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5-Formylcytosine Is Not a Prevalent RNA Modification in Mammalian Cells

GSE288507 Mus musculus (mouse) RNA-seq (gene expression) 73 samples Submitted 2025/10/21 Platform GPL19057Platform GPL30172Platform GPL34290Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 73 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
73 samples: 24 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
5-Formylcytosine is not a prevalent RNA modification in mammalian cellsNature communications · 2025
Summary (written by the submitters)
The RNA modification 5-formylcytidine (f5C) is poorly explored in mammals. Low f5C levels reported in mRNA may reflect spurious 5-methylcytidine (m5C) oxidation or targeted demethylation by TET or ALKBH1 dioxygenases. Here we analyze f5C in RNA of mouse embryonic stem cells (mESCs) using LC-MS/MS and chemical-assisted sequencing. We reveal that the previously reported pyridine-borane-sequencing method misidentifies N4-acetylcytidine (ac4C) and unmodified, hyper-reactive cytidines in a CUMC context as f5C.
Read the full summary ↓
To overcome these limitations, we developed FIBo-seq with enhanced specificity and sensitivity for f5C-sequencing. We find no evidence for a role of TET enzymes in generating f5C, unlike for ALKBH1. Moreover, no f5C sites are detectable in mRNA. Instead, the bulk of mammalian f5C resides in the well-established mitochondrial tRNA Methionine (mt-tRNAMet) and is mediated by ALKBH1. The results argue against an instructive function for f5C outside tRNA in mammals. This SuperSeries is composed of the SubSeries listed below.
Published in
5-Formylcytosine is not a prevalent RNA modification in mammalian cells
Dehnen JA, Gopanenko AV, Scholz C et al. · Nature communications 2025 · PMID 41219180 · doi:10.1038/s41467-025-66090-3
This dataset
Open GSE288507 in finder → Find more mouse 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 GSE288507_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 PRJNA1217884 and SRA study SRP560774. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41219180) ↗
Study design
24 conditions, mostly in triplicate
mESC Tet1/2/3 CTRL, RIP, PyBo, clone6, ×3 mESC Tet1/2/3 CTRL, RIP, mock, clone ×3 mESC Tet1/2/3 CTRL, Input, PyBo, clone4, ×3 mESC Tet1/2/3 CTRL, Input, PyBo, clone6, ×3 mESC Tet1/2/3 TKO, RIP, PyBo, clone26, ×3 mESC Tet1/2/3 TKO, RIP, PyBo, clone29, ×3 mESC Tet1/2/3 TKO, RIP, mock, clone ×3 mESC Tet1/2/3 TKO, Input, PyBo, clone26, ×3 +22 more

Supports a between-group comparison across 67 samples.

How we read this: 24 replicated groups read from 73 sample titles; they account for 67 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

+ 33 more — browse all 73 samples with per-sample file links →

Datasets on a similar topic

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