GEO DataSets

(Submitter supplied) Transcriptome profiling of de novo-derived ccRCC cell cultures and their matching parental tumours. VHL-mutant and VHL wild-type cultures were established by isolating CA9+ and CA9- cells from tumor samples using FACS.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

18 Samples

Download data: TXT

(Submitter supplied) This study investigates the genes that promote clear cell renal cell carcimoma (ccRCC) metastasis using 4 primary metastatic and 5 non-metastatic tumor samples. U133 plus 2.0 array was used to identify the diffrently expressed genes between the primary metastatic and non metastatic ccRCC samples

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

9 Samples

Download data: CEL

(Submitter supplied) The pituitary tumor-transforming gene (PTTG1) is a recently discovered oncogene implicated in the malignant progression of a number of neoplasms. It has been shown to drive both endocrine and non-endocrine malignancies, but has not yet been studied in the context of renal cell carcinoma (RCC). Clear cell RCC (ccRCC) is cytogenetically characterized by deletion of chromosome 3p, harboring the von-Hippel Lindau tumor suppressor gene, and amplification of chromosome 5q. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10175

4 Samples

Download data: CEL

(Submitter supplied) The pituitary-tumor transforming gene (PTTG1) is a recently discovered oncogene implicated in the malignant progression of a number of neoplasms. It has been shown to drive both endocrine and non-endocrine malignancies, but has not yet been studied in the context of renal cell carcinoma. Here we show that PTTG1 is frequently amplified and overexpressed in clear cell renal cell carcinoma, the most common form of kidney cancer. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platforms:

GPL2004 GPL2005

90 Samples

Download data: CEL, TXT

(Submitter supplied) Metastatic clear cell renal cell carcinoma (ccRCC) has a poor prognosis and unpredictable course and there are no molecular markers that reliably predict ccRCC metastasis. In this study, specimens from 84 patients with ccRCC were directly cultured in vitro. The primary cultures from 38 of 94 specimens contained more than 90% tumor cells at 4th passages. After identified by immunostaining, the primary cultures of metastatic- and nonmetastatic ccRCC specimens from the age-, gender-matched patients were subjected to cDNA microrray assays. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6259

12 Samples

Download data: TXT

(Submitter supplied) This dataset complements GSE76207. Formalin-fixed, paraffin-embedded (FFPE) tissues are an underused resource for molecular analyses. This proof of concept study aimed to compare RNAseq results from FFPE biopsies (Eikrem et al., PLoS One. 2016 Feb 22;11(2):e0149743. doi: 10.1371/journal.pone.0149743. eCollection 2016. PMID: 26901863) with FFPE confirmation dataset from clear cell renal cell carcinoma (ccRCC) patients. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

24 Samples

Download data: TXT

(Submitter supplied) Formalin-fixed, paraffin-embedded (FFPE) tissues are an underused resource for molecular analyses. This proof of concept study aimed to compare RNAseq results from FFPE biopsies with the corresponding RNAlater® (Qiagen, Germany) stored samples from clear cell renal cell carcinoma (ccRCC) patients, to enable the decision of whether or not it is feasible to apply RNAseq technology to archival tissue. Core biopsies were obtained with a 16g needle from 16 patients undergoing partial or full nephrectomy. The RNA sequencing libraries were generated applying the new Illumina TruSeq® Access library preparation protocol.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

64 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL9101

160 Samples

Download data: CEL, TXT

(Submitter supplied) Systematic somatic mutation screening of 4000 genes in human clear cell renal cell carcinoma. Information on corresponding somatic mutations in each sample can be found at http://www.sanger.ac.uk/genetics/CGP/Studies/.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL9101

115 Samples

Download data: CEL, TXT

(Submitter supplied) Systematic somatic mutation screening of 4000 genes in human clear cell renal cell carcinoma. Information on corresponding somatic mutations in each sample can be found at http://www.sanger.ac.uk/genetics/CGP/Studies/. These samples were run at a different facility than VARI - scmmlab.com

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL9101

45 Samples

Download data: CEL, TXT

(Submitter supplied) Patients with clear cell renal cell carcinoma (ccRCC) are often diagnosed with both von Hippel-Lindau (VHL) mutations and the constitutive activation of hypoxia-inducible factor-dependent signaling. In this study, we investigated the effects of long-term hypoxia in 786-O, a VHL-defective renal cell carcinoma cell line, to identify potential genes and microRNAs associated with tumor malignancy. The transcriptomic profiles of 786-O under normoxia, short-term hypoxia, and long-term hypoxia were analyzed using next-generation sequencing. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: XLSX

(Submitter supplied) Clear-cell renal cell carcinoma (ccRCC) is the most prevalent subtype of renal cell carcinoma (up-to 70% of all RCC types). There is a very close causal correlation between ccRCC and inactivation of the tumor suppressor gene von Hippel-Lindau (VHL) located on chromosome 3p25‐26. Up to 80% of sporadic ccRCC carry genomic mutations or epigenetic inactivation of VHL and nearly 100% familial ccRCC (in VHL disease) contain VHL deficiency. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: XLSX

(Submitter supplied) Although renal cell carcinoma (RCC) is the sixth-leading cause of cancer death, the molecular events leading to disease onset and progression are not well understood. Genomic profiling of clear cell RCC (cRCC) patients indicated that loss of a negative regulator of the Wnt pathway, secreted frizzled-related protein 1 (sFRP1), occurred in the majority of more than 100 patients tested. To our knowledge, this is the first report of loss of sFRP1 expression in patients diagnosed with cRCC; this loss occurs in early stage cRCC, suggesting that it may be an important early event in renal carcinogenesis. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Datasets:

GDS2880 GDS2881

Platforms:

GPL96 GPL97

40 Samples

Download data: CEL, PDF, TXT, ZIP

Analysis of patient matched normal and stage 1 or stage 2 clear cell renal cell carcinoma (cRCC) tumors. Results provide insight into the molecular pathogenesis of cRCC.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 3 disease state, 10 individual sets

Platform:

GPL97

Series:

GSE6344

20 Samples

Download data: CEL

Analysis of patient matched normal and stage 1 or stage 2 clear cell renal cell carcinoma (cRCC) tumors. Results provide insight into the molecular pathogenesis of cRCC.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 3 disease state, 10 individual sets

Platform:

GPL96

Series:

GSE6344

20 Samples

Download data: CEL

(Submitter supplied) The PDGF and mTOR pathways are clinically relevant therapeutic targets in clear cell renal cell carcinoma (ccRCC), but the molecular mechanisms that lead to their activation has remained poorly understood. By chromatin and transcriptomic profiling and functional analysis we have identified Kruppel like factor 6 (KLF6), a transcription factor of the zinc-finger family, as a critical regulator of the PDGF-mTOR axis in ccRCC. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

20 Samples

Download data: TXT

(Submitter supplied) The PDGF and mTOR pathways are clinically relevant therapeutic targets in clear cell renal cell carcinoma (ccRCC), but the molecular mechanisms that lead to their activation has remained poorly understood. By chromatin and transcriptomic profiling and functional analysis we have identified Kruppel like factor 6 (KLF6), a transcription factor of the zinc-finger family, as a critical regulator of the PDGF-mTOR axis in ccRCC. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

17 Samples

Download data: BW

(Submitter supplied) The complete transcriptomes of kidney cortex from 3 TRACK/γ-HIF1αM3 ~15 month old TG+ male mice and 3 age matched TG- C57BL/6 male mice were sequenced on an Illumina HiSeq2000 Sequencer.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

12 Samples

Download data: TSV

(Submitter supplied) Both cigarette smoking and obesity have been implicated in increased risk of clear cell renal cell carcinoma (ccRCC); however, there are limited data regarding the molecular mechanisms that underlie these associations. We used a multi-stage design to identify and validate specific molecular targets that are associated with smoking or obesity-related ccRCC.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

130 Samples

Download data: CEL

(Submitter supplied) By analyzing RNAseq data from TCGA in ccRCC and metabolomics data from CCLE, we identified the strong correlation of GPX8 with the lipid and glycogen metabolism, which are highly upregulated in ccRCC. We validated this observation by knocking out GPX8 in Caki1 (ccRCC cell line). Using transcript profiling, we confirmed the association of GPX8 with de novo lipogenesis and suppressed fatty acid oxidation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: CSV