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Establishment of Human Formative Pluripotent Stem Cell Like Cells Exhibiting Amniotic Differentiation Potentials [bulk RNA-seq]

GSE298429 Homo sapiens (human) Single-cell RNA-seq 13 samples Submitted 2026/03/01 Platform GPL34281Platform GPL34328
At a glance

Single-cell RNA-seq · human · 13 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Homo sapiens (human)
Samples
13 samples: 2 × hALSCs vs 2 × hESCs_sus vs 2 × 3D_to_2D_P1 vs 2 × 3D_to_2D_P2Groups 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.
Summary (written by the submitters)
Human embryos undergo pivotal morphogenetic remodelling shortly after implantation. The understanding of this crucial stage is severely impeded by the scarcity of embryonic samples and ethical constraints. Pluripotent stem cells with the competence for somatic and germline differentiation serve as in vitro models of epiblast.
Read the full summary ↓
In this study, we established human formative pluripotent stem cells-like cell (hfPSC-LCs) from naive human embryonic stem cells (hESCs), conventional hESCs, human induced pluripotent stem cells (hiPSCs), as well as human blastocysts using the three dimensional (3D) Matrigel culture system. Similar to pre gastrula stage epiblast hfPSC-LCs self-organize into self-renewing colonies with an apical lumen and exhibit several hallmarks of formative pluripotency, consistent with the properties observed in mouse fPSCs. Notably, single cells of hfPSC-LCs could differentiate into amnion-like precursor cells (hALPCs) which are transcriptionally and morphologically similar to the bona fide amnion. Meanwhile, hfPSC-LCs directly respond to primordial germ cell (PGC) induction signals, generating PGC-like cells (PGCLCs) either as single - cell aggregates or intact colonies, with an efficiency of approximately 50%. Chromatin accessibility analysis revealed that the differentiation capacity of hfPSC-LCs for gametes and amnion lineages might correlate with the accessible chromatin architecture of PGC and amnion associated genes. Loss of 3D-Matrigel niche disrupts formative pluripotency in both mouse and human, manifesting as downregulated formative markers and compromised differentiation capacity. Collectively, our findings establish hfPSC-LCs as a 3D model for investigating formative pluripotency of humans, thereby probably addressing a critical gap in the understanding of human pluripotency transitions.
This dataset
Open GSE298429 in finder → Find more 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 GSE298429_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1269438 and SRA study SRP588755. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
2 × hALSCs vs 2 × hESCs_sus vs 2 × 3D_to_2D_P1 vs 2 × 3D_to_2D_P2

Supports a between-group comparison across 8 samples.

How we read this: 4 replicated groups read from 13 sample titles; they account for 8 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
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