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Series GSE167118 Query DataSets for GSE167118
Status Public on Feb 20, 2021
Title Clonal expansion and activation of tissue-resident memory-like Th17 cells expressing GM-CSF in the lung of severe COVID-19 patients
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Other
Summary Hyperinflammation contributes to lung injury and subsequent acute respiratory distress syndrome (ARDS) with high mortality in severe COVID-19. To understand the underlying mechanisms, we investigated the role of the lung-specific immune response. Here we profiled lymphocytes and myeloid cells in the bronchoalveolar lavage (BAL) fluid and blood of COVID-19 patients. By tracking T cell clones across tissues, we identified clonally expanded tissue-resident memory-like Th17 cells (Trm17 cells) in the lung even after viral clearance. These Trm17 cells are characterized by a potentially pathogenic cytokine profile with expression of IL17A and CSF2 (GM-CSF). Interactome analysis revealed that Trm17 cells interact with macrophages and cytotoxic CD8+ T cells, which have been associated with disease severity and lung damage. High IL-17A and GM-CSF protein levels in the serum of COVID-19 patients correlated with severe clinical course. This study suggests pulmonary Trm17 cells as one of the orchestrators of the hyperinflammation in severe COVID-19 and that these cells and their cytokines, such as GM-CSF, are promising biomarkers and potential targets for a COVID-19 therapy.
 
Overall design SRA accession: SRP306287; BioProject accession: PRJNA701725; Sort CD45 positive cells the bronchoalveolar lavage fluid and blood of COVID-19 patients and bacteria pnemonia patients, then perform 5'-RNA single cell transcriptome, CITE-seq and TCR sequening (10x genomics).
 
Contributor(s) Zhao Y, Hausmann F, Gagliani N, Krebs CF
Citation(s) 33622974
BioProject PRJNA701725
Submission date Feb 19, 2021
Last update date Mar 03, 2021
Contact name Yu Zhao
E-mail(s) yu.zhao@zmnh.uni-hamburg.de
Organization name University Medical Center Hamburg-Eppendorf
Department Institute of Medical Systems Biology
Street address Falkenried 94
City Hamburg
ZIP/Postal code 20251
Country Germany
 
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (93)
GSM5093883 Bac17B_CD3pos_ADT
GSM5093884 Bac17B_CD3pos_GEX
GSM5093885 Bac17B_CD3pos_TCR
Relations
SRA SRP306287

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
GSE167118_Bac17B_CD3pos_barcodes.tsv.gz 16.8 Kb (ftp)(http) TSV
GSE167118_Bac17B_CD3pos_features.tsv.gz 297.9 Kb (ftp)(http) TSV
GSE167118_Bac17B_CD3pos_matrix.mtx.gz 19.1 Mb (ftp)(http) MTX
GSE167118_Bac17B_TCR_all_contig_annotations.csv.gz 246.0 Kb (ftp)(http) CSV
GSE167118_Bac17L_CD3neg_barcodes.tsv.gz 16.8 Kb (ftp)(http) TSV
GSE167118_Bac17L_CD3neg_features.tsv.gz 297.9 Kb (ftp)(http) TSV
GSE167118_Bac17L_CD3neg_matrix.mtx.gz 21.8 Mb (ftp)(http) MTX
GSE167118_Bac17L_CD3pos_barcodes.tsv.gz 19.3 Kb (ftp)(http) TSV
GSE167118_Bac17L_CD3pos_features.tsv.gz 297.9 Kb (ftp)(http) TSV
GSE167118_Bac17L_CD3pos_matrix.mtx.gz 21.6 Mb (ftp)(http) MTX
GSE167118_Bac17L_TCR_all_contig_annotations.csv.gz 314.1 Kb (ftp)(http) CSV
GSE167118_Bac18B_CD3pos_barcodes.tsv.gz 9.4 Kb (ftp)(http) TSV
GSE167118_Bac18B_CD3pos_features.tsv.gz 297.9 Kb (ftp)(http) TSV
GSE167118_Bac18B_CD3pos_matrix.mtx.gz 15.7 Mb (ftp)(http) MTX
GSE167118_Bac18B_TCR_all_contig_annotations.csv.gz 326.0 Kb (ftp)(http) CSV
GSE167118_Bac18L_CD3neg_barcodes.tsv.gz 13.2 Kb (ftp)(http) TSV
GSE167118_Bac18L_CD3neg_features.tsv.gz 297.9 Kb (ftp)(http) TSV
GSE167118_Bac18L_CD3neg_matrix.mtx.gz 17.9 Mb (ftp)(http) MTX
GSE167118_Bac18L_CD3pos_barcodes.tsv.gz 8.6 Kb (ftp)(http) TSV
GSE167118_Bac18L_CD3pos_features.tsv.gz 297.9 Kb (ftp)(http) TSV
GSE167118_Bac18L_CD3pos_matrix.mtx.gz 10.3 Mb (ftp)(http) MTX
GSE167118_Bac18L_TCR_all_contig_annotations.csv.gz 144.5 Kb (ftp)(http) CSV
GSE167118_Bac19B_CD3pos_barcodes.tsv.gz 34.7 Kb (ftp)(http) TSV
GSE167118_Bac19B_CD3pos_features.tsv.gz 297.9 Kb (ftp)(http) TSV
GSE167118_Bac19B_CD3pos_matrix.mtx.gz 50.7 Mb (ftp)(http) MTX
GSE167118_Bac19B_TCR_all_contig_annotations.csv.gz 968.0 Kb (ftp)(http) CSV
GSE167118_Bac19L_CD3pos_barcodes.tsv.gz 17.7 Kb (ftp)(http) TSV
GSE167118_Bac19L_CD3pos_features.tsv.gz 297.9 Kb (ftp)(http) TSV
GSE167118_Bac19L_CD3pos_matrix.mtx.gz 19.1 Mb (ftp)(http) MTX
GSE167118_Bac19L_TCR_all_contig_annotations.csv.gz 257.3 Kb (ftp)(http) CSV
GSE167118_Bac20B_CD3pos_barcodes.tsv.gz 50.7 Kb (ftp)(http) TSV
GSE167118_Bac20B_CD3pos_features.tsv.gz 297.9 Kb (ftp)(http) TSV
GSE167118_Bac20B_CD3pos_matrix.mtx.gz 61.3 Mb (ftp)(http) MTX
GSE167118_Bac20B_TCR_all_contig_annotations.csv.gz 2.1 Mb (ftp)(http) CSV
GSE167118_Bac20L_CD3neg_barcodes.tsv.gz 4.6 Kb (ftp)(http) TSV
GSE167118_Bac20L_CD3neg_features.tsv.gz 297.9 Kb (ftp)(http) TSV
GSE167118_Bac20L_CD3neg_matrix.mtx.gz 3.7 Mb (ftp)(http) MTX
GSE167118_Bac20L_CD3pos_barcodes.tsv.gz 3.2 Kb (ftp)(http) TSV
GSE167118_Bac20L_CD3pos_features.tsv.gz 297.9 Kb (ftp)(http) TSV
GSE167118_Bac20L_CD3pos_matrix.mtx.gz 2.1 Mb (ftp)(http) MTX
GSE167118_Bac20L_TCR_all_contig_annotations.csv.gz 65.9 Kb (ftp)(http) CSV
GSE167118_Sar01B_CD3pos_barcodes.tsv.gz 53.5 Kb (ftp)(http) TSV
GSE167118_Sar01B_CD3pos_features.tsv.gz 297.9 Kb (ftp)(http) TSV
GSE167118_Sar01B_CD3pos_matrix.mtx.gz 62.5 Mb (ftp)(http) MTX
GSE167118_Sar01B_TCR_all_contig_annotations.csv.gz 1.0 Mb (ftp)(http) CSV
GSE167118_Sar01L_CD3neg_barcodes.tsv.gz 19.0 Kb (ftp)(http) TSV
GSE167118_Sar01L_CD3neg_features.tsv.gz 297.9 Kb (ftp)(http) TSV
GSE167118_Sar01L_CD3neg_matrix.mtx.gz 20.5 Mb (ftp)(http) MTX
GSE167118_Sar01L_CD3pos_barcodes.tsv.gz 41.6 Kb (ftp)(http) TSV
GSE167118_Sar01L_CD3pos_features.tsv.gz 297.9 Kb (ftp)(http) TSV
GSE167118_Sar01L_CD3pos_matrix.mtx.gz 57.8 Mb (ftp)(http) MTX
GSE167118_Sar01L_TCR_all_contig_annotations.csv.gz 827.8 Kb (ftp)(http) CSV
GSE167118_Sar02B_CD3pos_barcodes.tsv.gz 48.4 Kb (ftp)(http) TSV
GSE167118_Sar02B_CD3pos_features.tsv.gz 297.9 Kb (ftp)(http) TSV
GSE167118_Sar02B_CD3pos_matrix.mtx.gz 72.9 Mb (ftp)(http) MTX
GSE167118_Sar02B_TCR_all_contig_annotations.csv.gz 1.0 Mb (ftp)(http) CSV
GSE167118_Sar02L_CD3neg_barcodes.tsv.gz 8.2 Kb (ftp)(http) TSV
GSE167118_Sar02L_CD3neg_features.tsv.gz 297.9 Kb (ftp)(http) TSV
GSE167118_Sar02L_CD3neg_matrix.mtx.gz 4.3 Mb (ftp)(http) MTX
GSE167118_Sar02L_CD3pos_barcodes.tsv.gz 4.9 Kb (ftp)(http) TSV
GSE167118_Sar02L_CD3pos_features.tsv.gz 297.9 Kb (ftp)(http) TSV
GSE167118_Sar02L_CD3pos_matrix.mtx.gz 3.2 Mb (ftp)(http) MTX
GSE167118_Sar02L_TCR_all_contig_annotations.csv.gz 46.5 Kb (ftp)(http) CSV
GSE167118_Sar03B_CD3pos_barcodes.tsv.gz 42.7 Kb (ftp)(http) TSV
GSE167118_Sar03B_CD3pos_features.tsv.gz 297.9 Kb (ftp)(http) TSV
GSE167118_Sar03B_CD3pos_matrix.mtx.gz 60.5 Mb (ftp)(http) MTX
GSE167118_Sar03B_TCR_all_contig_annotations.csv.gz 855.1 Kb (ftp)(http) CSV
GSE167118_Sar03L_CD3neg_barcodes.tsv.gz 3.9 Kb (ftp)(http) TSV
GSE167118_Sar03L_CD3neg_features.tsv.gz 297.9 Kb (ftp)(http) TSV
GSE167118_Sar03L_CD3neg_matrix.mtx.gz 3.6 Mb (ftp)(http) MTX
GSE167118_Sar03L_CD3pos_barcodes.tsv.gz 2.5 Kb (ftp)(http) TSV
GSE167118_Sar03L_CD3pos_features.tsv.gz 297.9 Kb (ftp)(http) TSV
GSE167118_Sar03L_CD3pos_matrix.mtx.gz 2.9 Mb (ftp)(http) MTX
GSE167118_Sar03L_TCR_all_contig_annotations.csv.gz 58.3 Kb (ftp)(http) CSV
GSE167118_Sar04B_CD3pos_barcodes.tsv.gz 54.4 Kb (ftp)(http) TSV
GSE167118_Sar04B_CD3pos_features.tsv.gz 297.9 Kb (ftp)(http) TSV
GSE167118_Sar04B_CD3pos_matrix.mtx.gz 63.3 Mb (ftp)(http) MTX
GSE167118_Sar04B_TCR_all_contig_annotations.csv.gz 1.1 Mb (ftp)(http) CSV
GSE167118_Sar04L_CD3neg_barcodes.tsv.gz 17.5 Kb (ftp)(http) TSV
GSE167118_Sar04L_CD3neg_features.tsv.gz 297.9 Kb (ftp)(http) TSV
GSE167118_Sar04L_CD3neg_matrix.mtx.gz 22.7 Mb (ftp)(http) MTX
GSE167118_Sar04L_CD3pos_barcodes.tsv.gz 10.6 Kb (ftp)(http) TSV
GSE167118_Sar04L_CD3pos_features.tsv.gz 297.9 Kb (ftp)(http) TSV
GSE167118_Sar04L_CD3pos_matrix.mtx.gz 13.7 Mb (ftp)(http) MTX
GSE167118_Sar04L_TCR_all_contig_annotations.csv.gz 177.7 Kb (ftp)(http) CSV
GSE167118_Sar05B_CD3pos_barcodes.tsv.gz 33.1 Kb (ftp)(http) TSV
GSE167118_Sar05B_CD3pos_features.tsv.gz 297.9 Kb (ftp)(http) TSV
GSE167118_Sar05B_CD3pos_matrix.mtx.gz 58.8 Mb (ftp)(http) MTX
GSE167118_Sar05B_TCR_all_contig_annotations.csv.gz 887.0 Kb (ftp)(http) CSV
GSE167118_Sar05L_CD3neg_barcodes.tsv.gz 23.4 Kb (ftp)(http) TSV
GSE167118_Sar05L_CD3neg_features.tsv.gz 297.9 Kb (ftp)(http) TSV
GSE167118_Sar05L_CD3neg_matrix.mtx.gz 28.4 Mb (ftp)(http) MTX
GSE167118_Sar05L_CD3pos_barcodes.tsv.gz 44.8 Kb (ftp)(http) TSV
GSE167118_Sar05L_CD3pos_features.tsv.gz 297.9 Kb (ftp)(http) TSV
GSE167118_Sar05L_CD3pos_matrix.mtx.gz 69.0 Mb (ftp)(http) MTX
GSE167118_Sar05L_TCR_all_contig_annotations.csv.gz 995.1 Kb (ftp)(http) CSV
GSE167118_Sar07B_CD3pos_barcodes.tsv.gz 29.8 Kb (ftp)(http) TSV
GSE167118_Sar07B_CD3pos_features.tsv.gz 297.9 Kb (ftp)(http) TSV
GSE167118_Sar07B_CD3pos_matrix.mtx.gz 40.1 Mb (ftp)(http) MTX
GSE167118_Sar07B_TCR_all_contig_annotations.csv.gz 485.8 Kb (ftp)(http) CSV
GSE167118_Sar07L_CD3neg_barcodes.tsv.gz 8.7 Kb (ftp)(http) TSV
GSE167118_Sar07L_CD3neg_features.tsv.gz 297.9 Kb (ftp)(http) TSV
GSE167118_Sar07L_CD3neg_matrix.mtx.gz 6.5 Mb (ftp)(http) MTX
GSE167118_Sar07L_CD3pos_barcodes.tsv.gz 16.8 Kb (ftp)(http) TSV
GSE167118_Sar07L_CD3pos_features.tsv.gz 297.9 Kb (ftp)(http) TSV
GSE167118_Sar07L_CD3pos_matrix.mtx.gz 20.8 Mb (ftp)(http) MTX
GSE167118_Sar07L_TCR_all_contig_annotations.csv.gz 318.1 Kb (ftp)(http) CSV
GSE167118_Sar08B_CD3pos_barcodes.tsv.gz 35.6 Kb (ftp)(http) TSV
GSE167118_Sar08B_CD3pos_features.tsv.gz 297.9 Kb (ftp)(http) TSV
GSE167118_Sar08B_CD3pos_matrix.mtx.gz 45.8 Mb (ftp)(http) MTX
GSE167118_Sar08B_TCR_all_contig_annotations.csv.gz 562.0 Kb (ftp)(http) CSV
GSE167118_Sar08L_CD3neg_barcodes.tsv.gz 15.8 Kb (ftp)(http) TSV
GSE167118_Sar08L_CD3neg_features.tsv.gz 297.9 Kb (ftp)(http) TSV
GSE167118_Sar08L_CD3neg_matrix.mtx.gz 16.1 Mb (ftp)(http) MTX
GSE167118_Sar08L_CD3pos_barcodes.tsv.gz 14.4 Kb (ftp)(http) TSV
GSE167118_Sar08L_CD3pos_features.tsv.gz 297.9 Kb (ftp)(http) TSV
GSE167118_Sar08L_CD3pos_matrix.mtx.gz 17.6 Mb (ftp)(http) MTX
GSE167118_Sar08L_TCR_all_contig_annotations.csv.gz 143.7 Kb (ftp)(http) CSV
GSE167118_Sar09L_CD45ne_barcodes.tsv.gz 40.3 Kb (ftp)(http) TSV
GSE167118_Sar09L_CD45ne_features.tsv.gz 297.9 Kb (ftp)(http) TSV
GSE167118_Sar09L_CD45ne_matrix.mtx.gz 8.3 Mb (ftp)(http) MTX
GSE167118_Sar09L_CD45po_barcodes.tsv.gz 2.3 Kb (ftp)(http) TSV
GSE167118_Sar09L_CD45po_features.tsv.gz 297.9 Kb (ftp)(http) TSV
GSE167118_Sar09L_CD45po_matrix.mtx.gz 2.0 Mb (ftp)(http) MTX
GSE167118_Sar09L_EpCAM_barcodes.tsv.gz 904 b (ftp)(http) TSV
GSE167118_Sar09L_EpCAM_features.tsv.gz 297.9 Kb (ftp)(http) TSV
GSE167118_Sar09L_EpCAM_matrix.mtx.gz 1.7 Mb (ftp)(http) MTX
GSE167118_Sar09L_TCR_all_contig_annotations.csv.gz 21.9 Kb (ftp)(http) CSV
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