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Hypoxia increases susceptibility of human intestinal epithelial cells to rotavirus infection through repression of interferon induction

GSE300313 Homo sapiens (human) RNA-seq (gene expression) 32 samples Submitted 2025/11/13 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 32 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
32 samples: 8 conditions, mostly with about 4 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
Hypoxia increases susceptibility of human intestinal epithelial cells to rotavirus infection through repression of interferon inductionGut microbes · 2025
Summary (written by the submitters)
Intestinal epithelial cells (IECs) serve as both a physical barrier and a source of robust antiviral interferon (IFN) response. As such, they constitute the primary barrier that enteric viruses, such as rotavirus, need to overcome to initiate infection. The gut is characterized by very low oxygen levels (hypoxia) within the lumen, resulting in a unique hypoxic physiological environment in which rotavirus infection occurs.
Read the full summary ↓
Depending on the tissues or viruses, conflicting results have been described for the role of hypoxia in regulating viral infections, where hypoxia could have either a proviral or antiviral function. Since intestinal epithelial cells naturally exist in a hypoxic environment, it is essential to investigate how these conditions affect rotavirus infection. We found that hypoxia promotes rotavirus infection, resulting in increased virus replication and production of infectious virus particles. We showed that this increased production of rotavirus particles under hypoxia is due to a decreased induction of both type I and III IFNs leading to a decreased expression of IFN stimulated genes (ISGs) and antiviral protection. RNA sequencing showed a robust decrease in ISG production in hypoxia for both rotavirus infection and poly I:C transfection, suggesting a conserved inhibition of IFN responses in hypoxia for IECs. Functional analyses revealed that hypoxia impairs signal transduction leading to IFN expression by negatively regulating the activation of the master signaling molecule TBK1. Mechanistically, we determined that hypoxia induces the expression of the protein phosphatase PP2A which is responsible for the hypoxia-induced impairment of TBK1 activation. Importantly, we observed that this hypoxia-mediated dampening of immune response was not restricted to rotavirus infection but dampened the IFN induction of a broad range of viruses and immune stimuli. Together, we propose that hypoxia creates an immune-suppressive environment through downregulation of IFN, representing a novel proviral mechanism for hypoxia in the human gastro-intestinal tract.
Published in
Hypoxia increases susceptibility of human intestinal epithelial cells to rotavirus infection through repression of interferon induction
Jacobs SO, Muenchau S, Uckeley ZM et al. · Gut microbes 2025 · PMID 40977474 · doi:10.1080/19490976.2025.2560593
This dataset
Open GSE300313 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 GSE300313_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 PRJNA1280075 and SRA study SRP593496. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40977474) ↗
Study design
8 conditions, mostly with about 4 replicates each
mock, normoxia, ×4 C transfection, 8hr, normoxia, ×4 rotavirus infection, 8hr, normoxia, ×4 rotavirus infection, 16hr, normoxia, ×4 mock, hypoxia, ×4 C transfection, 8hr, hypoxia, ×4 rotavirus infection, 8hr, hypoxia, ×4 rotavirus infection, 16hr, hypoxia, ×4

Supports a between-group comparison across 32 samples.

How we read this: 8 replicated groups read from 32 sample titles; they account for 32 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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