Project description:To functionally characterize the role of miR-17 family in HCC, lentiviral vector-based miR inhibitor TuD was used to inhibit miR-17 family of microRNAs in Hep3B cell line Methods: Hep3B HCC cell line was acquired from American Type Culture Collection (ATCC) and miR-17 TuD or NC TuD expressing lines were generated. Microarray profiling of miR-17 TuD or NC TuD expressing samples was performed using Affymetrix HG-U133Plus2 arrays. Briefly, starting with 1 ug total RNA, amplified biotin-labeled cRNA targets were produced using the Enzo Target Labeling method. Fragmented, biotin-labeled cRNA was hybridized to the Affymetrix GeneChip® HG-U133Plus2 Genome Arrays overnight at 45C for 16 to 18 hours according to the manufacturer’s recommendations. Stain, wash (GeneChip Fluidics Station 450, EukGE-WS2v5_450 script) and scan (GCS 3000 7G with the GeneChip® AutoLoader) were performed according to the manufacturer’s recommendations. Microarray data were GC Robust Multiarray Average (GCRMA) normalized using R and the bioconductor.org package gcrma and Log2 transformed.
Project description:A compiled human gene expression, ontology-annotated dataset from publicly available data including 27887 Affymetrix HG-U133Plus2 arrays, filtered for quality control. The dataset contains samples from healthy individuals, from individuals with disease (including cancer) and cell lines.
Project description:The human kinome is incolved in multiple function in the life cycle of cells, and ther differntial expression in cacner suggests that protein kinases play an important role in tumor progression and proliferation. To delineate pathways that may be important for neoplastic change in women at high risk for ovarian cancer, we compared the expression signature of surface kinases in normal ovarian surface epithelium with ovarian epithelium from patients at high risk, and epithelial ovarian cancer using Affymetrix expresion array HG U133Plus2.
Project description: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.
Project description:An integrated genomic and expression analysis of 7q deletion in splenic marginal zone lymphoma (Affymetrix HG-U133plus2 gene expression microarray)
Project description: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 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 Plus 2 array. It also includes the Chromsome and Cytoband CINdex matrices.
Project description:Baseline gene expression for cell lines growing in culture were measured by Affymetrix U133Plus2 arrays. Copy Number Variation for selected cell lines was also measured.