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Functional callus organoids reveal distinct cartilage to bone transition mechanisms across donors and a role for biological sex

GSE271551 Homo sapiens (human) RNA-seq (gene expression) 15 samples Submitted 2025/03/13 Platform GPL20301
At a glance

RNA-seq (gene expression) · human · 15 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
15 samples: 15 samples, each with a distinct title — no replicated groupsGroups 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
Callus organoids reveal distinct cartilage to bone transition mechanisms across donors and a role for biological sexBone research · 2025
Summary (written by the submitters)
Engineering a cartilage tissue intermediate in vitro that closely mimics the characteristics of the native fracture callus in vivo, ensures a high potency to undergo cartilage-to-bone transition when implanted in vivo. However, there is a lack of critical quality attributes that can be defined in vitro to predict in vivo functionality across donors, which is a significant limitation for the development of autologous tissue engineered implants according to Quality by Design (QbD) principles.
Read the full summary ↓
In addition, for clinical translation, regulatory bodies require in-process biological data acquisition, preferably noninvasive, to enable closed system manufacturing. In this study, we produced cartilaginous callus organoids of 10 human donors, both male and female, assembled scaffold-free donor-specific cartilaginous implants. We found two distinct organoid morphologies and transcriptome signatures, with 6 donors (5 male, 1 female) generating hypertrophic cartilage and 4 female donors producing organoids with a fibrocartilage phenotype. This distinction was already detectable early in the differentiation process with differences in proliferation and organoid morphology, leading to differential regulation of gene panels specific for reported periosteal progenitor populations. Further, we compared the secretome of bone-forming and non-bone-forming organoids, identifying a robust panel of 83 proteins that could be measured noninvasively as potency monitoring biomarkers. These findings provide new insights in donor variability and outlines a quality-driven pathway for the translation of organoid-based tissue engineered implants. The addition of noninvasive quality metrics paves the way towards data-driven closed-system manufacturing of patient-specific living implants.
Published in
Callus organoids reveal distinct cartilage to bone transition mechanisms across donors and a role for biological sex
Decoene I, Svitina H, Hamed MB et al. · Bone research 2025 · PMID 40140357 · doi:10.1038/s41413-025-00418-z
This dataset
Open GSE271551 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 GSE271551_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 PRJNA1132207 and SRA study SRP518147. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40140357) ↗
Study design
15 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 15 sample titles: 15 distinct titles with little repetition. 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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