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m6Am methyltransferase PCIF1 regulates osteogenesis via WNT signaling

GSE324998 Homo sapiens (human) Single-cell RNA-seq 14 samples Submitted 2026/03/19 Platform GPL24676
At a glance

Single-cell RNA-seq · human · 14 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Homo sapiens (human)
Samples
14 samples: 14 × Human femoral head, osteoarthritis, donoGroups 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
The m6Am methyltransferase PCIF1 promotes osteogenic differentiation of mesenchymal stem cells through stabilization of Wnt-related transcriptsPLoS biology · 2026
Summary (written by the submitters)
Skeletal development depends on the self-renewal and differentiation of MSCs. Emerging research underscores the regulatory functions of RNA methylation on bone homeostasis. Here, we show PCIF1, the N6,2′-O-dimethyladenosine (m6Am) methyltransferase, is essential for maintaining bone mass and promoting osteogenic differentiation of MSCs.
Read the full summary ↓
Multiple complementary analyses—including GWAS, TWAS, and single-cell transcriptomics—collectively point to PCIF1 as a regulator of human bone mineral traits and a marker of early mesenchymal stem cells. Global or MSC-specific Pcif1 deletion elicits osteoporotic pathology in mice, although myeloid cell-specific Pcif1 knockout does not induce femur bone alternation alterations. Mechanistically, Pcif1 knockout decreases m6Am signals of Wnt-related genes (Wnt11, Fzd4, Fgfr2) and accelerates mRNA degradation. This down-regulates active β-Catenin protein, and thus impairs osteogenic function of MSCs. Additionally, the WNT agonist attenuates the osteoporosis-like phenotype induced by Pcif1 deletion. These findings highlight the crucial role of PCIF1-mediated m6Am modification in regulating osteogenesis and suggest potential therapeutic implications for bone disorders.
Published in
The m6Am methyltransferase PCIF1 promotes osteogenic differentiation of mesenchymal stem cells through stabilization of Wnt-related transcripts
Song W, Su KJ, Pan Z et al. · PLoS biology 2026 · PMID 41941537 · doi:10.1371/journal.pbio.3003739
This dataset
Open GSE324998 in finder → Find more human 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 GSE324998_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 PRJNA1438204 and SRA study SRP684133. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41941537) ↗
Study design
14 × Human femoral head, osteoarthritis, dono

Supports a between-group comparison across 14 samples.

How we read this: 1 replicated groups read from 14 sample titles; they account for 14 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

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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.