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HAND1 controls the lineage divergence between amnion and trophoblast from human pluripotent stem cells

GSE299501 Homo sapiens (human) RNA-seq (gene expression) 27 samples Submitted 2026/03/02 Platform GPL29480
At a glance

RNA-seq (gene expression) · human · 27 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
27 samples: 9 conditions, mostly in triplicateGroups 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
HAND1 controls the lineage bifurcation of trophoblast and amnion from human pluripotent stem cellsCellular and molecular life sciences : CMLS · 2026
Summary (written by the submitters)
Trophoblasts and amnion, as extra-embryonic lineages, can be differentiated from human pluripotent stem cells (PSCs) under defined culture conditions, but the regulatory mechanisms that coordinate the cell fate decisions between these lineages during PSC differentiation remain poorly defined. In this study, leveraging CRISPR/Cas9-mediated targeted screening and lineage reporter pluripotent stem cells (PSCs), we identified the transcription factor HAND1 as a critical determinant governing the divergence of trophoblast and amnion lineages in PSCs.
Read the full summary ↓
Genetic ablation of HAND1 effectively suppressed the amnion differentiation capacity of EPSCs while enhancing their trophoblast differentiation potential. Conversely, ectopic overexpression of HAND1 have adverse effects. Notably, forced expression of HAND1 activated amnionic transcription program in human trophoblast stem cells (TSCs), demonstrating its lineage-reprogramming capability. Mechanistic analyses revealed that HAND1 cooperates with Wnt signaling pathway co-factors TCF/b-catenin to form a transcriptional complex that antagonistically regulates trophoblast- and amnion-associated gene networks. Collectively, our findings establish HAND1 as a pivotal regulator that orchestrates the fate choice between amnionic and trophoblast lineages during human PSC differentiation, providing insights into the molecular logic of extra-embryonic lineage specification.
Published in
HAND1 controls the lineage bifurcation of trophoblast and amnion from human pluripotent stem cells
Pang C, Yang Q, Zhong Y et al. · Cellular and molecular life sciences : CMLS 2026 · PMID 41805859 · doi:10.1007/s00018-026-06120-5
This dataset
Open GSE299501 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 GSE299501_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 PRJNA1274861 and SRA study SRP591320. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41805859) ↗
Study design
9 conditions, mostly in triplicate
M1, Wild-type, Day8, ×3 M1, HAND1-knockout, Day8, ×3 M1, HAND1-knockout, ROSA26-DOX-HAND1, ×3 M1, HAND1-knockout, ROSA26-DOX-HAND1, 24h wit… ×3 M1, HAND1-knockout, ROSA26-DOX-HAND1, 24h wit… ×3 M1, HAND1-knockout, ROSA26-DOX-HAND1, 48h wit… ×3 M1, HAND1-knockout, ROSA26-DOX-HAND1, 48h wit… ×3 M1, HAND1-knockout, ROSA26-DOX-HAND1, 72h wit… ×3 +1 more

Supports a case/control comparison: 24 samples read as cases, 3 as controls.

How we read this: 9 replicated groups read from 27 sample titles; they account for 27 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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