Agilent 4 44k expression arrays

Gene expression profiling was performed as described in a previous study (Thu et al., 2014 (link)). In previous study, expression profiling for PDAC and HPDE cell lines was performed using Agilent 4 × 44K expression arrays (Agilent, Canada). Normalization of expression values for each array was calculated using the following formula: (median intensity - background intensity) / (median array intensity value). To reduce overestimation resulting from poor probe performance, the lowest 2% of genes, calculated based on expression values in the HPDE cell line, were eliminated.
To compare publically available genomic data with our proteomic data, our proteomic data were converted from IPI numbers (1931) to gene symbols (1910). Among 1910 gene symbols, 1695 gene symbols overlapped between the genomic (30,484 total gene symbols) and proteomic (1910 total gene symbols) data. Of these, 697 gene symbols for the differentially expressed in our proteomic dataset were subjected to Pearson correlation analysis. The fold-changes between dataset comparisons were transformed to log₂ scales.

Expression profiles were generated using Agilent 4 × 44 K expression arrays (Agilent, Mississauga, ON, USA). Total RNA was extracted, checked and purified by RNeasy mini kit (QIAGEN, GmBH, Hilden, Germany). After RNA amplification and labeling, each slide was hybridized with 1.65 μg labeled sample. Slides were washed in staining dishes after 17-h hybridization, and scanned using an Agilent Microarray Scanner (Agilent Technologies, Santa Clara, CA, USA). Data were extracted with the Feature Extraction software 10.7 (Agilent Technologies) and normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent Technologies). Genes with fold changes>or <2.0 were considered to be of biological significance.