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Series GSE158356 Query DataSets for GSE158356
Status Public on Mar 24, 2021
Title Pancreatic cancer is marked by complement-high blood monocytes and tumor-associated macrophages
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary 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.
Contributor(s) di Magliano MP, Crawford HC, Kemp SB
Citation(s) 33782087
Submission date Sep 22, 2020
Last update date May 12, 2021
Contact name Marina Pasca di Magliano
Organization name University of Michigan
Department Surgery
Street address 1500 E Medical Center Drive
City Ann Arbor
State/province Michigan
ZIP/Postal code 48109
Country USA
Platforms (3)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (15)
GSM4798240 Control_Scaff
GSM4798241 Tumor_Scaff
GSM4798242 OT_Tumor_1
BioProject PRJNA664962
SRA SRP284880

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Supplementary file Size Download File type/resource
GSE158356_RAW.tar 1.0 Gb (http)(custom) TAR (of H5, MTX, TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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