GEO series

Feeder-free culture of naive human pluripotent stem cells retaining embryonic, extraembryonic and blastoid generation potential [RNA-Seq]

GSE284368 Homo sapiens (human) RNA-seq (gene expression) 10 samples Submitted 2025/12/22 Platform GPL30173Platform GPL18573

At a glance

RNA-seq (gene expression) · human · 10 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: 10 samples: 5 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.
Paper: Serum coating enables feeder-free culture of naive human pluripotent stem cells preserving developmental potentialThe EMBO journal · 2026

Summary (written by the submitters)

Conventional human pluripotent stem cells (hPSCs) are widely used to study early embryonic development, generate somatic cells, and model diseases, with differentiation potential aligned to a post-implantation epiblast identity. In the past decade, naive hPSCs, representing a pre-implantation stage, have been derived, exhibiting broader differentiation potential, including embryonic and extraembryonic lineages such as trophectoderm, primitive endoderm, and extraembryonic mesoderm.

Read the full summary ↓

Naive hPSCs can also self-organize into blastocyst-like structures called blastoids. However, their culture typically relies on mouse embryonic fibroblasts (MEFs), which are variable, resource-intensive, and can contaminate analyses. We report the long-term maintenance of naive hPSCs in a feeder-free, serum-coated system. Growth rate, clonogenicity, and gene expression profiles on serum coating were comparable to MEF-based cultures, but serum coating minimised fibroblast contamination. Naive hPSCs cultured on serum exhibited faster exit from pluripotency, more efficient germ layer specification, and retained trophectoderm potential with high blastoid formation efficiency. Exome sequencing revealed fewer mutations in serum-cultured cells, and mass spectrometry identified extracellular matrix proteins like vitronectin, fibronectin, and collagens in the serum coating. Overall, serum coating offers a scalable, cost-effective alternative for naive hPSC culture, maintaining developmental potential, reducing DNA mutations, and eliminating MEF-related confounding factors. We believe serum coating will expand the use of naive hPSCs to large-scale studies and mechanistic insights of developmental and disease modelling.

Published in

Serum coating enables feeder-free culture of naive human pluripotent stem cells preserving developmental potential

Rossignoli G, Oberhuemer M, Brun IS et al. · The EMBO journal 2026 · PMID 41820618 · doi:10.1038/s44318-026-00714-2

This dataset

Open GSE284368 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 GSE284368_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 PRJNA1198900 and SRA study SRP551747. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41820618) ↗

Study design

5 conditions, mostly in duplicate

HPD06 on MEFs, RNA-Seq, ×2 HPD06_on serum, RNA-Seq, ×2 HPD03 on MEFs, RNA-Seq, ×2 HPD03 on serum, RNA-Seq, ×2 Shef6 on serum, RNA-Seq, ×2

Supports a between-group comparison across 10 samples.

How we read this: 5 replicated groups read from 10 sample titles; they account for 10 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

GSM8682886 HPD06 on MEFs, RNA-Seq, Replicate 1 HPD06 on MEFs, RNA-Seq,
GSM8682887 HPD06 on MEFs, RNA-Seq, Replicate 2 HPD06 on MEFs, RNA-Seq,
GSM8682888 HPD06_on serum, RNA-Seq, Replicate 1 HPD06_on serum, RNA-Seq,
GSM8682889 HPD06_on serum, RNA-Seq, Replicate 2 HPD06_on serum, RNA-Seq,
GSM8682890 HPD03 on MEFs, RNA-Seq, Replicate 1 HPD03 on MEFs, RNA-Seq,
GSM8682891 HPD03 on MEFs, RNA-Seq, Replicate 2 HPD03 on MEFs, RNA-Seq,
GSM8682892 HPD03 on serum, RNA-Seq, Replicate 1 HPD03 on serum, RNA-Seq,
GSM8682893 HPD03 on serum, RNA-Seq, Replicate 2 HPD03 on serum, RNA-Seq,
GSM8682894 Shef6 on serum, RNA-Seq, Replicate 1 Shef6 on serum, RNA-Seq,
GSM8682895 Shef6 on serum, RNA-Seq, Replicate 2 Shef6 on serum, RNA-Seq,

Datasets on a similar topic

GSE324673 Feeder-Free Generation of Lymphatic Endothelial Cells from Human Induced Pluripotent Stem Cells 15 samples shares feeder-free, pluripotent, generation
GSE269571 Generation of Stable Chambered Cardioids from human Pluripotent Stem Cells [bulk RNA-seq] 24 samples shares pluripotent, generation
GSE216593 Generation of megakaryocytes and functional platelets from human embryonic stem cells 18 samples shares generation, embryonic
GSE334362 Generation of spermatogonia from human and non-human primate pluripotent stem cells 21 samples shares pluripotent, generation
GSE262419 Informing Hazard Identification and Risk Characterization of Environmental Chemicals by Combining Transcriptomic and Functional Data from Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes 4558 samples shares pluripotent
GSE226482 Single cell RNA sequencing of spinal motor neurons and interneurons differentiated from isogenic FUS and TARDBP human induced pluripotent stem cell lines harbouring ALS-causative mutations 1415 samples shares pluripotent
GSE261648 Unraveling Novel Drug candidate for ALS through an Integrative Network Analysis of approved Drug-Gene Expression Signatures in Human Pluripotent Stem Cell-Based Model 151 samples shares pluripotent
GSE272333 TOWARDS THE GENERATION OF A LASER CAPTURE MICRODISSECTION-BASED HUMAN ANAGEN HAIR FOLLICLE TRANSCRIPTOME ATLAS 110 samples shares generation

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.