GEO series

Trophoblast stem cell derivation from naive and primed hPSC enables ELF5 functional analysis (scRNAseq)

GSE281595 Homo sapiens (human) Single-cell RNA-seq 12 samples Submitted 2025/09/15 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 12 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Homo sapiens (human)
Samples: 12 samples: 12 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: Trophoblast stem cell derivation from naive and primed hPSC enables ELF5 functional analysisStem cell reports · 2025

Summary (written by the submitters)

Human pluripotent stem cells (hPSCs) are valuable tools for studying placental biology, yet their differentiation into bona fide trophoblast stem cells (TSCs) remains challenging. In this study, we established and thoroughly compared naive and primed-derived TSC-like cells with primary human TSCs derived from pre-implantation blastocyst and first-trimester placenta.

Read the full summary ↓

Comprehensive analyses confirmed expression of trophoblast lineage-specific genes and typical placental features. Detailed transcriptional analyses revealed that naive-derived TSC-like cells resembled embryo and placenta-derived cell lines and differentiated faster and more directly into TSC than primed-derived cells. We used these TSC-like models to study the role of ELF5, a transcription factor indispensable for maintenance and differentiation in mouse TSC. In contrast to the mouse, knockout and knockdown experiments revealed that ELF5 is dispensable for human TSC-like cells self-renewal and differentiation. Our study provides valuable transcriptional data and highlights the utility of hPSC-derived TSC-like cells for modeling the placenta and studying gene function.

Published in

Trophoblast stem cell derivation from naive and primed hPSC enables ELF5 functional analysis

Sokka J, Lapinsuo E, Kvist J et al. · Stem cell reports 2025 · PMID 40939596 · doi:10.1016/j.stemcr.2025.102637

This dataset

Open GSE281595 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 GSE281595_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 PRJNA1184766 and SRA study SRP544501. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40939596) ↗

Study design

12 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 12 sample titles: 12 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

GSM8624424 bTS5
GSM8624425 CT30
GSM8624426 ESCn
GSM8624427 ESCp
GSM8624428 TSCKO
GSM8624429 TSCWT
GSM8624430 TSCn
GSM8624431 Day 3 TSCn
GSM8624432 Day 6 TSCn
GSM8624433 TSCp
GSM8624434 Day 3 TSCp
GSM8624435 Day 6 TSCp

Datasets on a similar topic

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GSE306221 Transient inhibition of MEK/ERK and WNT pathways enhances direct differentiation of primed hPSCs into functional trophoblast stem cells 18 samples shares trophoblast, primed, stem
GSE314863 Repertoire FLEX (REFLEX) Enables High-Throughput Multiomic scRNAseq with AIR Detection 127 samples shares scrnaseq, enables
GSE276594 Hypoxia and loss of GCM1 expression prevents differentiation and contact inhibition in human trophoblast stem cells [RNA-Seq 2] 45 samples shares trophoblast, stem
GSE278375 PPARG-centric transcriptional re-wiring during differentiation of human trophoblast stem cells into extravillous trophoblasts [RNA-seq] 32 samples shares trophoblast, stem
GSE299501 HAND1 controls the lineage divergence between amnion and trophoblast from human pluripotent stem cells 27 samples shares trophoblast, stem
GSE280832 Chromosomal instability in human trophoblast stem cells and placenta 26 samples shares trophoblast, stem

Search all human RNA-seq datasets in GEO →

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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.