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Series GSE155698 Query DataSets for GSE155698
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.
 
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
Web link https://www.nature.com/articles/s43018-020-00121-4
 
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
 
Platforms (2)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (41)
GSM4710689 PDAC_TISSUE_1
GSM4710690 PDAC_TISSUE_2
GSM4710691 PDAC_TISSUE_3
Relations
BioProject PRJNA655238

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE155698_RAW.tar 876.8 Mb (http)(custom) TAR (of TAR)
Processed data provided as supplementary file
Raw data not provided for this record

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