Affymetrix human gene 1.0 st array

In the discovery phase, high-throughput screening was performed using Affymetrix Human Gene 1.0 ST Array (Affymetrix, Santa Clara, CA), Nimblegen 3×720 K CpG Island Plus RefSeq Promoter Array (Roche NimbleGen, Madison, WI) and Affymetrix GeneChip Human Mapping 6.0 array (Affymetrix) to measure mRNA expression, DNA methylation and copy number changes in HCCs and paired non-tumor specimens, respectively. Referring to the corresponding array design database, we confirmed that the Affymetrix Human Gene 1.0 ST Array interrogates all 1,027 inflammation-related genes described by Loza et al. [10 (link)] with 1,108 transcripts; and the Nimblegen 3×720 K CpG Island Plus RefSeq Promoter Array and Affymetrix GeneChip Human Mapping 6.0 array interrogate 38,179 probes covering 1,024 genes and 33,855 probes covering 938 genes, respectively.

Gene expression information of PADA patients was acquired from the Cancer Genome Atlas (TCGA) database and Gene Expression Omnibus (GEO), including GSE62452 [17 (link)] and GSE28735 [18 (link)]. TCGA contains 172 PADA patients with a follow-up time of more than one month, among including of 171 primary tumors and one metastatic tumor. These samples were divided into the discovery set (n = 120) and validation set (n = 52). GSE62452 contains 69 PADA and adjacent non-tumor samples, among which 65 PADA samples had a follow-up time of more than one month. These samples were snap-frozen and sequenced using Affymetrix Human Gene 1.0 ST Array (GPL6244). GSE28735 contains 45 PAD patients, among which 42 PADA patients had a follow-up time of more than one month. These samples were also snap-frozen and sequenced using Affymetrix Human Gene 1.0 ST Array (GPL6244). Gene expression information was got through Cancer Cell Line Encyclopedia (CCLE) database. IC50 values of pancreatic cancer cell lines was got from Genomics of Drug Sensitivity in Cancer (GDSC). In the present study, gene expression profiling from TCGA was subjected to TPM normalization, and all arrays were subjected to RMA normalized in GSE62452 and GSE28735. A total of 104 circadian clock-associated genes that were retrieved in MSigDB database [19 (link)]. Basic information for gene expression data was shown in the Table 1.

According to the information included in the Gene Expression Omnibus (GEO) database [15 (link)] (https://www.ncbi.nlm.nih.gov/geo/ accessed on 15 February 2022), we downloaded the PI-related GSE33774 and GSE57631 genome-wide expression datasets. The GSE33774 dataset included 8 healthy samples and 7 PI samples. GSE33774 platform is GPL6244 [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version]. The GSE57631 dataset comprised 2 healthy samples and 6 PI samples, and the platform is GPL15034 [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [HuGene10stv1_Hs_ENTREZ, Brainarray v14].