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Repeats mimic pathogen-associated patterns across a vast evolutionary landscape [RIP-Seq]

GSE305618 Homo sapiens (human) RNA-seq (gene expression) 16 samples Submitted 2025/08/20 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 16 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
16 samples: 8 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
Repeats mimic pathogen-associated patterns across a vast evolutionary landscapeCell genomics · 2025
Summary (written by the submitters)
An emerging hallmark of many human diseases is transcription of typically silenced repetitive DNA containing pathogen-associated molecular patterns (PAMPs). These PAMPs engage the innate immune system via pattern recognition receptors (PRRs) – a phenomenon known as “viral mimicry.” We propose a statistical physics framework to quantify viral mimicry by measuring “selective forces” that enrich PAMPs compared to a genome-wide reference distribution.
Read the full summary ↓
We validate our predictions by identifying repeats that bind different PRRs and show viral mimicry in different repeat families across eukaryotic genomes, suggesting shared mechanisms drive emergence and retention. We propose two non-exclusive evolutionary hypotheses. The first ‘repeat-centric’ hypothesis posits PAMPs are integral to the repeat lifecycle and are therefore enriched as they mediate repeat expansion. The second ‘organism-centric’ hypothesis proposes viral mimicry functions as a cell-intrinsic feedback mechanism for sensing and reacting to transcriptional dysregulation, which provides a selective pressure to maintain PAMPs in genomes.
Published in
Repeats mimic pathogen-associated patterns across a vast evolutionary landscape
Šulc P, Di Gioacchino A, Solovyov A et al. · Cell genomics 2025 · PMID 40997813 · doi:10.1016/j.xgen.2025.101011
This dataset
Open GSE305618 in finder → Find more human 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 GSE305618_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 PRJNA1307287 and SRA study SRP609574. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40997813) ↗
Study design
8 conditions, mostly in duplicate
RIP-Seq, anti-ZCCHC3 antibody, 300mM salt con… ×2 RIP-Seq, anti-ZCCHC3 antibody, 500mM salt con… ×2 RIP-Seq, mock antibody, 300mM salt concentrat… ×2 RIP-Seq, mock antibody, 500mM salt concentrat… ×2 RIP-Seq, anti-ORFP1p antibody, 300mM salt con… ×2 RIP-Seq, anti-ORFP1p antibody, 500mM salt con… ×2 total RNA control, 300mM salt concentration, ×2 total RNA control, 500mM salt concentration, ×2

Supports a between-group comparison across 16 samples.

How we read this: 8 replicated groups read from 16 sample titles; they account for 16 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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