Pancreatic cancer is marked by complement-high blood monocytes and tumor-associated macrophages

We utilized biomaterial scaffolds to identify a unique gene expression signature of immune cells in tumor-bearing mice. Single cell RNA sequencing analysis then revealed two distinct macrophage populations that exist at both the primary tumor and systemically in both mice and pancreatic cancer patients, marked by the expression of C1qa, C1qb, and Trem2. This 10X Genomics single cell RNA sequencing repository includes raw and processed data files from biomaterial scaffolds from control (n=2) and tumor-bearingmice using an orthotopic model of pancreatic cancer (PDA) (n=1) and the iKras* p53* (n=1) genetically engineered model of PDA, mouse orthotopic pancreatic tumors (n=2), mouse normal pancreas samples (n=2), mouse iKras* p53* tumors (n=2), and human liver metastasis samples (n=5). Orthotopic tumors were formed from implantation of the 7940b cell line derived from the KrasLSL-G12D/+; Trp53LSL-R172H/+; Pdx1-Cre (KPC) model of pancreatic cancer. Single-cell cDNA libraries were prepared and sequenced at the University of Michigan Sequencing Core using the 10x Genomics Platform. Samples were run using paired end 50 cycle reads on HiSeq 4000 or the NovaSeq 6000 (Illumina) to a depth of 100,000 reads. The raw data were processed and aligned by the University of Michigan DNA Sequencing Core. Cellranger count version 2.2.0, 3.0.0, or 3.1.0 with default settings was used, with an initial expected cell count of 10,000.