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Effect of Notch1 signaling on muscle engraftment and maturation from pluripotent stem cells

GSE271221 Mus musculus (mouse) RNA-seq (gene expression) 23 samples Submitted 2025/02/02 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 23 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
23 samples
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
Effect of Notch1 signaling on muscle engraftment and maturation from pluripotent stem cellsStem cell reports · 2025
Summary (written by the submitters)
Pluripotent stem cell-derived iPax3 myogenic progenitors display an embryonic molecular signature but become postnatal upon transplantation. Because this correlates with upregulation of Notch signaling, here we probed whether Notch1 is required for in vivo maturation by performing gain- and loss-of-function studies in iPax3 myogenic progenitors.
Read the full summary ↓
Transplantation studies revealed comparable myofiber engraftment. However, assessment of fiber type composition revealed more mature myofiber grafts in the overexpression cohort, as shown by the lower expression of embryonic MHC and increased levels of type IIX MHC. Surprisingly, more mature myofiber were also observed in the absence of Notch1, suggesting its dispensability for in vivo maturation. Donor-derived Pax7+ cells were detected in all transplants, however, in the absence of Notch1, secondary grafts exhibited a high fraction of these cells in the interstitial space. RNA-sequencing showed changes in extracellular matrix organization, cell cycle, and metabolism, suggesting that Notch1 is required for satellite cell homing.
Published in
Effect of Notch1 signaling on muscle engraftment and maturation from pluripotent stem cells
Yamashita AMS, Garay BI, Kim H et al. · Stem cell reports 2025 · PMID 39889709 · doi:10.1016/j.stemcr.2024.102396
This dataset
Open GSE271221 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 GSE271221_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 PRJNA1130477 and SRA study SRP517321. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39889709) ↗
Samples in this study

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