GEO series

Generation of transient totipotent blastomere-like stem cells by short-term high-dose Pladienolide B treatment

GSE252206 Mus musculus (mouse) RNA-seq (gene expression) 19 samples Submitted 2025/04/02 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 19 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: 19 samples: 7 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: Generation of transient totipotent blastomere-like stem cells by short-term high-dose Pladienolide B treatmentScience China. Life sciences · 2025

Summary (written by the submitters)

As an alternative model for study of the dynamic process of early mammalian embryonic development, multiple progresses have been made in using mouse embryonic stem cells (mESCs) to generate embryo-like structure, especially by modifying the starting cells. A previous study has shown that as long as continuously treating mESCs with a low-dose splicing inhibitor, pladienolide B (PlaB), a totipotent state comparable to 2- and 4-cell embryos at molecular levels can be reached.

Read the full summary ↓

However, these totipotent mESCs mare less proliferative, with the culture time being limited to about 10-15 passages. Here we reported that transiently PlaB-treated mESCs were sufficient for generating a novel type of totipotent-like stem cells from classical mESCs, and these cells were endowed with the ability to differentiate into both embryonic and extra-embryonic cell lineages, we termed them as transient totipotent-like stem cells (TTLCs). Similarly, TTLCs could self-organize to blastoids and recapitulated key preimplantation developmental processes. Transcriptome analysis also showed that TTLC-blastoids bear similarities with mouse E3.5, E4.5 blastocyst and TBLC-blastoids. Moreover, we found that TTLC-blastoids could develop beyond implantation stage, forming egg-cylinder structures both in vivo and in vitro. In summary, our findings provided a rapidly alternative cell type to generate blastoids for the study of early mouse embryogenesis.

Published in

Generation of transient totipotent blastomere-like stem cells by short-term high-dose Pladienolide B treatment

Zhang W, An S, Hou S et al. · Science China. Life sciences 2025 · PMID 40024996 · doi:10.1007/s11427-024-2774-2

This dataset

Open GSE252206 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 GSE252206_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 PRJNA1058557 and SRA study SRP480521. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40024996) ↗

Study design

7 conditions, mostly in triplicate

TT2_Blastoid_D1 ×3 TT2_Blastoid_D2 ×3 TT2_Blastoid_D3 ×3 TT2_Blastoid_D4 ×3 TT2_Blastoid_D5 ×3 TT2_54h_Ctrl ×2 TT2_54h_PlaB ×2

Supports a between-group comparison across 19 samples.

How we read this: 7 replicated groups read from 19 sample titles; they account for 19 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

GSM7996653 TT2_54h_Ctrl_Rep1 TT2_54h_Ctrl
GSM7996654 TT2_54h_Ctrl_Rep2 TT2_54h_Ctrl
GSM7996655 TT2_54h_PlaB_Rep1 TT2_54h_PlaB
GSM7996656 TT2_54h_PlaB_Rep2 TT2_54h_PlaB
GSM7996657 TT2_Blastoid_D1_Rep1 TT2_Blastoid_D1
GSM7996658 TT2_Blastoid_D1_Rep2 TT2_Blastoid_D1
GSM7996659 TT2_Blastoid_D1_Rep3 TT2_Blastoid_D1
GSM7996660 TT2_Blastoid_D2_Rep1 TT2_Blastoid_D2
GSM7996661 TT2_Blastoid_D2_Rep2 TT2_Blastoid_D2
GSM7996662 TT2_Blastoid_D2_Rep3 TT2_Blastoid_D2
GSM7996663 TT2_Blastoid_D3_Rep1 TT2_Blastoid_D3
GSM7996664 TT2_Blastoid_D3_Rep2 TT2_Blastoid_D3
GSM7996665 TT2_Blastoid_D3_Rep3 TT2_Blastoid_D3
GSM7996666 TT2_Blastoid_D4_Rep1 TT2_Blastoid_D4
GSM7996667 TT2_Blastoid_D4_Rep2 TT2_Blastoid_D4
GSM7996668 TT2_Blastoid_D4_Rep3 TT2_Blastoid_D4
GSM7996669 TT2_Blastoid_D5_Rep1 TT2_Blastoid_D5
GSM7996670 TT2_Blastoid_D5_Rep2 TT2_Blastoid_D5
GSM7996671 TT2_Blastoid_D5_Rep3 TT2_Blastoid_D5

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