Computational protocol: Combination treatment of prostate cancer with FGF receptor and AKT kinase inhibitors

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Protocol publication

[…] Samples were obtained from castration resistant PCa under an Institutional Review Board approved protocol and RNA prepared as described previously []. RNA concentration, purity, and integrity was assessed by NanoDrop (Thermo Fisher Scientific Inc) and Agilent Bioanalyzer. RNA-seq libraries were constructed from 1 ug total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer's protocol. Barcoded libraries were pooled and sequenced six per lane on the Illumina HiSeq 2500 generating 50 bp paired end reads. Sequencing reads were mapped to the hg19 human genome using TopHat v2.0.12 []. Gene level abundance was quantitated from the filtered human alignments in R using the Genomic Alignments Bioconductor package []. Differential expression was assessed using transcript abundances as inputs to the edgeR Bioconductor package in R [] which first corrects for transcripts per million, then normalizes for exonic size. […]

Pipeline specifications

Software tools TopHat, edgeR
Application RNA-seq analysis
Organisms Homo sapiens/Mus musculus xenograft
Diseases Neoplasms, Prostatic Neoplasms