GEO series

Enhancement of Chikungunya virus genome replication in mammalian cells at sub-physiological temperatures

GSE264494 Mus musculus (mouse) RNA-seq (gene expression) 45 samples Submitted 2025/04/10 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 45 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: Mus musculus (mouse)
Samples: 45 samples
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.

Summary (written by the submitters)

Chikungunya virus (CHIKV) is an Alphavirus transmitted by Aedes mosquitoes, causing fever, rash and arthralgia in mammals. The function of the CHIKV non-structural protein 3 (nsP3) remains enigmatic. Building on previous studies, we generated a panel of mutants in a conserved and surface-exposed cluster in the nsP3 alphavirus unique domain (AUD) and tested their replication using a sub-genomic replicon (SGR).

Read the full summary ↓

Three of these SGR mutants replicated well in mosquito cells but poorly in mammalian cells. We observed that this difference was due to cell culture temperature (mosquito cells: 28 °C; mammalian cells: 37 °C) as the mutants exhibited no replication defect in mammalian cells grown at a sub-physiological temperature (28 °C). Similar effects were observed for infectious CHIKV and the closely related O'nyong-nyong virus. Intriguingly, the wildtype SGR replicated more efficiently in mammalian cells at 28 °C compared to 37 °C. To explore the mechanism behind this difference, we focused on two known antiviral pathways: interferon-stimulated genes (ISGs) and stress granules (SG). SGR replication correlated strongly with increased expression of ISGs at 37°C, but only weakly correlated at 28 °C. We also observed enhanced recruitment of SG proteins (G3BP, eIF4G, and TIA-1) into cytoplasmic sites of genome replication at 28 °C. These findings may have real-world implications as when a mosquito bites a mammal, the virus first infects cells in peripheral tissues which are often at sub-physiological temperatures. We propose that alphaviruses such as CHIKV have evolved mechanisms to both promote viral genome replication and concomitantly limit antiviral responses in these cells.

This dataset

Open GSE264494 in finder → Find more mouse 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 GSE264494_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 PRJNA1102705 and SRA study SRP503027. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Samples in this study

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+ 45 more — browse all 45 samples with per-sample file links →

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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.