Sentrix human 6v3 whole genome expression beadchips sentrix human wg 6

Expression profiling data are available from extensive previous studies (Bauer et al., 2018). In summary, there are data on 195 cases of PDAC, 30 cases of peritumoral tissue from next to PDAC (N.PDAC), 24 CT, 22 peritumoral tissues from next to cystic tumors, 59 samples of CP, and 41 healthy pancreatic tissues from noncancer patients (N). Total RNA from individual samples was analyzed on the Sentrix Human‐6v3 Whole Genome Expression BeadChips (Sentrix Human WG‐6; Illumina, San Diego, CA, USA). Differential expression analysis was performed using the LIMMA package by pairwise comparisons of the groups (Ritchie et al., 2015). The resulting P‐values were adjusted for multiple testing using Benjamini–Hochberg's false discovery rate (FDR) method; features with a FDR < 0.01 and an absolute log₂‐fold change (log₂FC) > 0.5 were considered significant.

Sentrix Human-6v3 Whole Genome Expression BeadChips (Sentrix Human WG-6; Illumina) were used to identify genes expressed in pancreatic cancer tissue. To synthesize first and second strand cDNA and amplify biotinylated cRNA from the total RNA we used an Illumina TotalPrep RNA Amplification Kit. Hybridization to the BeadChip was performed without modification according to the manufacturer’s instructions. A maximum of 10 µl cRNA was mixed with a 20 µL GEX-HYB hybridization solution. The preheated 30 µl assay sample was dispensed onto the large sample port of each array and incubated for 18 hours at 58°C. Following hybridization, the samples were washed according to the protocol and scanned with a Bead Array Reader (Illumina, San Diego, CA). Raw data were exported from the Bead studio software to R. The data were quantile normalized and log2 transformed. The data have been uploaded to ArrayExpress under accession number E-MTAB-1791.