GEO series

A Single Small-Molecule-Based Human Embryo Model Reveals V-ATPase Requirement in Mammalian Blastocyst Cavitation

GSE316552 Homo sapiens (human) RNA-seq (gene expression) 1 samples Submitted 2026/03/11 Platform GPL34281

At a glance

RNA-seq (gene expression) · human · 1 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: 1 samples
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: A single small molecule-based human embryo model reveals V-ATPase requirement in mammalian blastocyst cavitationCell research · 2026

Summary (written by the submitters)

Human naïve pluripotent stem cells (nPSCs) can be indued by various combinations of signaling factors to genearte blastocyst-like structures known as blastoids. Despite the rapid advances in human blastoid models, their potential to uncover fundamental mechanisms of early development remains limited, leaving key morphogenetic processes poorly understood.

Read the full summary ↓

Here, we present a simple and robust system in which dimethyl sulfoxide (DMSO) alone induces blastoid formation from human nPSCs. This model faithfully recapitulates pre- and post-implantation features, including amniotic cavity formation, and reveals a previously unrecognized mechanism of trophectoderm (TE) cavitation. Using this system, we identified lysosome-related genes—particularly those encoding subunits of the proton pump V-ATPase—are essential for blastoid cavitation. DMSO treatment upregulates key V-ATPase subunits (ATP6V0A4 and ATP6V1B1), which are also enriched in the TE of human embryos. Inhibition of V-ATPase disrupted lysosomal acidification, blocked intracellular vacuole formation, and impaired blastoid cavitation. Furthermore, both genetic and pharmacological disruption of V-ATPase function significantly impaired cavitation in mouse and human blastocysts. Thus, our simple DMSO model recapitulates key aspects of human blastocyst development and reveals a conserved mechanism involving V-ATPase–mediated lysosomal acidification during early mammalian embryogenesis.

Published in

A single small molecule-based human embryo model reveals V-ATPase requirement in mammalian blastocyst cavitation

Alsolami S, Chandrasekaran AP, Jin Y et al. · Cell research 2026 · PMID 41936702 · doi:10.1038/s41422-026-01239-3

This dataset

Open GSE316552 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 GSE316552_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 PRJNA1403381 and SRA study SRP662685. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41936702) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 1 more — browse all 1 samples with per-sample file links →

Datasets on a similar topic

GSE237669 A single small molecule-based human embryo model reveals V-ATPase requirement in mammalian blastocyst cavitation 18 samples shares requirement, blastocyst, cavitation, mammalian, v-atpase, embryo
GSE236961 A single small molecule-based human embryo model reveals a requirement for V-ATPase in mammalian blastocyst cavitation 18 samples shares requirement, blastocyst, cavitation, mammalian, v-atpase, embryo
GSE239744 A single small molecule-based human embryo model reveals a requirement for V-ATPase in mammalian blastocyst cavitation 10 samples shares requirement, blastocyst, cavitation, mammalian, v-atpase, embryo
GSE291369 DMSO-induced human embryo model reveals V-ATPase requirement in cavitation 7 samples shares requirement, cavitation, v-atpase, embryo
GSE239821 Endometrial extracellular vesicles regulate processes related to embryo development and implantation in human blastocysts. 24 samples shares blastocyst, embryo
GSE239843 Suppression of ERK signalling promotes pluripotent epiblast in the human blastocyst [RNA-seq I] 134 samples shares blastocyst
GSE297052 Suppression of ERK signalling promotes pluripotent epiblast in the human blastocyst 100 samples shares blastocyst
GSE309100 Reconstitution of human fetal ovaries reveals niche requirements for primordial germ cell-like cell progression 6 samples shares requirement

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.