GEO series

Transcriptomic analysis of Multicellular spheroids from 10 Ehlers-Danlos SYndrome (EDS) patients.

GSE270410 Homo sapiens (human) RNA-seq (gene expression) 14 samples Submitted 2025/06/10 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 14 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: 14 samples: 14 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: Multi-OMICs analysis on tridimensional fibroblast spheroids to model vascular Ehlers-Danlos syndrome pathogenesisBiochimica et biophysica acta. Molecular basis of disease · 2025

Summary (written by the submitters)

Multicellular spheroid from 10 Ehlers-Danlos SYndrome (EDS) patients were used to perform transcritomic experiment. These were compared to 4 control healty samples with the aim to identify dysregulated genes and pathways and to use this information to propose potential drugs that could be repurposed for the treatment, based on computational approaches to drug repositioning.In summary, this comprehensive study expands our understanding of the molecular basis of Ehlers-Danlos syndrome, particularly relating to COL3A1 mutations.

Read the full summary ↓

The integration of transcriptomic analysis, pathway studies, and drug repurposing strategies provides a robust framework for identifying potential therapeutic strategies for EDS.

Published in

Multi-OMICs analysis on tridimensional fibroblast spheroids to model vascular Ehlers-Danlos syndrome pathogenesis

Micale L, Di Muro E, De Cegli R et al. · Biochimica et biophysica acta. Molecular basis of disease 2025 · PMID 40345454 · doi:10.1016/j.bbadis.2025.167896

This dataset

Open GSE270410 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 GSE270410_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 PRJNA1126320 and SRA study SRP515092. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40345454) ↗

Study design

14 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 14 sample titles: 14 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

GSM8342164 C1A_3D
GSM8342165 C2B_3D
GSM8342166 C3B_3D
GSM8342167 RR_3D
GSM8342168 GAU_3D
GSM8342169 VL_3D
GSM8342170 19_1597_3D
GSM8342171 SF_3D
GSM8342172 22_0548_3D
GSM8342173 20_4456_3D
GSM8342174 20_A222_3D
GSM8342175 20_3156_3D
GSM8342176 20_3154_3D
GSM8342177 22_0547_3D

Datasets on a similar topic

GSE270199 Transcriptomic analysis of fibroblast from 10 Ehlers-Danlos SYndrome (EDS) patients. 14 samples shares eds, ehlers-danlos
GSE277910 10 Ehlers-Danlos SYndrome (EDS) patients 28 samples shares eds, ehlers-danlos
GSE278813 Intervertebral disc spheroids as an in vitro multicellular platform for recapitulating the microenvironment of intervertebral disc degeneration 3 samples shares multicellular, spheroids
GSE248105 Transcriptional profiling sheds light on the cellular and fibrotic aspects of idiopathic subglottic tracheal stenosis 5 samples shares eds
GSE295854 Single nucleus analysis of post-mortem brain tissues from Adult-onset leukoencephalopathy with axonal spheroids and pigmented glia (ALSP) patients 29 samples shares spheroids
GSE99951 Maturation of Human iPSC-derived Astrocytes in 3D Cortical Spheroids 730 samples shares spheroids
GSE247455 Single-nucleus chromatin and gene expression profiling across hundreds of skeletal muscle samples reveals context-specific regulation 8 samples shares eds
GSE311065 RNA seq analysis comparing uninfected to MCPyV-infected 2D monolayer or 3D spheroids 12 samples shares spheroids

Search all human RNA-seq datasets in GEO →

Share this dataset

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.