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Disc-Derived Induced Pluripotent Stem Cells and Environmental Cues for Nucleus Pulposus Regeneration

GSE273124 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2025/11/24 Platform GPL30173
At a glance

RNA-seq (gene expression) · human · 12 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
12 samples: 3 × PBMC-NCM vs 3 × PBMC-TGF vs 3 × TIE2-NCM vs 3 × TIE2-TGFGroups 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
Disc-Derived Induced Pluripotent Stem Cells and Environmental Cues for Nucleus Pulposus RegenerationTissue engineering. Part A · 2026
Summary (written by the submitters)
Notochordal cells (NCs) are linked to a healthy state of the nucleus pulposus (NP) and are therefore considered a promising candidate for cell-based regenerative therapies. However, NCs are scarcely available as they are lost early in life, and attempts at in vitro expansion have failed because NCs lose their specific phenotype. The generation of notochordal-like cells (NLCs) from human induced pluripotent stem cells (hiPSCs) is considered a viable alternative.
Read the full summary ↓
Therefore, this study aimed to build on the instructive capacity of decellularized notochordal cell-derived matrix (dNCM) and the epigenetic memory of tissue-specific hiPSCs derived from TIE2+ nucleus pulposus-progenitor cells (NPPCs) to improve hiPSC differentiation towards mature, healthy matrix-producing NLCs. As a comparison, donor-matched minimally invasive peripheral blood mononuclear cell (PBMC)-derived hiPSCs were generated. The results showed that the use of tissue-specific derived hiPSCs instructed by a mix of natural cues provided by dNCM allowed for an improved differentiation capacity, indicated by the increased expression of key phenotypic and functional NC/NPC markers. Additionally, within this in vitro environment, the cell-source influenced off-target differentiation resulting in increased neural- and immune-cell fate for the PBMC-derived hiPSC lines. In the end, Understanding how in vivo microenvironmental cues will direct differentiation and maturation of the hMEPCs is imperative to refine the differentiation protocol also taking into account the hiPSC-derived NLC functionality and survival within the challenging environment of the intervertebral disc.
Published in
Disc-Derived Induced Pluripotent Stem Cells and Environmental Cues for Nucleus Pulposus Regeneration
Laagland LT, Poramba Liyanage DWL, Desprat R et al. · Tissue engineering. Part A 2026 · PMID 40644334 · doi:10.1177/19373341251359106
This dataset
Open GSE273124 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 GSE273124_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 PRJNA1140209 and SRA study SRP522235. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40644334) ↗
Study design
3 × PBMC-NCM vs 3 × PBMC-TGF vs 3 × TIE2-NCM vs 3 × TIE2-TGF

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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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