Bulk RNA sequencing of murine pancreatic ductal adenocarcinoma cell lines with and without C1galt1c1 knockout

Pancreatic ductal adenocarcinoma (PDAC) frequently displays aberrant O-glycosylation that contributes to tumor progression and immune evasion. To investigate the transcriptional consequences of altered O-glycosylation, we performed bulk RNA sequencing of murine PDAC (mPDAC) cell lines derived from the KPC model (Kras^LSL-G12D/+; Trp53^LSL-R172H/+; Pdx1-Cre) and their isogenic C1galt1c1 knockout (KO) counterparts. C1galt1c1 encodes Cosmc, an essential chaperone for core 1 O-glycan synthesis, and its loss leads to expression of the Tn antigen. Cells were harvested under standard culture conditions, RNA was extracted, and libraries were prepared and sequenced on an Illumina HiSeq platform (20–30 million reads per sample). Reads were processed and mapped to the mouse reference genome (mm39), and gene-level counts were generated. This dataset provides a resource for understanding how truncated O-glycosylation reshapes the transcriptome of PDAC cells and may influence tumor biology and immune interactions.