Virus Dataset Detail

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Dataset Information
Accession GSE164690
Status 2021/11/8
Title Investigating Immune and Non-Immune Cell Interactions in Head and Neck Tumors by Single-Cell RNA Sequencing
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Head and neck squamous cell carcinoma (HNSCC) is characterized by complex relations between stromal, epithelial, and immune cells within the tumor microenvironment (TME). To enable the development of more efficacious therapies, we aim to study the heterogeneity, signatures of unique cell populations, and cell-cell interactions of suppressive non-immune and immune cell populations in 6 human papillomavirus (HPV)+ and 12 HPV- HNSCC patient tumor and matched peripheral blood specimens using single-cell RNA sequencing (scRNAseq). Using this dataset of 134,606 cells, we show cell type-specific signatures associated with inflammation and HPV status, describe the negative prognostic value of fibroblasts with elastic differentiation specifically in the HPV+ TME, predict therapeutically targetable checkpoint receptor-ligand interactions, and show that tumor-associated macrophages are dominant contributors of PD-L1 and other immune checkpoint ligands in the TME. We present a comprehensive single-cell view of cell-intrinsic mechanisms and cell-cell communication shaping the HNSCC microenvironment.
Samples
GSM ID Sample info Characteristics Description
GSM5017021 HN01_PBL cells tiisue:PBL; sorting:CD45+ -
GSM5017022 HN01_CD45+ cells tiisue:Tumor; sorting:CD45+ -
GSM5017023 HN01_CD45- cells tiisue:Tumor; sorting:CD45- -
GSM5017024 HN02_PBL cells tiisue:PBL; sorting:CD45+ -
GSM5017025 HN02_CD45+ cells tiisue:Tumor; sorting:CD45+ -
GSM5017026 HN03_PBL cells tiisue:PBL; sorting:CD45+ -
GSM5017027 HN03_CD45+ cells tiisue:Tumor; sorting:CD45+ -
GSM5017028 HN04_PBL cells tiisue:PBL; sorting:CD45+ -
GSM5017029 HN04_CD45+ cells tiisue:Tumor; sorting:CD45+ -
GSM5017030 HN05_PBL cells tiisue:PBL; sorting:CD45+ -
GSM5017031 HN05_CD45+ cells tiisue:Tumor; sorting:CD45+ -
GSM5017032 HN05_CD45- cells tiisue:Tumor; sorting:CD45- -
GSM5017033 HN06_PBL cells tiisue:PBL; sorting:CD45+ -
GSM5017034 HN06_CD45+ cells tiisue:Tumor; sorting:CD45+ -
GSM5017035 HN06_CD45- cells tiisue:Tumor; sorting:CD45- -
GSM5017036 HN07_PBL cells tiisue:PBL; sorting:CD45+ -
GSM5017037 HN07_CD45+ cells tiisue:Tumor; sorting:CD45+ -
GSM5017038 HN07_CD45- cells tiisue:Tumor; sorting:CD45- -
GSM5017039 HN08_PBL cells tiisue:PBL; sorting:CD45+ -
GSM5017040 HN08_CD45+ cells tiisue:Tumor; sorting:CD45+ -
GSM5017041 HN08_CD45- cells tiisue:Tumor; sorting:CD45- -
GSM5017042 HN09_PBL cells tiisue:PBL; sorting:CD45+ -
GSM5017043 HN09_CD45+ cells tiisue:Tumor; sorting:CD45+ -
GSM5017044 HN09_CD45- cells tiisue:Tumor; sorting:CD45- -
GSM5017045 HN10_PBL cells tiisue:PBL; sorting:CD45+ -
GSM5017046 HN10_CD45+ cells tiisue:Tumor; sorting:CD45+ -
GSM5017047 HN10_CD45- cells tiisue:Tumor; sorting:CD45- -
GSM5017048 HN11_PBL cells tiisue:PBL; sorting:CD45+ -
GSM5017049 HN11_CD45+ cells tiisue:Tumor; sorting:CD45+ -
GSM5017050 HN11_CD45- cells tiisue:Tumor; sorting:CD45- -
GSM5017051 HN12_PBL cells tiisue:PBL; sorting:CD45+ -
GSM5017052 HN12_CD45+ cells tiisue:Tumor; sorting:CD45+ -
GSM5017053 HN12_CD45- cells tiisue:Tumor; sorting:CD45- -
GSM5017054 HN13_PBL cells tiisue:PBL; sorting:CD45+ -
GSM5017055 HN13_CD45+ cells tiisue:Tumor; sorting:CD45+ -
GSM5017056 HN13_CD45- cells tiisue:Tumor; sorting:CD45- -
GSM5017057 HN14_PBL cells tiisue:PBL; sorting:CD45+ -
GSM5017058 HN14_CD45+ cells tiisue:Tumor; sorting:CD45+ -
GSM5017059 HN14_CD45- cells tiisue:Tumor; sorting:CD45- -
GSM5017060 HN15_PBL cells tiisue:PBL; sorting:CD45+ -
GSM5017061 HN15_CD45+ cells tiisue:Tumor; sorting:CD45+ -
GSM5017062 HN15_CD45- cells tiisue:Tumor; sorting:CD45- -
GSM5017063 HN16_PBL cells tiisue:PBL; sorting:CD45+ -
GSM5017064 HN16_CD45+ cells tiisue:Tumor; sorting:CD45+ -
GSM5017065 HN16_CD45- cells tiisue:Tumor; sorting:CD45- -
GSM5017066 HN17_PBL cells tiisue:PBL; sorting:CD45+ -
GSM5017067 HN17_CD45+ cells tiisue:Tumor; sorting:CD45+ -
GSM5017068 HN17_CD45- cells tiisue:Tumor; sorting:CD45- -
GSM5017069 HN18_PBL cells tiisue:PBL; sorting:CD45+ -
GSM5017070 HN18_CD45+ cells tiisue:Tumor; sorting:CD45+ -
GSM5017071 HN18_CD45- cells tiisue:Tumor; sorting:CD45- -
Platform GPL18573  : Illumina NextSeq 500 (Homo sapiens)
Literature 34921143  35392082  39773563  
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scRNA-seq UMAP