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An ITGA11 expressing subpopulation as predictor for the donor-specific osteogenic capacity of stromal cells

GSE317531 Homo sapiens (human) RNA-seq (gene expression) 56 samples Submitted 2026/03/02 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 56 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
56 samples: 9 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.
Summary (written by the submitters)
Stromal progenitor cells of bone marrow origin are non-hematopoietic cells that give rise to osteoblasts and adipocytes in the postnatal organism. Marrow stromal cells (also known as mesenchymal stem cells - MSCs) are currently being employed in a large number of clinical trials for regenerative purposes post in vitro expansion. However, the clinical outcome has been variable, which might in part be due to the heterogeneity of the cells and the lack of a defined cell product with a molecular signature that favors tissue regeneration.
Read the full summary ↓
In this study, we determined the cellular heterogeneity of primary stromal cultures and examined how inter-donor variation in subpopulation composition contributes to the differentiation potential of primary cultures. We profiled 136,014 stromal progenitors from 26 donors and identified 5 subpopulations that were linked to distinct bone-related pathways and genetic traits of bone mineral density and morphology. Abundancy of one cluster characterized by high expression of ITGA11 (integrin alpha-11) and genes related to matrix function, collagen organization, and elevated expression upon lineage commitment was positively correlated with osteoblastic differentiation capacity in vitro. In addition, ITGA11 protein expression in progenitor cells was a predictive marker for matrix mineralization in vitro and ectopic bone formation in vivo. Sorting stromal progenitors into ITGA11high and ITGA11low cells established cultures with high and low osteoblastic differentiation potential and revealed transcriptional differences reflective of the subpopulation-specific signature, which was not affected by siRNA mediated knockdown of ITGA11 expression. Our findings corroborate the presence of an extensive donor-dependent cellular heterogeneity that persists in cultured stromal cells, and that ITGA11 can be employed as a marker for isolating cells with high bone-forming potential, a feature likely to benefit clinical trials of bone regeneration.
This dataset
Open GSE317531 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 GSE317531_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 PRJNA1414428 and SRA study SRP666391. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
9 conditions, mostly in duplicate
Primary stromal cells, undifferentiated, dono… ×14 Primary stromal cells, undifferentiated, dono… ×6 Primary stromal cells, undifferentiated, dono… ×5 Primary stromal cells, undifferentiated, cont… ×2 Primary stromal cells, undifferentiated, ITGA… ×2 Primary stromal cells, undifferentiated, ITGA… ×2 Primary stromal cells, undifferentiated, ITGA… ×2 Primary stromal cells, undifferentiated, ITGA… ×2 +20 more

Supports a between-group comparison across 37 samples.

How we read this: 9 replicated groups read from 56 sample titles; they account for 37 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

+ 16 more — browse all 56 samples with per-sample file links →

Datasets on a similar topic

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