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Interferon signaling in the nasal epithelium distinguishes among lethal and common cold respiratory viruses and is critical for viral clearance

GSE253542 Homo sapiens (human) RNA-seq (gene expression) 26 samples Submitted 2024/03/25 Platform GPL20301
At a glance

RNA-seq (gene expression) · human · 26 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
26 samples: 6 conditions, mostly in triplicateGroups 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
Interferon signaling in the nasal epithelium distinguishes among lethal and common cold coronaviruses and mediates viral clearanceProceedings of the National Academy of Sciences of the United States of America · 2024
Summary (written by the submitters)
All respiratory viruses establish primary infections in the nasal epithelium, where efficient innate immune induction may prevent dissemination to the lower airway and thus minimize pathogenesis. Human coronaviruses (HCoVs) cause a range of pathologies, but the host and viral determinants of disease during common cold versus lethal HCoV infections are poorly understood.
Read the full summary ↓
We model the initial site of infection using primary nasal epithelial cells cultured at air-liquid interface (ALI). HCoV-229E, HCoV-NL63 and human rhinovirus-16 are common cold-associated viruses that exhibit unique features in this model: early induction of antiviral interferon (IFN) signaling, IFN-mediated viral clearance, and preferential replication at nasal airway temperature (33ºC) which confers muted host IFN responses. In contrast, lethal SARS-CoV-2 and MERS-CoV encode antagonist proteins that prevent IFN-mediated clearance in nasal cultures. Our study identifies features shared among common cold-associated viruses, highlighting nasal innate immune responses as predictive of infection outcomes and nasally-directed IFNs as potential therapeutics.
Published in
Interferon signaling in the nasal epithelium distinguishes among lethal and common cold coronaviruses and mediates viral clearance
Otter CJ, Renner DM, Fausto A et al. · Proceedings of the National Academy of Sciences of the United States of America 2024 · PMID 38758698 · doi:10.1073/pnas.2402540121
This dataset
Open GSE253542 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 GSE253542_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 PRJNA1066261 and SRA study SRP484458. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38758698) ↗
Study design
6 conditions, mostly in triplicate
Primary nasal epithelial cells, MERS-CoV infe… ×3 Primary nasal epithelial cells, HCoV-NL63 inf… ×3 Primary nasal epithelial cells, SARS-CoV-2 in… ×3 Primary nasal epithelial cells, HCoV-229E inf… ×3 Primary nasal epithelial cells, HRV-16 infect… ×3 Primary nasal epithelial cells, IAV infected,… ×2 Primary nasal epithelial cells, mock infected… ×1 Primary nasal epithelial cells, mock infected… ×1 +7 more

Supports a between-group comparison across 17 samples.

How we read this: 6 replicated groups read from 26 sample titles; they account for 17 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
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