Illumina NovaSeq 6000 paired end sequencing; RNA-Seq of hamster PDAC cancer (HapT1 cell line) biopsies taken after treatment with either an IgG control or new hamster specific anti-PD-L1 monoclonal antibody.
RNA-Seq of hamster PDAC cancer (HapT1 cell line) biopsies taken after treatment with either an IgG control or new hamster specific anti-PD-L1 monoclonal antibody.
HapT1 cell line described in this publication DOI: 10.18632/oncotarget.9729 Thin needle biospies were taken from PDAC tumours on the day before the last injection. Biopsies were placed in RNA-later for extraction. 5-6 week old Syrian hamsters were engrafted with HapT1 cells grown in culture. The cells were grown (3x passages) in RPMI (10%FBS, 1%L-Glut, 1% P/s) until 80% confluency and were washed three times before engraftment. Hamsters were intraperitoneally injected with either 300ug of IgG2a or anti-PD-L1 every three days for a total of 8 injections. After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison. Below are the results of the number of significantly differentially expressed genes for all comparisons provided. RNAeasy mini kit (qiagen) was used according to the manufacturers instructions PolyA selection