GSE158356
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. Overall design: 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.