Computational protocol: Mapping of the chromosomal amplification 1p21-22 in bladder cancer

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Protocol publication

[…] Total RNA from bladder cancer cell lines was collected and extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA), according to the manufacturer’s protocol. The samples were then amplified and hybridized using the Agilent whole genome oligo microarray platform (Agilent Technologies, Palo Alto, CA, USA) and Xpress Ref ™ Human Universal Reference Total RNA (SuperArray Bioscience Corporation) was used as a reference. The resulting data files from Agilent Feature Extraction Software (version 9.5.1.1) were imported into the Agilent GeneSpring GX software (version 11.0) for further analysis. A fold-change cutoff of 2 was used to determine differential gene expression. […]

Pipeline specifications

Software tools Agilent Feature Extraction, GeneSpring GX
Application Gene expression microarray analysis
Organisms Homo sapiens
Diseases Urinary Bladder Neoplasms, Carcinoma, Squamous Cell