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Origin of extra-embryonic mesenchyme points to evolutionary novelty in primate early development [RNA-seq]

GSE219290 Homo sapiens (human) RNA-seq (gene expression) 33 samples Submitted 2024/12/02 Platform GPL20301
At a glance

RNA-seq (gene expression) · human · 33 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
33 samples: 11 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, partially mediated through ape-specific LTR binding, is essential for human extra-embryonic mesenchyme derivation from iPSCsCell reports · 2025
Summary (written by the submitters)
As ontogeny does not recapitulate phylogeny and little developmental restraint exists prior to gastrulation, early mammalian development differs significantly between species. A prime example is the temporal difference in the first emergence of extra-embryonic mesenchymal cells (ExMC) between mouse and human. Here, we report a fast and efficient in vitro cell model of human ExMC formation from induced pluripotent stem cells.
Read the full summary ↓
This ExMC emerges from the apparent late blastocystic trophoblast. We define HAND1 as an essential regulator of ExMC specification, with HAND1 null cells reverting to the trophoblast lineage. Regulatory phenotyping defines primary target genes of, and primate-specific genomic regions bound by, HAND1. These data emphasize the nascent evolutionary innovation in early development relevant to human health but, through pleiotropy, also to later in life human biology. The novel findings that trophectoderm is a source of ExMC lineage and how recently evolved young transposable elements regulate this process emphasize the evolutionary novelties of our model to explore the primate embryogenesis.
Published in
HAND1, partially mediated through ape-specific LTR binding, is essential for human extra-embryonic mesenchyme derivation from iPSCs
Liu Z, Tan Y, Flynn WF et al. · Cell reports 2025 · PMID 40220298 · doi:10.1016/j.celrep.2025.115568
This dataset
Open GSE219290 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 GSE219290_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 PRJNA907858 and SRA study SRP411104. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40220298) ↗
Study design
11 conditions, mostly in triplicate
BSA-83-DAY6 ×3 BSA-DAY6 ×3 BS-DAY6 ×3 KOLF2-BSA-DAY2 ×3 KOLF2-BSA-DAY3 ×3 KOLF2-BSA-DAY4 ×3 KOLF2-BSA-DAY6 ×3 KOLF2-HAND1KO-BSA-DAY2 ×3 +3 more

Supports a between-group comparison across 33 samples.

How we read this: 11 replicated groups read from 33 sample titles; they account for 33 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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