GEO series

Respiratory syncytial virus nonstructural protein 1 inhibits secretion of cytokines and chemokines by differentiated primary nasal epithelial cells cultured at air-liquid interface

GSE309353 Homo sapiens (human) RNA-seq (gene expression) 24 samples Submitted 2025/10/22 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 24 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: 24 samples: 12 conditions, mostly in duplicateGroups 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: Respiratory Syncytial Virus Nonstructural Protein 1 Inhibits Production of Cytokines and Chemokines by Differentiated Primary Nasal Epithelial Cells Cultured at Air-Liquid InterfaceJournal of innate immunity · 2026

Summary (written by the submitters)

Respiratory syncytial virus (RSV) is a major cause of severe respiratory infections in children and older adults. Several vaccines have recently been approved, which are all based on the RSV fusion (F) protein. Among the strategies to induce a broader immune response is the development of live-attenuated RSV vaccines, for example by disabling nonstructural protein 1 (NS1).

Read the full summary ↓

RSV NS1 has been found to modulate the host immune response by repression of interferon (IFN) production. However, functional characterization of this protein was mainly performed in immortalized cell lines, which do not necessarily represent the in vivo situation. Here, we assessed the effect of NS1 mutations on replication and host responses in differentiated primary human nasal epithelial cells (HNEC) cultured at air-liquid interface (ALI), which mimic several physiological properties of the human airways. Using a newly developed yeast-based RSV reverse genetics system, inactivating mutations in the NS1 gene were introduced. These mutations did not affect viral replication in Vero and A549 cells. However, in HNEC we observed a delayed replication of the NS1 mutants compared to the WT virus. Bulk RNA sequencing data from early post infection revealed a stronger antiviral signature in HNEC that were infected with NS1 mutants compared to WT, characterized by upregulation of IFN-β and IFN-λ1/2/3 and chemokines CXCL11 and CCL5. This signature was confirmed by analysis of the cytokines that were released into the HNEC basal medium. Finally, the basal medium containing these cytokines was used for an indirect immune cell migration assay. In this set-up, both WT and NS1 mutant viruses induce migration of mainly neutrophils. In conclusion, this study shows that RSV NS1 supports viral replication not only via inhibition of the production of IFNs, but also by reducing early chemokine production and secretion by epithelial cells. Furthermore, our data highlight the suitability of the ALI transwell model for preclinical assessment of live-attenuated vaccine candidates.

Published in

Respiratory Syncytial Virus Nonstructural Protein 1 Inhibits Production of Cytokines and Chemokines by Differentiated Primary Nasal Epithelial Cells Cultured at Air-Liquid Interface

Koutstaal RW, Munoz Garcia A, Ebert N et al. · Journal of innate immunity 2026 · PMID 41758737 · doi:10.1159/000550987

This dataset

Open GSE309353 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 GSE309353_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 PRJNA1335223 and SRA study SRP628144. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41758737) ↗

Study design

12 conditions, mostly in duplicate

Donor 1, mock, ×2 Donor 1, wt, ×2 Donor 1, NS-Y, ×2 Donor 1, NS-LL, ×2 Donor 2, mock, ×2 Donor 2, wt, ×2 Donor 2, NS-Y, ×2 Donor 2, NS-LL, ×2 +4 more

Supports a between-group comparison across 24 samples.

How we read this: 12 replicated groups read from 24 sample titles; they account for 24 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

GSM9266066 Donor 1, mock, rep 1 Donor 1, mock,
GSM9266067 Donor 1, mock, rep 2 Donor 1, mock,
GSM9266068 Donor 1, wt, rep 1 Donor 1, wt,
GSM9266069 Donor 1, wt, rep 2 Donor 1, wt,
GSM9266070 Donor 1, NS-Y, rep1 Donor 1, NS-Y,
GSM9266071 Donor 1, NS-Y, rep2 Donor 1, NS-Y,
GSM9266072 Donor 1, NS-LL, rep1 Donor 1, NS-LL,
GSM9266073 Donor 1, NS-LL, rep2 Donor 1, NS-LL,
GSM9266074 Donor 2, mock, rep 1 Donor 2, mock,
GSM9266075 Donor 2, mock, rep 2 Donor 2, mock,
GSM9266076 Donor 2, wt, rep 1 Donor 2, wt,
GSM9266077 Donor 2, wt, rep 2 Donor 2, wt,
GSM9266078 Donor 2, NS-Y, rep1 Donor 2, NS-Y,
GSM9266079 Donor 2, NS-Y, rep2 Donor 2, NS-Y,
GSM9266080 Donor 2, NS-LL, rep1 Donor 2, NS-LL,
GSM9266081 Donor 2, NS-LL, rep2 Donor 2, NS-LL,
GSM9266082 Donor 3, mock, rep 1 Donor 3, mock,
GSM9266083 Donor 3, mock, rep 2 Donor 3, mock,
GSM9266084 Donor 3, wt, rep 1 Donor 3, wt,
GSM9266085 Donor 3, wt, rep 2 Donor 3, wt,
GSM9266086 Donor 3, NS-Y, rep1 Donor 3, NS-Y,
GSM9266087 Donor 3, NS-Y, rep2 Donor 3, NS-Y,
GSM9266088 Donor 3, NS-LL, rep1 Donor 3, NS-LL,
GSM9266089 Donor 3, NS-LL, rep2 Donor 3, NS-LL,

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