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Series GSE162097 Query DataSets for GSE162097
Status Public on Jan 27, 2021
Title The identity of human tissue-emigrant CD8+ T cells (scRNAseq, scTCRseq, bulk RNA-seq)
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Other
Summary Lymphocyte migration is essential for adaptive immune surveillance. However, ourcurrent understanding of this process is rudimentary, because most human studieshave been restricted to immunological analyses of blood and various tissues. Toaddress this, we used an integrated approach to characterize tissue-emigrant immunecells in thoracic duct lymph (TDL). The most prevalent immune cells in human andnon-human primate efferent lymph were T cells. Cytolytic CD8+ T cell subsets witheffector-like epigenetic and transcriptional signatures were clonotypically skewed andselectively confined to the intravascular circulation, whereas non-cytolytic CD8+ T cellsubsets with stem-like epigenetic and transcriptional signatures predominated intissues and TDL. Moreover, these anatomically distinct gene expression profiles wererecapitulated within individual antigen-specific clonotypes, suggesting paralleldifferentiation programs independent of the expressed antigen receptor. Our collectivedataset provides a framework of the migratory immune system and defines the natureof tissue-emigrant CD8+ T cells that recirculate via TDL.
 
Overall design scRNAseq and scTCRseq of 1) HIV-specific or CMV-specific CD8+ T-cells and 2) memory CD8+ T-cells between TDL and blood

bulk RNA-seq of FACS sorted CD8+ Tcell memory subsets from human peripheral blood (samples re-used from GSE148234).
 
Contributor(s) Wu VH, Nguyen SN, Buggert M
Citation(s) 33306960
Submission date Nov 24, 2020
Last update date Apr 28, 2021
Contact name Marcus Buggert
E-mail(s) [email protected]
Organization name Karolinska Institutet
Department Microbiology
Street address C2:94; Karolinska Universitetssjukhuset Huddinge
City Stockholm
State/province PA
ZIP/Postal code 141 86
Country Sweden
 
Platforms (3)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL21697 NextSeq 550 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (36)
GSM4933103 scRNAseq of Blood memory CD8+ T-cells from HUP213
GSM4933104 scRNAseq of TDL memory CD8+ T-cells from HUP213
GSM4933105 scRNAseq of Blood memory CD8+ T-cells from HUP217
This SubSeries is part of SuperSeries:
GSE162180 The identity of human tissue-emigrant CD8+ T cells
Relations
BioProject PRJNA680565
SRA SRP293779

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
GSE162097_RAW.tar 203.7 Mb (http)(custom) TAR (of TAR)
GSE162097_bulk_RNA-seq_buggert_pbmc_RNAseq_deseq2_norm.csv.gz 1.7 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record
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