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.
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. Bisulphite converted DNA from the 92 samples were hybridised to the Illumina Infinium 450 Human Methylation Beadchip v1.2
Project description:Aberrant DNA methylation is common in cancer. To associate DNA methylation with gene function, we performed RNAseq upon tumor tissue and matched normal tissues of two ccRCC (clear cell renal cell carcinoma) patients. To quantify 5mC and 5hmC level in each CG site at genome-wide level, we performed BS-seq and TAB-seq upon tumor tissue and matched normal tissues of two ccRCC (clear cell renal cell carcinoma) patients, respectively.
Project description:Aberrant DNA methylation is common in cancer. To associate DNA methylation with gene function, we performed RNAseq upon tumor tissue and matched normal tissues of two ccRCC (clear cell renal cell carcinoma) patients. To quantify 5mC and 5hmC level in each CG site at genome-wide level, we performed BS-seq and TAB-seq upon tumor tissue and matched normal tissues of two ccRCC (clear cell renal cell carcinoma) patients, respectively. mRNA profiles of tumor and matched normal tissues from two ccRCC patients were generated by deep sequencing, using Hiseq 2000. Single-nucleotide-resolution, whole-genome, 5mC and 5hmC profiles of tumor and matched normal tissues from two ccRCC (clear cell renal cell carcinoma) patients were generated by deep sequencing, using Hiseq 2000.
Project description:Uncovering a protein abundance-based gene panel specific to clear cell Renal Cell Carcinoma (ccRCC) could provide support for the everyday clinical decision-making process. We used proteomic data to differentiate between normal kidney and ccRCC tissues. By using datasets of patients with paired normal tissue samples from gene array cohorts, we uncovered the top genes over-expressed in ccRCC. We collected surgically resected ccRCC specimens at Semmelweis University to validate the strongest genes. Differential expression was evaluated at the protein level using targeted mass spectrometry (MS).
Project description:Each total RNA sample is hybridized to two different arrays: Affymetrix U133A (GPL96) and U133B (GPL97). For most of the normal tissue samples there is a renal clear cell carcinoma sample from the same patient. There is no matching tumor sample for normal sample N1. For most of the renal clear cell carcinoma samples there is a corresponding adjacent normal tissue sample from the same patient. There are no matching normal tissue samples for C011 or C032. Keywords = kidney Keywords = renal Keywords = RCC Keywords = carcinoma Keywords = cancer Keywords: parallel sample
Project description:Each total RNA sample is hybridized to two different arrays: Affymetrix U133A (GPL96) and U133B (GPL97). For most of the normal tissue samples there is a renal clear cell carcinoma sample from the same patient. There is no matching tumor sample for normal sample N1. For most of the renal clear cell carcinoma samples there is a corresponding adjacent normal tissue sample from the same patient. There are no matching normal tissue samples for C011 or C032. Keywords = kidney Keywords = renal Keywords = RCC Keywords = carcinoma Keywords = cancer Keywords: parallel sample