GSE172303
Identification and characterization of new pancreatic cancer stem cells marker
To identify gene transcripts that were responsible for the stemness formation in pancreatic cancer cells, spheroid PANC1 and BXPC3 cells from primary sphere formation were enriched and then used for RNA-seq analysis. A gemcitabine-resistant SW1990 cell line was also established and used for RNA-seq analysis. In order to ensure the data quality, raw reads were preprocessed by removing low quality sequences, dejunction contamination(Trimmomatic), A/T/G/C Content Distribution(RSeQC), rRNA removal(bowtie2), etc to obtain high quality sequences (clean reads) and all subsequent analyses were based on clean reads. Clean Data was aligned to the reference genome by HISAT, and gene expression quantification was done via software FeatureCounts. DESseq2 package in the R software was introduced to analysis differentially expressed genes between comparisons using read counts estimated by FeatureCounts. Genes with adjusted pvalue<?0.05 and |log2(Fold Change) |?>?1 were defined as differentially expressed genes. Totally, we identified 108 DEGs whose expression changes were almost similar in all the data sets. Overall design: Identification of DEGs between wilt type (WT) and spheroid-forming (Sphere) pancreatic cancer cells (BXBP3, PANC1), and  between wilt type (WT) and gemcitabine-resistant (GR) SW1990 cell line.