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Therapeutic application of circular RNA aptamers in a mouse model of psoriasis

GSE248680 synthetic construct; Mus musculus RNA-seq (gene expression) 40 samples Submitted 2024/03/04 Platform GPL26526Platform GPL24247
At a glance

RNA-seq (gene expression) · synthetic construct; Mus musculus · 40 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
synthetic construct; Mus musculus
Samples
40 samples: 15 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
Therapeutic application of circular RNA aptamers in a mouse model of psoriasisNature biotechnology · 2025
Summary (written by the submitters)
Efforts to advance RNA aptamers as a novel therapeutic modality have been limited by their susceptibilty to degradation and immunogenicity. In a previous study, we demonstrated synthesized double-stranded circular RNAs (ds-cRNAs) with minimal immunogenicity targeted to dsRNA-activated Protein Kinase R (PKR). Here, we test the therapeutic potential of ds-cRNAs in a mouse model of imiquimod-induced psoriasis.
Read the full summary ↓
We find that genetic supplementation of ds-cRNAs leads to inhibition of PKR, resulting in alleviation of downstream interferon alpha (IFNα)/dsRNA signals and attenuation of psoriasis phenotypes. Delivery of ds-cRNAs by lipid nanoparticles to the spleen attenuates PKR activity in examined splenocytes, resulting in reduced epidermal thickness. These findings suggest that ds-cRNAs represent a promising approach to mitigate excessive PKR activation for therapeutic purposes.
Published in
Therapeutic application of circular RNA aptamers in a mouse model of psoriasis
Guo SK, Liu CX, Xu YF et al. · Nature biotechnology 2025 · PMID 38653797 · doi:10.1038/s41587-024-02204-4
This dataset
Open GSE248680 in finder → Find more 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 GSE248680_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 PRJNA1045575 and SRA study SRP474428. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38653797) ↗
Study design
15 conditions, mostly in duplicate
WT mouse with 0 day IMQ treatment ,repeat ×2 WT mouse with 1 day IMQ treatment ,repeat ×2 WT mouse with 2 days IMQ treatment ,repeat ×2 WT mouse with 5 days IMQ treatment ,repeat ×2 PKR KO mouse with 0 day IMQ treatment ,repeat ×2 PKR KO mouse with 1 day IMQ treatment ,repeat ×2 PKR KO mouse with 2 days IMQ treatment ,repeat ×2 PKR KO mouse with 5 days IMQ treatment ,repeat ×2 +17 more

Supports a between-group comparison across 30 samples.

How we read this: 15 replicated groups read from 40 sample titles; they account for 30 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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