GEO series
Feeder-free culture of naive human PSCs preserving embryonic, extraembryonic and blastoid potential
GSE287199
Homo sapiens (human)
RNA-seq (gene expression)
38 samples
Submitted 2025/12/22
Platform GPL30173
At a glance
RNA-seq (gene expression) · human · 38 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
- 38 samples: 19 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
Rossignoli G, Oberhuemer M, Brun IS et al.
· The EMBO journal 2026
· PMID 41820618
· doi:10.1038/s44318-026-00714-2
This dataset
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.
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 GSE287199_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1211590 and SRA study SRP557860. Searching any of these in the dataset finder brings you back here.
Study design
19 conditions, mostly in duplicate
Naive serum-adapted Shef6 on serum, PXGL d0, … ×2
Naive serum-adapted Shef6 on Geltrex, PXGL d0… ×2
Naive serum-adapted Shef6 on Geltrex, N2B27 d… ×2
Naive serum-adapted Shef6 on Geltrex, N2B27 d… ×2
Naive serum-adapted Shef6 on Geltrex, N2B27 d… ×2
Naive serum-adapted Shef6 on Geltrex, N2B27 d… ×2
Naive serum-adapted Shef6 on Geltrex, N2B27 d… ×2
Naive serum-adapted Shef6 on Geltrex, E8 d2, … ×2
+11 more
Supports a between-group comparison across 38 samples.
How we read this: 19 replicated groups read from 38 sample titles; they account for 38 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
- GSM8741212 Naive serum-adapted Shef6 on serum, PXGL d0, RNA-Seq, Replicate 1 Naive serum-adapted She…
- GSM8741213 Naive serum-adapted Shef6 on serum, PXGL d0, RNA-Seq, Replicate 2 Naive serum-adapted She…
- GSM8741214 Naive serum-adapted Shef6 on Geltrex, PXGL d0, RNA-Seq, Replicate 1 Naive serum-adapted She…
- GSM8741215 Naive serum-adapted Shef6 on Geltrex, PXGL d0, RNA-Seq, Replicate 2 Naive serum-adapted She…
- GSM8741216 Naive serum-adapted Shef6 on Geltrex, N2B27 d2, RNA-Seq, Replicate 1 Naive serum-adapted She…
- GSM8741217 Naive serum-adapted Shef6 on Geltrex, N2B27 d2, RNA-Seq, Replicate 2 Naive serum-adapted She…
- GSM8741218 Naive serum-adapted Shef6 on Geltrex, N2B27 d3, RNA-Seq, Replicate 1 Naive serum-adapted She…
- GSM8741219 Naive serum-adapted Shef6 on Geltrex, N2B27 d3, RNA-Seq, Replicate 2 Naive serum-adapted She…
- GSM8741220 Naive serum-adapted Shef6 on Geltrex, N2B27 d4, RNA-Seq, Replicate 1 Naive serum-adapted She…
- GSM8741221 Naive serum-adapted Shef6 on Geltrex, N2B27 d4, RNA-Seq, Replicate 2 Naive serum-adapted She…
- GSM8741222 Naive serum-adapted Shef6 on Geltrex, N2B27 d6, RNA-Seq, Replicate 1 Naive serum-adapted She…
- GSM8741223 Naive serum-adapted Shef6 on Geltrex, N2B27 d6, RNA-Seq, Replicate 2 Naive serum-adapted She…
- GSM8741224 Naive serum-adapted Shef6 on Geltrex, N2B27 d8, RNA-Seq, Replicate 1 Naive serum-adapted She…
- GSM8741225 Naive serum-adapted Shef6 on Geltrex, N2B27 d8, RNA-Seq, Replicate 2 Naive serum-adapted She…
- GSM8741226 Naive serum-adapted Shef6 on Geltrex, E8 d2, RNA-Seq, Replicate 1 Naive serum-adapted She…
- GSM8741227 Naive serum-adapted Shef6 on Geltrex, E8 d2, RNA-Seq, Replicate 2 Naive serum-adapted She…
- GSM8741228 Naive serum-adapted Shef6 on Geltrex, E8 d3, RNA-Seq, Replicate 1 Naive serum-adapted She…
- GSM8741229 Naive serum-adapted Shef6 on Geltrex, E8 d3, RNA-Seq, Replicate 2 Naive serum-adapted She…
- GSM8741230 Naive serum-adapted Shef6 on Geltrex, E8 d4, RNA-Seq, Replicate 1 Naive serum-adapted She…
- GSM8741231 Naive serum-adapted Shef6 on Geltrex, E8 d4, RNA-Seq, Replicate 2 Naive serum-adapted She…
- GSM8741232 Naive serum-adapted Shef6 on Geltrex, E8 d6, RNA-Seq, Replicate 1 Naive serum-adapted She…
- GSM8741233 Naive serum-adapted Shef6 on Geltrex, E8 d6, RNA-Seq, Replicate 2 Naive serum-adapted She…
- GSM8741234 Naive serum-adapted Shef6 on Geltrex, E8 d8, RNA-Seq, Replicate 1 Naive serum-adapted She…
- GSM8741235 Naive serum-adapted Shef6 on Geltrex, E8 d8, RNA-Seq, Replicate 2 Naive serum-adapted She…
- GSM8741236 Naive serum-adapted Shef6 on Geltrex, mTeSR d4, RNA-Seq, Replicate 1 Naive serum-adapted She…
- GSM8741237 Naive serum-adapted Shef6 on Geltrex, mTeSR d4, RNA-Seq, Replicate 2 Naive serum-adapted She…
- GSM8741238 Naive serum-adapted Shef6 on Geltrex, mTeSR d6, RNA-Seq, Replicate 1 Naive serum-adapted She…
- GSM8741239 Naive serum-adapted Shef6 on Geltrex, mTeSR d6, RNA-Seq, Replicate 2 Naive serum-adapted She…
- GSM8741240 Naive serum-adapted Shef6 on Geltrex, mTeSR d8, RNA-Seq, Replicate 1 Naive serum-adapted She…
- GSM8741241 Naive serum-adapted Shef6 on Geltrex, mTeSR d8, RNA-Seq, Replicate 2 Naive serum-adapted She…
- GSM8741242 Naive serum-adapted Shef6 on Geltrex, N2B27 d4, Ex2, RNA-Seq, Replicate 1 Naive serum-adapted She…
- GSM8741243 Naive serum-adapted Shef6 on Geltrex, N2B27 d4, Ex2, RNA-Seq, Replicate 2 Naive serum-adapted She…
- GSM8741244 Naive serum-adapted Shef6 on Geltrex, XAV d4, Ex2, RNA-Seq, Replicate 1 Naive serum-adapted She…
- GSM8741245 Naive serum-adapted Shef6 on Geltrex, XAV d4, Ex2, RNA-Seq, Replicate 2 Naive serum-adapted She…
- GSM8741246 Naive serum-adapted Shef6 on Geltrex, FAX d4, Ex2, RNA-Seq, Replicate 1 Naive serum-adapted She…
- GSM8741247 Naive serum-adapted Shef6 on Geltrex, FAX d4, Ex2, RNA-Seq, Replicate 2 Naive serum-adapted She…
- GSM8741248 Naive serum-adapted Shef6 on Geltrex, PXGL d0, Ex2, RNA-Seq, Replicate 1 Naive serum-adapted She…
- GSM8741249 Naive serum-adapted Shef6 on Geltrex, PXGL d0, Ex2, RNA-Seq, Replicate 2 Naive serum-adapted She…
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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.