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Optimization of a Micro-scale Air-Liquid-Interface Model of Human Proximal Airway Epithelium for Moderate Throughput Drug Screening for SARS-CoV-2

GSE266907 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2025/01/22 Platform GPL21290
At a glance

RNA-seq (gene expression) · human · 12 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Homo sapiens (human)
Samples
12 samples: 3 × MKGaA#49 + virus vs 3 × Virus Only vs 3 × Mock vs 3 × Remdesivir + virusGroups 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
Optimization of a micro-scale air-liquid-interface model of human proximal airway epithelium for moderate throughput drug screening for SARS-CoV-2Respiratory research · 2025
Summary (written by the submitters)
Respiratory viruses (e.g. influenza, RSV, SARS, MERS etc.) attack the proximal airway (upper respiratory tract) and cause a wide spectrum of diseases for which we have limited therapies. To date, a few primary human stem cell-based models of the proximal airway have been reported for drug discovery but scaling them up to a high throughput platform remains a significant challenge.
Read the full summary ↓
Here we present a microscale, primary human stem cell-based proximal airway model of SARS-CoV-2 infection, which is amenable to moderate-to-high throughput drug screening. The model recapitulates the heterogeneity of infection seen among different patients and with different SARS-CoV-2 variants. Using this model, we screened 2100 compounds from targeted drug libraries. We characterized a new small molecule with antiviral properties that is effective against both Wuhan and Omicron variants
Published in
Optimization of a micro-scale air-liquid-interface model of human proximal airway epithelium for moderate throughput drug screening for SARS-CoV-2
Sen C, Rickabaugh TM, Jeyachandran AV et al. · Respiratory research 2025 · PMID 39819574 · doi:10.1186/s12931-025-03095-y
This dataset
Open GSE266907 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 GSE266907_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1108704 and SRA study SRP506419. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39819574) ↗
Study design
3 × MKGaA#49 + virus vs 3 × Virus Only vs 3 × Mock vs 3 × Remdesivir + virus

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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
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.