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Series GSE241292 Query DataSets for GSE241292
Status Public on May 23, 2024
Title SARS-CoV-2-infected human nasal epithelial air-liquid interface cultures
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Continuous assessment of the impact of SARS-CoV-2 on the host at the cell-type level is crucial for understanding key mechanisms involved in host defense responses to viral infection. We investigated host response to ancestral-strain and Alpha-variant SARS-CoV-2 infections within air-liquid-interface human nasal epithelial cells from younger adults (26-32 Y) and older children (12-14 Y) using single-cell RNA-sequencing. Ciliated and secretory-ciliated cells formed the majority of highly infected cell-types, where the latter derived from ciliated lineages. Strong innate immune responses were observed across lowly-infected and un-infected bystander cells and heightened in Alpha-infection. Alpha highly-infected cells showed increased expression of protein-refolding genes compared with ancestral-strain-infected cells in children. Furthermore, oxidative phosphorylation-related genes were down-regulated in bystander cells versus infected and mock-control, underscoring the importance of these biological functions for viral replication. Overall, this study highlights the complexity of cell-type-, age- and viral strain-dependent host epithelial responses to SARS-CoV-2.
 
Overall design Nasal epithelial ALI-cultures from three human adult and child donors (12-14 years) were infected with one of two strains of SARS-CoV-2 (ancestral strain VIC01, Alpha variant VIC17991).
Single-cell RNA-sequencing with 10X Chromium coupled with Illumina sequencing was carried out with infected samples harvested at 72 hpi with ancestral strain (VIC01) and Alpha variant (VIC17991) and also 48 hpi of the ancestral strain (VIC01). Mock-controls were also sequenced. Count matrices were produced using Cellranger and the cells from the three donors (per age-group) were demultiplexed using genotyping information. Differential expression analysis using pseudo-bulking was carried out using edgeR and limma-voom.
 
Contributor(s) Chang JJ, Grimley SL, Tran BM, Deliyannis G, Tumpach C, Nguyen AN, Zhang J, Schröder J, Caly L, McAuley J, Wong SL, Stinear TP, Pitt ME, Purcell D, Vincan E, Coin LJ
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BioProject PRJNA956316
Submission date Aug 21, 2023
Last update date May 24, 2024
Contact name Jessie Jie-Youen Chang
Organization name The Peter Doherty Institute at The University of Melbourne
Street address 792 Elizabeth Street
City Melbourne
ZIP/Postal code 3000
Country Australia
 
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (16)
GSM7720737 Illumina_MS_UK_72_adult_FASTQ
GSM7720738 Illumina_MS_uninfected_adult_FASTQ
GSM7720739 Illumina_MS_VIC01_72_adult_FASTQ

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
GSE241292_RAW.tar 2.1 Gb (http)(custom) TAR (of BEST, MTX, TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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