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Transcriptional plasticity of stromal cells amplifies their differentiation efficiency in vitro

GSE288316 Homo sapiens (human) Single-cell RNA-seq 51 samples Submitted 2026/02/03 Platform GPL24676
At a glance

Single-cell RNA-seq · human · 51 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
51 samples: 17 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.
Summary (written by the submitters)
Human bone marrow-derived stromal cells (also termed mesenchymal stem cells or MSCs) are progenitors capable of differentiating into bone-forming osteoblasts and fat-storing adipocytes. Due to the loss of bone mass being associated with increased marrow fat, the trans-differentiation of osteoblasts into adipocytes has been hypothesized as a contributor to osteoporotic bone loss and fragility.
Read the full summary ↓
Reprogramming of transcriptional networks is a prerequisite for cellular differentiation, however, to which extent cell-type specific transcriptional networks modulate cellular plasticity within stromal cells remains unknown. In this study, we performed global gene expression analysis at the single cell level in immortalized human stromal cells from bone marrow (hBMSC-TERT4) that were repeatedly exposed to osteogenic and adipogenic inducers in vitro. Surprisingly, cell-type specific gene networks are not suppressive but rather promote the development of an opposing phenotype; for example, osteoblast differentiation of adipogenic pre-stimulated stromal cells is enhanced compared to undifferentiated ones. This is supported by the presence of cells simultaneously showing an osteogenic and adipogenic phenotype highlighting a strong molecular plasticity of transcriptional networks in stromal cells. These observations provide a strong molecular support for the notion of not only progenitor speciation but also the plasticity of differentiated cells contributing to the balance of bone mass and marrow fat content.
This dataset
Open GSE288316 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 GSE288316_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 PRJNA1216910 and SRA study SRP560548. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
17 conditions, mostly in triplicate
hBMSC-TERT4 cells, day 0, ×3 hBMSC-TERT4 cells, Ob 4 hrs, ×3 hBMSC-TERT4 cells, Ob 1 day, ×3 hBMSC-TERT4 cells, Ad 1 day, ×3 hBMSC-TERT4 cells, Ob 3 days, ×3 hBMSC-TERT4 cells, Ad 3 days, ×3 hBMSC-TERT4 cells, Ob 7 days, ×3 hBMSC-TERT4 cells, Ad 7 days, ×3 +16 more

Supports a between-group comparison across 44 samples.

How we read this: 17 replicated groups read from 51 sample titles; they account for 44 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

+ 11 more — browse all 51 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

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