The REMBRANDT study – a large collection of genomic data from brain cancer patients [gene expression]

The Rembrandt brain cancer dataset and includes clinical and biospecimen data from this study for 671 patients collected from 14 contributing institutions in 2005. Such combined datasets would provide researchers with a unique opportunity to conduct integrative analysis of gene expression and copy number changes alongside clinical outcomes (overall survival) in this large brain cancer study. In 2015, the NCI retired the REMBRANDT data portal, and all molecular data including microarray gene expression, copy number, and clinical data, was migrated to the Georgetown Database of Cancer (G-DOC). The G-DOC platform can be accessed at: https://gdoc.georgetown.edu. G-DOC is a data integration platform that offers advanced computational tools to handle a variety of biomedical BIG DATA including gene expression arrays, NGS and medical images so that they can be analyzed in the full context of other omics and clinical information. After migration of the REMBRANDT dataset into G-DOC, we applied our novel algorithm for copy number data analysis called Chromosomal Instability Index (CINdex), published as an open source Bioconductor package . This submission includes the copy number data, processed on two Affymetrix 50K copy number arrays and gene expression data processed on the Affymetrix U133 Plus2 array. It also includes the Chromosome and Cytoband CINdex matrices. Total RNA was extracted from the tumor tissue (50-80 mg) using the Trizol reagent (Invitrogen) and following the manufacturer's instructions. The quality of RNA extracted was verified using Agilent’s Bioanalyzer System with the help of RNA Pico Chips. 5 μg RNA extracted from each sample was processed using the Affymetrix U1332 Plus gene expression microarray chips This series represents a different subset of REMBRANDT samples from those contained in GSE68848.