GEO series

A temporally resolved BMP4 response in the peri-implantation human embryonic disc is critical for the induction of multipotent TFAP2A + cells and EMT

GSE288389 Homo sapiens (human) RNA-seq (gene expression) 3 samples Submitted 2025/07/30 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 3 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: 3 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: TFAP2A+ embryonic progenitor cells undergo fate diversification to give rise to human amnion, germline, and mesodermbioRxiv : the preprint server for biology · 2025

Summary (written by the submitters)

The unilaminar embryonic disc, a sheet of epithelized SOX2+ epiblast cells, undergoes complex morphogenesis to create a multi-dimensional human gastrula. This process endows early lineage specification and spatial identities that begin at the posterior end of the disc to create a coordinate system for embryogenesis. Here, we find that simply adding basement membrane extracts (BMEs) to the stem cell media is sufficient to model the early peri-gastrulating embryonic disc.

Read the full summary ↓

We demonstrate that the emergence of amnion, primordial germ cells (PGCs), and mesoderm arise from BMP4-responsive disc cells that induce transient TFAP2A expression and SOX2 repression. We track the order of embryonic events that take place during disc morphogenesis and show that amnion-like cells (AMLCs) and PGC-like cells (PGCLCs) are specified first from epithelized TFAP2A+ progenitors. Shortly after, gastrulating mesoderm-like cells (MeLCs) arise from transiently expressed TFAP2A+ disc cells that then undergo EMT. We find that BMP4-responsiveness is critical to SOX2 repression, TFAP2A expression, lineage induction and EMT, while the process of EMT itself is not. Thus, we show that the extracellular matrix is necessary to promote disc morphogenesis and EMT.

Published in

TFAP2A+ embryonic progenitor cells undergo fate diversification to give rise to human amnion, germline, and mesoderm

Arabpour A, DiRusso JA, Wu QY et al. · bioRxiv : the preprint server for biology 2025 · PMID 40667219 · doi:10.1101/2025.06.26.661839

This dataset

Open GSE288389 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 GSE288389_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 PRJNA1217343 and SRA study SRP560707. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40667219) ↗

Samples in this study

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+ 3 more — browse all 3 samples with per-sample file links →

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