Computational protocol: Anti viral state segregates two molecular phenotypes of pancreatic adenocarcinoma: potential relevance for adenoviral gene therapy

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Protocol publication

[…] RNA from 8 xeno-grafted primary PDAC, 3 primary PDAC bulk tissues, 3 chronic pancreatitis and 3 normal pancreatic tissues was hybridized to a GeneChip HG-U133A containing 22,283 probe sets (21,430 genes, Affymetrix, Sacramento, CA). RNA quality and concentration were assessed using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). First- and second-strand cDNA were synthesized from 12.5 μg of total RNA according to manufacturer's instructions (Affymetrix). After in vitro transcription, labeling and fragmentation, probes were hybridized to the GeneChips that were then washed in a GeneChip Fluidics Station 400 (Affymetrix); results were visualized with a Gene Array scanner using Affymetrix software. Array data were normalized and summarized using the RMA method []http://bioconductor.org/packages/2.0/bioc/src/contrib/affy_1.14.0.tar.gz. Cluster analysis was based on cluster and Treeview software (Eisen's laboratory, Berkeley, CA). Functional interpretations were based on Gene Ontology and Ingenuity Pathways Analysis software http://www.ingenuity.com. […]

Pipeline specifications

Software tools affy, TreeView
Application Gene expression microarray analysis
Organisms unidentified adenovirus, Homo sapiens
Diseases Carcinoma, Neoplasms, Pancreatic Neoplasms, Carcinoma, Pancreatic Ductal