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| Status |
Public on Oct 01, 2020 |
| Title |
Multimodal Mapping of the Tumor and Peripheral Blood Immune Landscape in Human Pancreatic Cancer |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
This is a human single cell sequencing repository of pancreatic cancer tumor tissue and PBMCs of pancreatic cancer patients. The goal of this study was to thorough map the immune landscape of pancreatic ductal adenocarinoma patient tumors and peripheral blood.
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| Overall design |
This repository contains 16 PDA tissue samples, 3 adjacent normal pancreas samples, 16 PBMC samples isolated from human PDA patients, and 4 PBMC samples isolated from healthy volunteers. Tissues were mechanically minced and enzymatically digested with collagenase P (1mg/mL DMEM) and subsequently filtered through a 40μm mesh to obtain single cells. Dead cells were removed using MACS®Dead Cell Removal Kit (Miltenyi Biotec Inc.). 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 3.0.0 with default settings was used, with an initial expected cell count of 10,000.
Submitter states the raw data is deposted in the dbGaP: accession number phs002071.v1.p1
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| Web link |
https://www.nature.com/articles/s43018-020-00121-4
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| Contributor(s) |
di Magliano MP |
| Citation(s) |
34296197, 36411320 |
| |
| Submission date |
Aug 04, 2020 |
| Last update date |
Dec 15, 2022 |
| Contact name |
Marina Pasca Di Magliano |
| Organization name |
University of Michigan
|
| Street address |
1500 E Medical Center Dr.
|
| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48103 |
| Country |
USA |
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| Platforms (2) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (41)
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| Relations |
| BioProject |
PRJNA655238 |
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