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| Status |
Public on Nov 26, 2021 |
| Title |
Single-cell RNA-sequencing reveals pervasive but highly cell type-specific genetic ancestry effects on the response to viral infection |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Humans show remarkable variation in susceptibility to infectious diseases as well as chronic inflammatory and autoimmune disorders. This heterogeneity arises partially from variation in the immune response, which is responsible for preventing and controlling infection. To better understand the major factors driving antiviral immune response differences, we used single-cell RNA-sequencing to measure the effects of genetic ancestry and cis-regulatory variation on the transcriptional response to influenza infection in various immune cell types in 90 European and African American individuals. We show that monocytes are the most responsive to infection but that all cell types engage a conserved, type I IFN response, which is stronger in European individuals. Further, we detect directional, polygenic differences in expression phenotypes between populations that are under cis-genetic control and show that recent positive selection has acted on putatively causal risk loci associated with common autoimmune disorders. Our findings establish genetic ancestry and common cis-regulatory variants as important determinants governing the antiviral immune response, thus improving our understanding of the factors that contribute to differences in infectious and complex disease susceptibility.
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| Overall design |
Multiplexed single-cell RNA expression profiles of control (mock-infected) and influenza A virus (IAV)-infected peripheral blood mononuclear cells (PBMCs) collected from African and European American individuals
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| Contributor(s) |
Randolph HE, Fiege JK, Thielen BK, Cobb MS, Batista-Barroso J, Langlois RA, Barreiro LB |
| Citation(s) |
34822289 |
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| Submission date |
Dec 03, 2020 |
| Last update date |
Nov 10, 2022 |
| Contact name |
Luis B Barreiro |
| E-mail(s) |
[email protected]
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| Organization name |
University of Chicago
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| Lab |
Barreiro Lab
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| Street address |
900 E 57th Street
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| City |
Chicago |
| ZIP/Postal code |
60637 |
| Country |
USA |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (292)
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| Relations |
| BioProject |
PRJNA682434 |
| SRA |
SRP295709 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE162632_RAW.tar |
788.9 Mb |
(http)(custom) |
TAR (of MTX, TSV) |
| GSE162632_bulk_PBMCs.Homo_sapiens_with_flu.GRCh38.kallisto.gene_level.ScaledTPM.txt.gz |
22.0 Mb |
(ftp)(http) |
TXT |
| GSE162632_time_course_PBMCs.Homo_sapiens_with_flu.GRCh38.kallisto.gene_level.ScaledTPM.txt.gz |
9.5 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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