{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Yusuke Sato"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-2007"],"description":["DNA methylation profiling of 106 ccRCC tumors by the Illumina Infinium 450k Human Methylation Beadchip"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Labeling - Standard Illumina Protocol","Scaning - Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting","Nucleic Acid Extraction - Genomic DNA was extracted from fresh frozen tissues (tumor specimens and adjacent normal kidney) using DNeasy kit (Qiagen) according to the manufacturer's instructions.","Growth Protocol - Surgical specimens were stored in liquid nitrogen","Hybridization - bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol"],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Processed Data","MAGE-TAB Files","Array Designs"],"data_protocol":["Data Transformation - BeadStudio software"],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"pubmed_abstract":["Clear-cell renal cell carcinoma (ccRCC) is the most prevalent kidney cancer and its molecular pathogenesis is incompletely understood. Here we report an integrated molecular study of ccRCC in which ≥100 ccRCC cases were fully analyzed by whole-genome and/or whole-exome and RNA sequencing as well as by array-based gene expression, copy number and/or methylation analyses. We identified a full spectrum of genetic lesions and analyzed gene expression and DNA methylation signatures and determined their impact on tumor behavior. Defective VHL-mediated proteolysis was a common feature of ccRCC, which was caused not only by VHL inactivation but also by new hotspot TCEB1 mutations, which abolished Elongin C-VHL binding, leading to HIF accumulation. Other newly identified pathways and components rec"],"study_type":["methylation profiling by array"],"species":["Homo sapiens"],"pubmed_title":["Integrated molecular analysis of clear-cell renal cell carcinoma"],"pubmed_authors":["Yusuke Sato","Sato Y, Yoshizato T, Shiraishi Y, Maekawa S, Okuno Y, Kamura T, Shimamura T, Sato-Otsubo A, Nagae G, Suzuki H, Nagata Y, Yoshida K, Kon A, Suzuki Y, Chiba K, Tanaka H, Niida A, Fujimoto A, Tsunoda T, Morikawa T, Maeda D, Kume H, Sugano S, Fukayama M, Aburatani H, Sanada M, Miyano S, Homma Y, Ogawa S."],"additional_accession":[]},"is_claimable":false,"name":"ccRCC_methylation","description":"DNA methylation profiling of 106 ccRCC tumors by the Illumina Infinium 450k Human Methylation Beadchip","dates":{"release":"2013-06-24T00:00:00Z","modification":"2022-01-31T16:45:01.832Z","creation":"2022-01-31T16:45:01.832Z"},"accession":"E-MTAB-2007","cross_references":{"pubmed":["23797736"],"EFO":["EFO_0002759"]}}