Computational protocol: Prevention of Human Lymphoproliferative Tumor Formation in Ovarian Cancer Patient-Derived Xenografts12

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Protocol publication

[…] Purification of genomic RNA and DNA was simultaneously extracted following the manufacturer's protocol for Qiagen AllPrep DNA/RNA mini Kit (Cat#80204; Qiagen, Venlo, Netherlands). Nucleic acid concentration and purity were determined on a Thermo Scientific NanoDrop 2000c UV-Vis Spectrophotometer (Thermo Scientific, Wilmington, DE). All samples met RNA integrity number and validated Agilent (Agilent Technologies, Santa Clara, CA) criteria. Total tumorgraft RNA was analyzed by Affymetrix HG U133 plus 2.0 arrays at the Mayo Medical Genome Facility according to the manufacturer's protocol.Gene expression arrays were preprocessed and normalized by robust multichip analysis . For differential gene expression studies, epithelial versus lymphoma tumorgrafts were compared using the linear models and empirical Bayes methods that share information across genes to estimate variance (LIMMA) , and Java TreeView , . Study samples and the Stanford NCI60 Cancer arrays underwent unsupervised, hierarchical clustering. The NCI 60 contains expression data for 64 cancers, including ovarian and leukocyte derived (lymphoid). Tree-structured dendrograms and heat maps were surveyed in an unsupervised fashion for clustering. […]

Pipeline specifications

Software tools limma, TreeView
Application Gene expression microarray analysis
Organisms Homo sapiens, Mus musculus, Human gammaherpesvirus 4