GEO series

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

GSE237669 Homo sapiens (human) RNA-seq (gene expression) 18 samples Submitted 2026/03/11 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 18 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: 18 samples: 4 × PALLY_DM_SI_D vs 4 × impPALLY_DM_SI_D vs 4 × PALLY_SI_D vs 4 × impPALLY_SI_DGroups 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: 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 induced by various combinations of signaling factors to generate blastocyst-like structures, termed blastoids. Despite rapid progress in human blastoid models, their potential to uncover fundamental mechanisms of early human development remains limited, leaving key morphogenetic processes poorly understood.

Read the full summary ↓

Here, we describe a simple and robust system in which dimethyl sulfoxide (DMSO) alone induces blastoid formation from human nPSCs. This model recapitulates key pre- and post-implantation features and exhibits enhanced polar trophectoderm (TE) organization, more efficient attachment within an implantation-relevant window, improved epiblast lumenogenesis associated with amniotic cavity formation, and more robust, sustained expansion of embryonic lineages following attachment. Using this system, we reveal a previously unrecognized mechanism underlying TE cavitation and identify lysosome-associated genes - particularly subunits of the proton pump V-ATPase - as essential regulators of blastoid cavitation. DMSO treatment upregulates key V-ATPase subunits (ATP6V0A4 and ATP6V1B1), which are also enriched in the TE of human embryos. Genetic or pharmacological inhibition of V-ATPase activity disrupts lysosomal acidification, blocks intracellular vacuole formation, and impairs blastoid cavitation, whereas overexpression of V-ATPase subunits rescues this phenotype. Furthermore, genetic and pharmacological perturbations of V-ATPase function significantly compromise cavitation in both mouse and human blastocysts. Finally, DMSO treatment induces membrane biomechanical changes characteristic of early embryonic development, suggesting a mode of action distinct from conventional small-molecule, signaling pathway-based induction strategies. This simple DMSO-based blastoid model recapitulates key aspects of human blastocyst development and reveals a conserved requirement for 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 GSE237669 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 GSE237669_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 PRJNA996129 and SRA study SRP450265. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41936702) ↗

Study design

4 × PALLY_DM_SI_D vs 4 × impPALLY_DM_SI_D vs 4 × PALLY_SI_D vs 4 × impPALLY_SI_D

Supports a between-group comparison across 16 samples.

How we read this: 4 replicated groups read from 18 sample titles; they account for 16 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

GSM7635551 PALLY_DM_SI_D1 PALLY_DM_SI_D
GSM7635552 PALLY_DM_SI_D2 PALLY_DM_SI_D
GSM7635553 PALLY_DM_SI_D3 PALLY_DM_SI_D
GSM7635554 PALLY_DM_SI_D4 PALLY_DM_SI_D
GSM7635555 impPALLY_DM_SI_D1 impPALLY_DM_SI_D
GSM7635556 impPALLY_DM_SI_D2 impPALLY_DM_SI_D
GSM7635557 impPALLY_DM_SI_D3 impPALLY_DM_SI_D
GSM7635558 impPALLY_DM_SI_D4 impPALLY_DM_SI_D
GSM7635559 PALLY_SI_D1 PALLY_SI_D
GSM7635560 PALLY_SI_D2 PALLY_SI_D
GSM7635561 PALLY_SI_D3 PALLY_SI_D
GSM7635562 PALLY_SI_D4 PALLY_SI_D
GSM7635563 impPALLY_SI_D1 impPALLY_SI_D
GSM7635564 impPALLY_SI_D2 impPALLY_SI_D
GSM7635565 impPALLY_SI_D3 impPALLY_SI_D
GSM7635566 impPALLY_SI_D4 impPALLY_SI_D
GSM8383986 DMSO_D6
GSM8383987 DMSO_POSTIMP

Datasets on a similar topic

GSE236961 A single small molecule-based human embryo model reveals a requirement for V-ATPase in mammalian blastocyst cavitation 18 samples shares molecule-based, requirement, blastocyst, cavitation, mammalian, v-atpase, embryo, small
GSE316552 A Single Small-Molecule-Based Human Embryo Model Reveals V-ATPase Requirement in Mammalian Blastocyst Cavitation 1 samples shares molecule-based, requirement, blastocyst, cavitation, mammalian, v-atpase, embryo, small
GSE239744 A single small molecule-based human embryo model reveals a requirement for V-ATPase in mammalian blastocyst cavitation 10 samples shares molecule-based, requirement, blastocyst, cavitation, mammalian, v-atpase, embryo, small
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
GSE279752 Small molecule-based regulation of gene expression in human astrocytes switching on and off the G-quadruplex control systems 15 samples shares molecule-based, small
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

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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.