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

Integrative genome-wide gene expression profiling of clear cell renal cell carcinoma in Czech Republic

ABSTRACT: We conducted whole-genome expression profiling on 101 pairs of ccRCC tumours and adjacent non-tumour renal tissue from Czech patients using the Illumina HumanHT-12 v4 Expression BeadChips to explore the molecular variations underlying the biological and clinical heterogeneity of ccRCC. Total RNA obtained from frozen ccRCC tumour and adjacent non-tumour renal tissue.

ORGANISM(S): Homo sapiens

SUBMITTER: Magdalena Wozniak

PROVIDER: E-GEOD-40435 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Integrative genome-wide gene expression profiling of clear cell renal cell carcinoma in Czech Republic and in the United States.

Wozniak Magdalena B MB Le Calvez-Kelm Florence F Abedi-Ardekani Behnoush B Byrnes Graham G Durand Geoffroy G Carreira Christine C Michelon Jocelyne J Janout Vladimir V Holcatova Ivana I Foretova Lenka L Brisuda Antonin A Lesueur Fabienne F McKay James J Brennan Paul P Scelo Ghislaine G

PloS one 20130305 3

Gene expression microarray and next generation sequencing efforts on conventional, clear cell renal cell carcinoma (ccRCC) have been mostly performed in North American and Western European populations, while the highest incidence rates are found in Central/Eastern Europe. We conducted whole-genome expression profiling on 101 pairs of ccRCC tumours and adjacent non-tumour renal tissue from Czech patients recruited within the "K2 Study", using the Illumina HumanHT-12 v4 Expression BeadChips to exp ...[more]

PMID: 23526956

Similar Datasets

Impact of delay to cryopreservation on RNA integrity and genome-wide expression profiles in resected tumor samples.

Project description:Using Illumina HumanHT-12 v3 Expression BeadChips, providing a genome-wide coverage of over 24,000 genes, we have analysed gene expression variation in samples of 3 hepatocellular carcinomas (HCC) and 3 lung carcinomas (LC) cryopreserved at times up to 2 hours after resection. Total RNA obtained 3 frozen Hepatocellular Carcinomas and 3 Lung Carcinomas cryopreserved at 5 min, 15min, 30min and 120min after resection. Tissue samples from the center and the peripheral of the tumours were frozen for each time point.

2013-04-01 | E-GEOD-41160 | biostudies-arrayexpress

Integrative genome-wide gene expression profiling of clear cell renal cell carcinoma in Czech Republic

Project description:We conducted whole-genome expression profiling on 101 pairs of ccRCC tumours and adjacent non-tumour renal tissue from Czech patients using the Illumina HumanHT-12 v4 Expression BeadChips to explore the molecular variations underlying the biological and clinical heterogeneity of ccRCC.

2013-06-03 | GSE40435 | GEO

HIF-1α and HIF-2α differently regulate tumour development, metabolism and inflammation of clear cell renal cell carcinoma in mice

Project description:Mutational inactivation of VHL is the earliest genetic event in the majority of ccRCCs, leading to activation of the HIF-1α and HIF-2α transcription factors. While correlative studies of human ccRCCs and functional studies using human ccRCC cell lines have implicated HIF-1α as an inhibitor and HIF-2α as a promoter of aggressive tumour behaviours, their roles in tumour onset have not been functionally addressed. Using an autochthonous ccRCC model, we show genetically that Hif1a is necessary for tumour formation whereas Hif2a deletion has only minor effects on tumour initiation and growth. Both HIF-1α and HIF-2α are necessary for the clear cell phenotype. Transcriptomic and proteomic analyses revealed that HIF-1α regulates glycolysis while HIF-2α regulates genes associated with lipoprotein metabolism, ribosome biogenesis and E2F and MYC transcriptional activities. Deficiency of HIF-2α increased CD8+ T cell infiltration and activation. These studies reveal different functions of HIF-1α and HIF-2α in ccRCC. SIGNIFICANCE The roles of HIF-1α and HIF-2α in ccRCC pathogenesis remain unclear. Using a mouse genetic approach we show that HIF-1α but not HIF-2α is important for tumour formation, contrary to predictions from studies of human ccRCC. We show that HIF-1α and HIF-2α transcriptionally regulate different aspects of metabolism and identify HIF-2α as a suppressor of immune cell infiltration and activation.

2020-07-02 | PXD016630 | Pride

Expression data from spatially separated samples of different ccRCC patients

Project description:We have sampled several tumour regions from nine clear cell renal cell carcinoma (ccRCC) patients to investigate intra-tumour heterogeneity.

2014-01-06 | GSE53000 | GEO

Epigenome analysis of clear cell renal cell carcinoma (ccRCC) tissue versus matched normal kidney tissue

Project description:Genome wide DNA methylation profiling of clear cell renal cell carcinoma (ccRCC) tissue versus matched normal kidney tissue. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in tumor and adjacent normal kidney tissue samples from ccRCC patients. Samples included 46 paired fresh frozen ccRCC tumor and adjacent normal kidney tissues.

2015-10-26 | GSE61441 | GEO

microRNAseq of clear-cell renal cell carcinoma on surgical resection specimens of untreated primary tumors in humans

Project description:We aimed to assess differences in miRNA expression profiles in transcriptomic molecular subtypes of ccRCC (Beuselinck et al, Clinical Cancer Research 2015) and to correlate miRNAs with overal survival since diagnosis of ccRCC. Sequencing was done for 129 primary ccRCC (formalin-fixed paraffin-embedded surgical resection specimens, previously untreated) and 16 normal kidney specimens. Normal kidney was obtained from the nephrectomy specimens at time of ccRCC removal, in tissue blocks containing only normal kidney (so nót the normal kidney immediately adjacent to ccRCC). The samples were sequenced in 2 major batches (2014 and 2017).

2020-07-22 | E-MTAB-9380 | biostudies-arrayexpress

Epigenome analysis of clear cell renal cell carcinoma (ccRCC) tissue versus matched normal kidney tissue

Project description:Genome wide DNA methylation profiling of clear cell renal cell carcinoma (ccRCC) tissue versus matched normal kidney tissue. TheÂ IlluminaÂ Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximatelyÂ 450,000 CpGs in tumor and adjacent normal kidney tissue samples from ccRCC patients. Samples included 46 paired fresh frozen ccRCC tumor and adjacent normal kidney tissues. Bisulphite converted DNA from the 92 samples were hybridised to the Illumina Infinium 450 Human Methylation Beadchip v1.2

2015-10-26 | E-GEOD-61441 | biostudies-arrayexpress

Multi-region copy-number analysis

Project description:Intra-tumour heterogeneity (ITH) foster tumour adaptation and hamper the efficiency of personalised medicine approaches. We investigated the extent of ITH within individual clear cell renal cell carcinomas (ccRCC) by multi-region sampling and copy number analysis. We analyzed 63 tumour regions and 8 normal samples from eight clear cell renal cell carcinomas using Affymetrix SNP6 arrays.

2013-06-04 | GSE47077 | GEO

Expression data from spatially separated samples of different ccRCC patients

Project description:We have sampled several tumour regions from nine clear cell renal cell carcinoma (ccRCC) patients to investigate intra-tumour heterogeneity. We selected 56 tumour samples and 6 normal samples from the 9 patients for expression analysis using microarray data. All samples were fresh frozen upon extraction.

2014-01-06 | E-GEOD-53000 | biostudies-arrayexpress

Multi-region copy-number analysis

2013-06-04 | E-GEOD-47077 | biostudies-arrayexpress