GEO series

Modelling mouse embryogenesis from chemically induced totipotent stem cells

GSE292862 Mus musculus (mouse) RNA-seq (gene expression) 22 samples Submitted 2026/08/08 Platform GPL34328

At a glance

RNA-seq (gene expression) · mouse · 22 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: Mus musculus (mouse)
Samples: 22 samples: 15 distinct titles, 3 of them repeatedGroups 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.

Summary (written by the submitters)

The ability to faithfully initiate embryogenesis from a single, induced non-germline cell type, akin to the totipotent blastomeres, remains a significant challenge in developmental and synthetic biology. In this study, we established conditions that enabled the continuous ex utero development of mouse embryo models (EMs), starting solely from the very beginning of chemically induced totipotent-like stem cells (ciTotiSCs) and spanning the pre-implantation morula, blastocysts, and post-gastrulation stages with both embryonic and extraembryonic compartments.

Read the full summary ↓

These ciTotiSCs self-organized into blastocyst-like structures that closely resembled natural blastocysts in both morphology and lineage segregation. The resulting ciTotiSC-derived EMs (ciToti-EMs) successfully progressed through key developmental milestones, including gastrulation, embryonic axis formation, hematopoiesis and early organogenesis, closely resembling E8.5 natural embryos (NEs). Furthermore, extended culture led to the development of functional cardiac tissues in ciToti-EMs, highly comparable to that of E10.5-NEs. These findings demonstrate an extraordinary ability of a single induced cell type, ciTotiSCs, to autonomously recapitulate the complete spectrum of early mouse embryogenesis. Our ciToti-EM system provides a powerful new model for investigating mammalian embryonic development and opens new avenues for creating multicellular organisms from non-germline cells.

This dataset

Open GSE292862 in finder → Find more mouse 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 GSE292862_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 PRJNA1241770 and SRA study SRP573569. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

15 distinct titles, 3 of them repeated

ciToti ×5 ciToti8 ×3 ciToti10 ×2

How we read this: Read from 22 sample titles: 15 distinct titles with little repetition. 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

GSM8867616 ciToti7
GSM8867617 ciToti8_1
GSM8867618 ciToti8_2
GSM8867619 ciToti8_3
GSM8867620 ciToti10_1
GSM8867621 ciToti10_2
GSM8867622 ciToti12_H
GSM8867623 E3.5_In utero
GSM8867624 E6.5_In utero
GSM8867625 E7.5_In utero
GSM8867626 E8.5_In utero
GSM8867627 E10.5_H_In utero
GSM8867628 E4.5_Ex utero
GSM8867629 E6.5_Ex utero
GSM8867630 E7.5_Ex utero
GSM9859922 mESC
GSM9859923 ciTotiSCs_TAW
GSM9859924 ciTotiSCs_TAWa
GSM9859925 ciToti1
GSM9859926 ciToti2
GSM9859927 ciToti3
GSM9859928 ciToti4

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GSE68715 Global transcriptional analysis of mouse fibroblasts, chemically-induced neurons (neuron-like cells) from mouse fibroblasts and mouse primary cortical neurons by RNA-seq 15 samples shares chemically, induced
GSE243921 Modeling pre-implantation development using totipotent blastomere-like stem cells [bulk RNA-seq] 104 samples shares totipotent, stem
GSE287908 Totipotent-Like Cell-Based Embryo Model Recapitulating Mouse Embryogenesis from Pre-Implantation to Gastrulation [RNA-Seq] 52 samples shares embryogenesis, totipotent
GSE252206 Generation of transient totipotent blastomere-like stem cells by short-term high-dose Pladienolide B treatment 19 samples shares totipotent, stem
GSE232718 Employing totipotent cells to reconstruct embryogenesis 13 samples shares embryogenesis, totipotent
GSE232634 Employing totipotent cells to reconstruct embryogenesis [RNA-seq] 9 samples shares embryogenesis, totipotent
GSE287909 Totipotent-Like Cell-Based Embryo Model Recapitulating Mouse Embryogenesis from Pre-Implantation to Gastrulation [scRNA-Seq] 8 samples shares embryogenesis, totipotent

Search all mouse RNA-seq datasets in GEO →

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