Computational protocol: Up-Regulated Expression of LAMP2 and Autophagy Activity during Neuroendocrine Differentiation of Prostate Cancer LNCaP Cells

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Protocol publication

[…] Genome-wide transcriptomic analysis was performed using the whole human genome oligo microarray from Agilent platform GPL4133. Total RNA was isolated from LNCaP cells cultured in serum-free medium for 4 hours or 6 days using Trizol reagent according to the manufacturer’s recommended protocol. RNA labeling, hybridization and washing were carried out following Agilent's instructions. Images of hybridized microarrays were acquired with a DNA microarray scanner. Data were background corrected and normalized using the quantile method (Bolstadt et al., 2003). Differential expression analysis was assessed using the linear modeling features of the Limma package from Bioconductor open source software (http://www.bioconductor.org/. DNA microarray assays and bioinformatic data analyses were carried out in the Genomics Unit of the Spanish National Center for Cardiovascular Research (CNIC, Madrid, Spain). Results from differential expression analysis were further analyzed for functional enrichment by using GSEA (Gene Set Enrichment Analysis) v2.2.2 software [] an open source tool from the Broad Institute (http://software.broadinstitute.org/gsea/index.jsp). Gene Ontology Molecular Process, Cellular Components and Molecular Function gene sets (GO:MP, GO:CC and GO:MF) were downloaded from the Broad Institute’s Molecular Signature Database (version 4.0). […]

Pipeline specifications

Software tools limma, GSEA
Application Gene expression microarray analysis
Diseases Prostatic Neoplasms