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Series GSE128223 Query DataSets for GSE128223
Status Public on May 01, 2019
Title Single cell RNAseq of human TCRVdelta 1 and TCRVdelta 2 gammadelta T lymphocytes purified from healthy adults blood
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary γδ T lymphocytes represent ~1% of human PBMC and even more cells in most tissues of vertebrates. Although they have important anticancer functions, most current scRNA-Seq studies do not identify γδ T lymphocytes since their transcriptomes at the single cell level are unknown. Here we show that high resolution clustering of large scRNA-Seq data sets and a combination of gene signatures allow the specific detection of human γδ T lymphocytes and identification of their TCRVδ1 and TCRVδ2 subsets in large data sets from complex cell mixtures. In t-SNE plots from blood and tumor samples, the few γδ T lymphocytes appear collectively embedded between cytotoxic CD8 T and NK cells. Their TCRVδ1 and TCRVδ2 subsets form close yet distinct sub-clusters respectively neighbouring NK and CD8 T cells owing to expression of shared and distinct cytotoxic maturation genes. Similar pseudo-time maturation trajectories of TCRVδ1 and TCRVδ2 γδ T lymphocytes were discovered, unveiling in both subsets an unattended pool of TEMRA cells with preserved proliferative capacity, a finding confirmed by in vitro proliferation assays. Overall, the single cell transcriptomes of thousands of individual gd T lymphocytes from different CMV+ and CMV- donors reflect cytotoxic maturation stages driven by the immunological history of donors. This landmark study establishes the rationale for identification, subtyping and deep characterization of human γδ T lymphocytes in further scRNA-Seq studies of complex tissues in physiological and disease conditions.
Overall design 6 samples of purified human gd T cells from 3 donors (CMV+ and CMV-). Cell-sorted TCRVdelta1 and TCRVdelta2 T lymphocytes from each donor PBMC.
Contributor(s) Fournié J
Citation(s) 31118283
Submission date Mar 13, 2019
Last update date Apr 18, 2020
Contact name Jean Jacques FOURNIE
Phone +33619900602
Organization name INSERM
Department oncology
Lab Cancer Research Center of Toulouse
Street address 2 av Hubert Curien
City Toulouse
ZIP/Postal code 31037
Country France
Platforms (2)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
GPL21697 NextSeq 550 (Homo sapiens)
Samples (6)
GSM3667467 Donor_1_d1
GSM3667468 Donor_1_d2
GSM3667469 Donor_2_d1
BioProject PRJNA526841
SRA SRP188300

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Supplementary file Size Download File type/resource
GSE128223_3donors_d1_d2_v2.tsv.gz 11.3 Mb (ftp)(http) TSV
GSE128223_RAW.tar 12.2 Mb (http)(custom) TAR (of TSV)
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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