GEO series

High resolution multi-scale profiling of embryonic germ cell-like cell derivation reveals pluripotent state transitions in humans [RNA-Seq]

GSE286998 Homo sapiens (human) RNA-seq (gene expression) 26 samples Submitted 2026/03/04 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 26 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: 26 samples: 8 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: High resolution multi-scale profiling of embryonic germ cell-like cell derivation reveals pluripotent state transitions in humansStem cell reports · 2026

Summary (written by the submitters)

Primordial germ cells (PGCs) are the embryonic precursors of the gametes. In mice and rats, PGCs can readily acquire pluripotency in vitro by forming embryonic germ cells (EGCs). To date, a comparable in vitro system has not been established in humans, despite the fact that human PGCs (hPGCs) readily undergo pluripotent conversion in the context of germ cell tumorigenesis.

Read the full summary ↓

Here we report that hPGC-like cells (hPGCLCs) undergo conversion to human embryonic germ-like cells (hEGCLCs) upon exposure to the same inductive signals previously used to derive mouse EGCs. This defined, feeder-free culture system allows efficient derivation of human EGCLCs which can be expanded and maintained in standard human pluripotent stem cell medium. hEGCLCs are transcriptionally similar to human pluripotent stem cells (hPSCs) and can differentiate into all three germ layers, as well as giving rise to PGCLCs once more - demonstrating the interconvertibility of pluripotent states. This is also evident at the epigenetic level, as the initial DNA demethylation that occurs in hPGCLCs is largely reversed in hEGCLCs, restoring DNA methylation to the level observed in hPSCs. This new in vitro model captures the transition from the pluripotent stem cell state to a germ cell identity and back again, and therefore represents a highly tractable system to study pluripotent and epigenetic transitions, including those which occur during human germ cell tumorigenesis.

Published in

High resolution multi-scale profiling of embryonic germ cell-like cell derivation reveals pluripotent state transitions in humans

Stucchi S, Sepulveda-Rincon LP, Dion C et al. · Stem cell reports 2026 · PMID 41418783 · doi:10.1016/j.stemcr.2025.102746

This dataset

Open GSE286998 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 GSE286998_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 PRJNA1210644 and SRA study SRP557326. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41418783) ↗

Study design

8 conditions, mostly in triplicate

hIPSC ×3 hEGCLC3_P3 ×3 hEGCLC2_P3 ×3 hEGCLC1_P3 ×3 hEGCLC3_P5 ×3 hEGCLC2_P5 ×3 hEGCLC1_P5 ×3 hPGCLC ×2 +3 more

Supports a between-group comparison across 23 samples.

How we read this: 8 replicated groups read from 26 sample titles; they account for 23 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

GSM8736079 hIPSC3 hIPSC
GSM8736080 hIPSC2 hIPSC
GSM8736081 hIPSC1 hIPSC
GSM8736082 hPGCLC2 hPGCLC
GSM8736083 hPGCLC1 hPGCLC
GSM8736084 hEGCLC3_P0
GSM8736085 hEGCLC2_P0
GSM8736086 hEGCLC1_P0
GSM8736087 hEGCLC3_P3_1 hEGCLC3_P3
GSM8736088 hEGCLC3_P3_2 hEGCLC3_P3
GSM8736089 hEGCLC3_P3_3 hEGCLC3_P3
GSM8736090 hEGCLC2_P3_1 hEGCLC2_P3
GSM8736091 hEGCLC2_P3_2 hEGCLC2_P3
GSM8736092 hEGCLC2_P3_3 hEGCLC2_P3
GSM8736093 hEGCLC1_P3_1 hEGCLC1_P3
GSM8736094 hEGCLC1_P3_2 hEGCLC1_P3
GSM8736095 hEGCLC1_P3_3 hEGCLC1_P3
GSM8736096 hEGCLC3_P5_1 hEGCLC3_P5
GSM8736097 hEGCLC3_P5_2 hEGCLC3_P5
GSM8736098 hEGCLC3_P5_3 hEGCLC3_P5
GSM8736099 hEGCLC2_P5_1 hEGCLC2_P5
GSM8736100 hEGCLC2_P5_2 hEGCLC2_P5
GSM8736101 hEGCLC2_P5_3 hEGCLC2_P5
GSM8736102 hEGCLC1_P5_1 hEGCLC1_P5
GSM8736103 hEGCLC1_P5_2 hEGCLC1_P5
GSM8736104 hEGCLC1_P5_3 hEGCLC1_P5

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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.