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Single cell landscape of transdifferentiation using chemical components

GSE179357 Mus musculus (mouse) Single-cell RNA-seq 139 samples Submitted 2025/03/21 Platform GPL21273Platform GPL28330
At a glance

Single-cell RNA-seq · mouse · 139 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism
Mus musculus (mouse)
Samples
139 samples: 49 conditions, mostly in duplicateGroups 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
Dynamics of Cell Fate Decisions during Chemically Induced Multi-Lineage Trans-Differentiation at Single-Cell LevelAdvanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025
Summary (written by the submitters)
We construct a time-series atlas of in vitro mouse cell transdifferentiating atlas (MCTA) using chemical components, to reveal the gene regulatory networks which govern lineage development.
Published in
Dynamics of Cell Fate Decisions during Chemically Induced Multi-Lineage Trans-Differentiation at Single-Cell Level
E W, Fei L, Wang J et al. · Advanced science (Weinheim, Baden-Wurttemberg, Germany) 2025 · PMID 40051350 · doi:10.1002/advs.202409642
This dataset
Open GSE179357 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 GSE179357_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA743338 and SRA study SRP326697. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40051350) ↗
Study design
49 conditions, mostly in duplicate
day4 ×10 day0 ×6 day8 ×6 day35 ×6 day16 ×5 scATAC_Day6 ×4 d28_RNA ×4 d35_RNA ×4 +41 more

Supports a between-group comparison across 139 samples.

How we read this: 49 replicated groups read from 139 sample titles; they account for 139 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

+ 99 more — browse all 139 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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