← BioTransfer GEO Dataset Finder
GEO series

Modulation of host gene expression by the zinc finger antiviral protein [RNA-seq]

GSE274578 Mus musculus (mouse) RNA-seq (gene expression) 36 samples Submitted 2024/09/01 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 36 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
36 samples: 9 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
Modulation of host gene expression by the zinc finger antiviral proteinProceedings of the National Academy of Sciences of the United States of America · 2025
Summary (written by the submitters)
The zinc finger antiviral protein (ZAP) depletes non-self RNAs through recognition of their elevated CpG dinucleotide content. CpG dinucleotides are sparse in most endogenous mammalian mRNAs, but a subset might potentially be modulated by ZAP. While CpG frequency alone is insufficient to predict ZAP-regulation, we developed an algorithm using experimentally determined compositional features to predict which endogenous mRNAs may be ZAP-regulated.
Read the full summary ↓
Using ZAP-knockout mice, we demonstrate that levels of many host mRNAs that are algorithmically predicted ZAP targets are indeed increased when ZAP is absent. ZAP is interferon-inducibel and we also identify genes that are downregulated by ZAP during an innate immune response. Many ZAP-regulated gene products are extracellular matrix or of nucleosome components, whose ZAP mediated control is conserved in human cells. Overall, we provide a new tool for the prediction of ZAP target genes and reveal host mRNAs that are ZAP-regulated.
Published in
Modulation of host gene expression by the zinc finger antiviral protein
Gonçalves-Carneiro D, Mastrocola E, Lei X et al. · Proceedings of the National Academy of Sciences of the United States of America 2025 · PMID 40146858 · doi:10.1073/pnas.2420819122
This dataset
Open GSE274578 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 GSE274578_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 PRJNA1147233 and SRA study SRP526272. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40146858) ↗
Study design
9 conditions, mostly in triplicate
C-treated, 6h, biol ×6 C-treated, 12h, biol ×6 C-treated, 24h, biol ×6 ZAP+/+ C57BL/6 mouse spleen, mock-treated, 6h… ×3 ZAP-/- C57BL/6 mouse spleen, mock-treated, 6h… ×3 ZAP+/+ C57BL/6 mouse spleen, mock-treated, 12… ×3 ZAP-/- C57BL/6 mouse spleen, mock-treated, 12… ×3 ZAP+/+ C57BL/6 mouse spleen, mock-treated, 24… ×3 +1 more

Supports a between-group comparison across 36 samples.

How we read this: 9 replicated groups read from 36 sample titles; they account for 36 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

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.