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SARS-CoV-2 infection of human lung ALI cultures reveals basal cells as relevant targets

GSE272756 Homo sapiens (human) Single-cell RNA-seq 54 samples Submitted 2025/10/01 Platform GPL24676
At a glance

Single-cell RNA-seq · human · 54 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Homo sapiens (human)
Samples
54 samples: 12 conditions, mostly with about 6 replicates eachGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper
SARS-CoV-2 Infection of Human Lung Air-Liquid Interface Cultures Reveals Basal Cells as Relevant TargetsThe Journal of infectious diseases · 2025
Summary (written by the submitters)
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) primarily targets ciliated cells during the initial infection of the upper respiratory tract, although uncertainties persist regarding other involved epithelial cell types. Herein, we utilized viral replication analysis, single-cell RNA sequencing, and spectral microscopy on infected air-liquid interface cultures of human primary nasal and bronchial epithelial cells to discern cell type proportions in relation to SARS-CoV-2 tropism and immune activation.
Read the full summary ↓
We revealed that, alongside ciliated and secretory cells, SARS-CoV-2 (wildtype and lineage B1.1.7 [Alpha variant]) strongly infects basal cells, significantly contributing to the epithelial immune response in a donor-specific manner. Moreover, local Camostat mesylate treatment was effective on both the basal and apical cell compartment, resulting in a notable reduction in viral load and reduced immune activation. Collectively, our data emphasize the critical role of basal cells in facilitating SARS-CoV-2 dissemination within the upper respiratory tract and their substantial contribution to the epithelial immune response. Furthermore, our results highlight the potential of local application of Camostat mesylate as an effective strategy for early inhibiting SARS-CoV-2 infection and mitigating associated immune activation.
Published in
SARS-CoV-2 Infection of Human Lung Air-Liquid Interface Cultures Reveals Basal Cells as Relevant Targets
Baumgardt M, Obermayer B, Balázs A et al. · The Journal of infectious diseases 2025 · PMID 40065723 · doi:10.1093/infdis/jiaf125
This dataset
Open GSE272756 in finder → Find more human RNA-seq datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE272756_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1138675. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40065723) ↗
Study design
12 conditions, mostly with about 6 replicates each
untreated, mock-infected primary nasal epithe… ×6 Camostattreated, mock-infected primary nasal … ×6 untreated, SARS-CoV-2-infected primary nasal … ×6 Camostattreated, SARS-CoV-2-infected primary … ×6 untreated, SARS-CoV-2(B1.1.7)-infected primar… ×6 Camostattreated, SARS-CoV-2(B1.1.7)-infected … ×6 untreated, mock-infected primary bronchial ep… ×3 Camostattreated, mock-infected primary bronch… ×3 +4 more

Supports a between-group comparison across 54 samples.

How we read this: 12 replicated groups read from 54 sample titles; they account for 54 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

+ 14 more — browse all 54 samples with per-sample file links →

Datasets on a similar topic

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.