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Next Generation Sequencing analysis of OC43 and EV1 viral infection on macrophage-augmented intestinal organoids following treatment with nirmatrelvir and acetate

GSE295767 Homo sapiens (human) RNA-seq (gene expression) 24 samples Submitted 2025/04/28 Platform GPL20795
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: 8 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.
Summary (written by the submitters)
The pathogenesis of enteric viral infections arises from dual mechanisms: intrinsic viral replication dynamics and dysregulated host immune-inflammatory cascades. To bridge this knowledge gap, we developed macrophage-augmented intestinal organoids (MaugOs), a physiologically relevant model engineered by co-culturing primary human intestinal organoids with autologous macrophages.
Read the full summary ↓
Using this platform, we interrogated five enteric viruses with distinct intestinal tropisms: Echovirus 1, Echovirus 6, Rotavirus, seasonal coronavirus OC43, and *SARS-CoV-2*. Key findings revealed that all tested viruses exhibited robust replication in MaugOs and activated canonical antiviral pathways (e.g., IFN-β/ISG15). Notably, Rotavirus, OC43, and *SARS-CoV-2* uniquely elicited inflammatory responses (IL-6/IL-8 upregulation), contrasting with the non-inflammatory phenotype of echoviruses. Mechanistically, acetate—a dominant gut microbial metabolite—dose-dependently attenuated virus-induced inflammation (NF-κB/STAT3 inhibition), while exhibiting cell-compartment-specific effects on viral replication: suppressing OC43 replication in macrophages but enhancing it in organoids. Furthermore, we established a combinatorial therapeutic strategy in MaugOs by pairing the antiviral agent nirmatrelvir with either anti-inflammatory drugs or acetate, achieving dual suppression of viral load (↓90%) and cytokine storm (IL-6/IL-8 ↓70%). These results position MaugOs as a transformative platform for 1) dissecting spatial virus-immune-epithelial interactions and 2) accelerating drug discovery targeting both viral pathogenesis and immunopathology.
This dataset
Open GSE295767 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 GSE295767_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 PRJNA1256333 and SRA study SRP581743. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
8 conditions, mostly in triplicate
mo ×3 eo ×3 oo ×3 mm ×3 em ×3 om ×3 mco ×3 eco ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 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
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.