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Series GSE161918 Query DataSets for GSE161918
Status Public on Feb 10, 2021
Title Time-resolved Systems Immunology Reveals a Late Juncture Linked to Fatal COVID-19
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary COVID-19 exhibits extensive clinical heterogeneity ranging from asymptomatic infection to death. Unraveling the basis of immune response differences across individuals is critical for developing effective therapeutics and prophylactics. We longitudinally assessed 192 surface protein markers, the transcriptome, and T-cell receptor sequence profiles simultaneously in single peripheral immune cells from COVID-19 patients, and compared to age-matched healthy control samples.
Overall design Peripheral blood mononuclear cells from 33 COVID19 patients and 14 age-matched healthy controls were profiled using multi-modal single cell RNAseq (surface protein staining (Biolegend TotalSeq-C lyophilized panel), mRNA, and T cell recpetor VDJ regions) using the 10x Genomics Chromium system. Individual patients samples, in some cases with multiple samples per donor from different timepoints during disease, were combined and ran together in several lanes of the 10x system, and assignment of the individual cells to a donor and timepoint was done using a combination of SNP and antibody hashtags. SNP calls per donor were determined from bulk level RNAseq data of the individual samples. A single sample, CHI014, was included across the three batches as a technical control, but not used in further analysis. Additionally, a healthy control donor, SHD8, was excluded from further analysis upon finding lymphoma-like B cells in this sample; the HDML_bc and HDVO_bc samples were included to test an alternate cell freezing protocol, and also not used in further analysis.
Contributor(s) Liu C, Martins AJ, Lau WW, Rachmaninoff N, Chen J, Imberti L, Mostaghimi D, Fink DL, Burbelo PD, Dobbs K, Delmonte OM, Bansal N, Failla L, Sottini A, Quiros-Roldan E, Han KL, Sellers BA, Cheung F, Sparks R, Chun T, Moir S, Lionakis M, Rossi C, NIAID-COVID-Consortium *, COVID-Clinicians *, Su HC, Kuhns DB, Notarangelo LD, Tsang JS
Citation(s) 33713619
Liu et. al. Time-resolved Systems Immunology Reveals a Late Juncture Linked to Fatal COVID-19. Cell. 2021.
Submission date Nov 20, 2020
Last update date Mar 17, 2021
Contact name Andrew James Martins
Phone 3017615289
Organization name National Institute of Allergy and Infectious Diseases
Department Laboratory of Immune System Biology
Lab Systems Genomics and Bioinformatics
Street address 4 Memorial Drive
City Bethesda
State/province Maryland
ZIP/Postal code 20892
Country USA
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (241)
GSM4929065 Batch 1 PBMC 10x Lane 1 CSP
GSM4929066 Batch 1 PBMC 10x Lane 2 CSP
GSM4929067 Batch 1 PBMC 10x Lane 3 CSP
BioProject PRJNA680293
SRA SRP293783

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE161918_AllBatches_SeuratObj.rds.gz 5.4 Gb (ftp)(http) RDS
GSE161918_B1TCR_filtered_contig_annotations.csv.gz 2.6 Mb (ftp)(http) CSV
GSE161918_B1bulkRNAseq_countmtx.csv.gz 1.0 Mb (ftp)(http) CSV
GSE161918_B2GSE161918_B3bulkRNAseq_countmtx.csv.gz 2.1 Mb (ftp)(http) CSV
GSE161918_B2TCR_filtered_contig_annotations.csv.gz 15.8 Mb (ftp)(http) CSV
GSE161918_B3TCR_filtered_contig_annotations.csv.gz 14.1 Mb (ftp)(http) CSV
GSE161918_RAW.tar 3.1 Gb (http)(custom) TAR (of H5)
GSE161918_allbatches.HTOandTimepointMetadata.csv.gz 2.5 Kb (ftp)(http) CSV
GSE161918_demuxletResults.tar.gz 71.2 Mb (ftp)(http) TAR
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Processed data provided as supplementary file
Raw data are available in SRA
Processed data are available on Series record

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