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Transcriptome-wide mapping of N3-methylcytidine modification at single-base resolution

GSE287299 synthetic construct; Homo sapiens Single-nucleus RNA-seq 22 samples Submitted 2025/03/19 Platform GPL24676Platform GPL26526
At a glance

Single-nucleus RNA-seq · synthetic construct; Homo sapiens · 22 samples

What it is
Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue). Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
synthetic construct; Homo sapiens
Samples
22 samples: 7 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
Transcriptome-wide mapping of N3-methylcytidine modification at single-base resolutionNucleic acids research · 2025
Summary (written by the submitters)
3-Methylcytidine (m3C), a prevalent modification of tRNAs, was recently identified in eukaryotic mRNAs. However, its precise distribution and formation mechanisms in mRNAs remain elusive. Here we develop a novel approach, m3C immunoprecipitation and sequencing (m3C-IP-seq), utilizing antibody enrichment to profile the m3C methylome at single-nucleotide resolution.
Read the full summary ↓
m3C-IP-seq captures 12 m3C modification sites in cytoplasmic tRNA isoacceptors and 2 in mitochondrial tRNA isoacceptors. Moreover, m3C-IP-seq permits the comprehensive profiling of m3C sites in mRNAs and lncRNAs, with their presence reliant on a nuclear isoform of METTL8. A significant proportion of m3C sites is concentrated in the 3’ untranslated region (3’ UTR) of mRNAs. Additionally, m3C methylation is dynamic and responds to hypoxia. Functionally, m3C formation in the 3’ UTR is associated with mRNA degradation. Collectively, our data demonstrate the widespread presence of m3C modification in the human transcriptome and provide a resource for functional studies of m3C-mediated RNA metabolism.
Published in
Transcriptome-wide mapping of N3-methylcytidine modification at single-base resolution
Gao Y, Hou J, Wei S et al. · Nucleic acids research 2025 · PMID 40071931 · doi:10.1093/nar/gkaf153
This dataset
Open GSE287299 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 GSE287299_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1212065 and SRA study SRP558110. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40071931) ↗
Study design
7 conditions, mostly in duplicate
m3C ×5 tRNA_m3C_Input ×2 tRNA_m3C_IP ×2 tRNA_m3C_Dm ×2 m3C_Input ×2 m3C_IP ×2 m3C_Dm ×2 tRNA_m3C_Input-mix ×1 +4 more

Supports a between-group comparison across 17 samples.

How we read this: 7 replicated groups read from 22 sample titles; they account for 17 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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