribution and dosage compensation in Drosophila

Project description:Dosage compensation ensures that males and females, despite unequal number of X chromosomes, equalize for X linked gene expression. In Drosophila, it is achieved by a two-fold up-regulation of most of the genes present on the male X chromosome, and requires the association of the Dosage Compensation Complex (DCC) on the X chromosome. One of the main intriguing aspects of dosage compensation is how this complex is able to target specifically hundreds of sites only on the X chromosome in order to ensure dosage compensation. In order to better understand the targeting of the DCC and the dosage compensation mechanism, we have then decided to analyze the distribution of the DCC as well as the expression levels in male and female in a more complete and precise manner, using microarrays. In this experiment, we present the data used to analyse the distribution of the MSL-1 and MSL-3 protein (part of the DCC complex) on the X chromosome in WT embryos aged from 0H-14H, as well as the distribution of MSL-1 in embryos aged from 4-6H and in male III instar salivary glands. The DNA amplified from the specific immunoprecipitation (MSL-1 or MSL-3 IP) were labelled using Cy5-dCTP and hybridized against DNA amplified from a non specific immunoprecipitation (mock IP), labeled with Cy3 dye. In parralel we present the data used to analyse the expression profile of X-linked genes in WT male or female III instar larvae salivary glands. The cDNA amplified from the RNA extracted from the male or female salivary glands were labelled using Cy5-dUTP and hybridized against the reference sample, labelled with Cy3-dUTP (pool RNA from ON embryos, adultes, and salivary glands mixed at a ratio 1:1:1.and amplified as the RNA from salivary glands). We used for this study a cDNA array developed by the Genecore facility in EMBL, covering the DGC1 and DGC2 cDNA libraries from the Berkeley Drosophila Genome Project, which represents more than 70% of the coding Drosophila genome.

2006-04-01 | E-MEXP-554 | biostudies-arrayexpress

RNA-SEQ analysis of single cells extracted from the metanephric mesenchyme of Embryonic day 11.5 (E11.5) Crym-EGFP transgenic mice.

Project description:We used micro-dissection with FACS sorting techniques to isolate single cells from the metanephric mesenchyme of the E11.5 developing kidney. A subset of these single cell populations is analysed individually via Fluidigm single cell analysis. This analysis will determine the transcriptional profile of each cell type, identify compartment specific transcripts, compartment specific transcript isoforms and cell-type specific long-noncoding RNAs. In addition the unbiased nature of RNA-SEQ will potentially identify novel transcripts that have not been annotated in the database. Kidneys are harvested from Tg(Crym-EGFP)GF82Gsat mice. Single cells are extracted from E11.5 metanephric mesenchyme using manual micro-dissection techniques. A subset of these cells is analyzed individually via Fluidigm single cell analysis. The long term goal is to generate a transcriptional atlas of the developing kidney.

2014-08-01 | E-GEOD-59129 | biostudies-arrayexpress

An antibiotic-sensing leader peptide regulates translation and premature Rho-dependent transcription termination of the topAI gene in Escherichia coli

Project description:The SHAPE-Seq experiment was used to determine accessible nucleotides in the 5' UTR of the topAI gene in the presence and absence of 0.2 ug/ml of tetracycline.

2019-10-03 | E-MTAB-8365 | biostudies-arrayexpress

Analysis of HIF and mTOR dependent translational regulation of mRNAs resolved by their transcription start sites, using HP5 technology

Project description:Changes in translational efficiency of mRNAs consequent on alteration of HIF and/or mTOR pathway activity in VHL-defective kidney cancer cell were analysed. High-resolution polysome profiling followed by sequencing of the 5′ ends of mRNAs (HP5) was used to measure translational efficiency of mRNAs resolved by their transcription start sites. HP5 was applied to VHL-defective kidney cancer cell lines with or without VHL reintroduction and/or mTOR inhibition with Torin 1 treatment. In addition, the contribution of HIF2A/EIF4E2 pathway was assessed using 786-O cells in which EIF4E2 was inactivated.

2022-05-14 | E-MTAB-10689 | biostudies-arrayexpress

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