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Series GSE222454 Query DataSets for GSE222454
Status Public on Nov 05, 2023
Title Multimodal profiling reveals site-specific adaptation and tissue residency hallmarks of γδ T cells across organs in mice
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary γδ T cells perform heterogeneous functions in homeostasis and disease across tissues. However, it is unclear whether these roles correspond to distinct γδ subsets or to a homogeneous population of cells exerting context-dependent functions. Here, by cross-organ multimodal single-cell profiling, we reveal that various mouse tissues harbor unique site-adapted γδ subsets. Epidermal and intestinal intraepithelial γδ T cells are transcriptionally homogeneous and exhibit epigenetic hallmarks of functional diversity. Through parabiosis experiments, we uncovered cellular states associated with cytotoxicity, innate-like rapid IFN-γ production and tissue repair functions displaying tissue residency hallmarks. Notably, our observations nuance the link between IL-17-producing γδ T cells and tissue residency. Moreover, transcriptional programs associated with tissue-resident γδ T cells are analogous to those of CD8+ tissue-resident memory T cells. Altogether, this study provides the first multimodal landscape of tissue-adapted γδ T cells, revealing heterogeneity, lineage relationships and their tissue residency program.

Overall design To identify and compare various subsets of γδ T cells present across different tissues, we took a single-cell multimodal approach and sorted gd T cells from lymph nodes, spleen, liver, lung, skin, small and large intestine using flow cytometry. Sorted cells were subjected to single-cell sequencing using two different approaches. In the first approach, γδ T cells from different organs were barcoded with distinct oligonucleotide-conjugated antibodies as well as 26 other antibodies. The transcriptomes and epitopes were simultaneously profiled using single-cell RNA sequencing (scRNA-seq) and TotalSeq, respectively. In the second approach, simultaneous single-nucleus RNA sequencing (snRNA-seq) and assay for transposase-accessible chromatin using sequencing (scATAC-seq) were performed on pooled γδ T cells from different organs without sample barcoding. Furthermore, simultaneous profiling of RNA and gamma delta T cell receptor (TCR) profiling was also performed at a single-cell resolution.
Web link
Contributor(s) Sagar -
Citation(s) 38177282
Submission date Jan 09, 2023
Last update date Jan 05, 2024
Contact name Sagar -
Organization name University Medical Center Freiburg
Department Department of Internal Medicine II
Lab Sagar
Street address Hugstetter Straße 55
City Freiburg
ZIP/Postal code 79106
Country Germany
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (21)
GSM6923614 gdTcells, mRNA-derived library DEC_GD_GEX
GSM6923615 gdTcells, HTO-derived library DEC_GD_HTO
GSM6923616 gdTcells, mRNA-derived library OCT_GD_GEX
BioProject PRJNA922136

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
GSE222454_DEC_GD_barcodes.tsv.gz 42.1 Kb (ftp)(http) TSV
GSE222454_DEC_GD_features.tsv.gz 284.2 Kb (ftp)(http) TSV
GSE222454_DEC_GD_matrix.mtx.gz 41.6 Mb (ftp)(http) MTX
GSE222454_MULTIOME_MPI_filtered_feature_bc_matrix.h5 206.7 Mb (ftp)(http) H5
GSE222454_MULTIOME_Paris_Lib1_filtered_feature_bc_matrix.h5 81.3 Mb (ftp)(http) H5
GSE222454_MULTIOME_Paris_Lib2_filtered_feature_bc_matrix.h5 92.2 Mb (ftp)(http) H5
GSE222454_OCT_GD_barcodes.tsv.gz 69.6 Kb (ftp)(http) TSV
GSE222454_OCT_GD_features.tsv.gz 284.4 Kb (ftp)(http) TSV
GSE222454_OCT_GD_matrix.mtx.gz 92.6 Mb (ftp)(http) MTX
GSE222454_RAW.tar 270.0 Kb (http)(custom) TAR (of CSV)
GSE222454_VDJ5PGD_barcodes.tsv.gz 93.8 Kb (ftp)(http) TSV
GSE222454_VDJ5PGD_features.tsv.gz 284.2 Kb (ftp)(http) TSV
GSE222454_VDJ5PGD_matrix.mtx.gz 149.0 Mb (ftp)(http) MTX
GSE222454_parabiosis_circulating_p1_2_2_barcodes.tsv.gz 42.7 Kb (ftp)(http) TSV
GSE222454_parabiosis_circulating_p1_2_2_features.tsv.gz 284.3 Kb (ftp)(http) TSV
GSE222454_parabiosis_circulating_p1_2_2_matrix.mtx.gz 48.4 Mb (ftp)(http) MTX
GSE222454_parabiosis_circulating_p2_1_1_barcodes.tsv.gz 28.6 Kb (ftp)(http) TSV
GSE222454_parabiosis_circulating_p2_1_1_features.tsv.gz 284.3 Kb (ftp)(http) TSV
GSE222454_parabiosis_circulating_p2_1_1_matrix.mtx.gz 27.6 Mb (ftp)(http) MTX
GSE222454_parabiosis_resident_p1_1_1_barcodes.tsv.gz 88.3 Kb (ftp)(http) TSV
GSE222454_parabiosis_resident_p1_1_1_features.tsv.gz 284.3 Kb (ftp)(http) TSV
GSE222454_parabiosis_resident_p1_1_1_matrix.mtx.gz 96.4 Mb (ftp)(http) MTX
GSE222454_parabiosis_resident_p2_2_2_barcodes.tsv.gz 65.8 Kb (ftp)(http) TSV
GSE222454_parabiosis_resident_p2_2_2_features.tsv.gz 284.3 Kb (ftp)(http) TSV
GSE222454_parabiosis_resident_p2_2_2_matrix.mtx.gz 67.7 Mb (ftp)(http) MTX
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