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Investigation of gene expression changes in normal human dermal fibroblasts after exposure to bone marrow mesenchymal stromal cell secretome

GSE251807 Homo sapiens (human) RNA-seq (gene expression) 32 samples Submitted 2025/06/16 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 32 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
32 samples: 5 conditions, mostly with about 8 replicates eachGroups 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
Small extracellular vesicles from human bone marrow mesenchymal stromal cells enhance migration and regulate reparative gene expression in dermal fibroblastsScientific reports · 2025
Summary (written by the submitters)
Mesenchymal stromal cells (MSCs) are been widely investigated in clinical trials for several clinical conditions. It is known that these cells do not promote their effects by engrafment and differentiation, as they die shortly after intravenous administration. Extracellular vesicles (EVs) are membrane bound particles that carry bioactive lipids, peptides and nucleic acids and act in cell-cell communication.
Read the full summary ↓
The aim of this study is to determine the transcriptomic effects of exposure of dermal fibroblasts to fractions of bone marrow MSCs, including conditioned medium (CM), non-small extracellular vesicles (NsEV), small extracellular vesicles (sEVs) and depleted medium (DM). Differential gene expression and gene ontology analysis showed that there enrichment of pathways related to migration and genes within the regulation of cell population proliferation pathway had their expression changed after exposure to MSC-sEVs. This indicates that MSC secretome promotes targeted gene expression change that can be of particular interest in wound healing studies and clinical trials.
Published in
Small extracellular vesicles from human bone marrow mesenchymal stromal cells enhance migration and regulate reparative gene expression in dermal fibroblasts
Lei R, da Silva TB, Cui Z et al. · Scientific reports 2025 · PMID 40461530 · doi:10.1038/s41598-025-04057-6
This dataset
Open GSE251807 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 GSE251807_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 PRJNA1055484 and SRA study SRP479494. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40461530) ↗
Study design
5 conditions, mostly with about 8 replicates each
DMEM ×8 EV ×8 NEXO ×8 CM ×4 DM ×4

Supports a between-group comparison across 32 samples.

How we read this: 5 replicated groups read from 32 sample titles; they account for 32 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.