Computational protocol: Pten Regulates Epithelial Cytodifferentiation during Prostate Development

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Protocol publication

[…] Total RNA was extracted from frozen P10 anterior and ventral prostates using an RNeasy Micro kit (Qiagen) according to the manufacturer’s instructions. 5 samples of each genotype (Nkx3.1:Cre; Pten Fl/Fl and control) were used. Microarray analysis (affymetrix based GeneChip Mouse Gene 1.0 ST Array) was carried out at the Paterson Institute Microarray Service (CRUK, Manchester). All data analysis was carried out at the Transcript Cluster ID level. DABG (detection above background) calling was done using Affymetrix Power Tools software. Individual CEL files were read into R using the Simpleaffy package and normalized using RMA. Cluster IDs were filtered according to DABG. The threshold used was a p value of < 0.01. If the p value was less than the threshold, the ID was present, if above the threshold, the ID was called absent. IDs were retained if they were called present in all samples, if they were called present in all samples in the control group and if they were called present in all samples in the mutant group. LIMMA was used to define differentially expressed transcript clusters, at a threshold of log2 fold change of 1 (linear fold change of 2). […]

Pipeline specifications

Software tools Simpleaffy, limma
Application Gene expression microarray analysis
Organisms Mus musculus, Homo sapiens
Diseases Neoplasms, Prostatic Neoplasms