GEO series

Extensive Crosstalk between BMP and Notch Signaling Pathways in Activated Adult Muscle Stem Cells [RNA-seq III]

GSE339586 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2026/07/22 Platform GPL28457

At a glance

RNA-seq (gene expression) · mouse · 24 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: 24 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.

Summary (written by the submitters)

Muscle stem cells (MuSC) are the cellular source for generation and regeneration of skeletal muscle. To ensure correct muscle growth, MuSC self-renewal and differentiation need to be tightly regulated. Several signaling systems have been implicated in the control of MuSCs, among them Bone Morphogenetic Proteins (BMPs) and Notch, both of which promote MuSC proliferation and suppress differentiation.

Read the full summary ↓

To better understand the mechanisms of function and the target genes regulated by BMP signaling in myogenesis, we investigated the transcriptional responses of adult mouse MuSCs to BMP6/4 using RNA-sequencing. BMP6/4-stimulation of freshly isolated MuSCs for one hour rapidly increased the expression of classical BMP target genes like Id1 and strongly induced expression of genes of the Notch pathway (Hes1, Hey1, Lfng, Snai1). In parallel, using Cleavage Under Targets and Tagmentation (CUT&Tag), we generated whole-genome binding profiles for the BMP pathway effectors pSMAD1/5/9 and SMAD4 and detected binding in promoters and potential regulatory elements of BMP targets and Notch pathway genes (Hes1, Hey1, Lfng, Snai1) indicating that BMP signaling directly influences Notch and that crosstalk between the two pathways regulates myogenesis.

This dataset

Open GSE339586 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 GSE339586_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 PRJNA1499245 and SRA study SRP720449. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

8 conditions, mostly in triplicate

MuSC RNA-seq III control 1h biol ×3 MuSC RNA-seq III BMP6 1h biol ×3 MuSC RNA-seq III BMP6+DAPT 1h biol ×3 MuSC RNA-seq III BMP6+CHX 1h biol ×3 MuSC RNA-seq III control 3h biol ×3 MuSC RNA-seq III BMP6 3h biol ×3 MuSC RNA-seq III BMP6+DAPT 3h biol ×3 MuSC RNA-seq III BMP6+CHX 3h biol ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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

GSM9897983 MuSC RNA-seq III control 1h biol rep 1 MuSC RNA-seq III contro…
GSM9897984 MuSC RNA-seq III BMP6 1h biol rep 1 MuSC RNA-seq III BMP6 1…
GSM9897985 MuSC RNA-seq III BMP6+DAPT 1h biol rep 1 MuSC RNA-seq III BMP6+D…
GSM9897986 MuSC RNA-seq III BMP6+CHX 1h biol rep 1 MuSC RNA-seq III BMP6+C…
GSM9897987 MuSC RNA-seq III control 1h biol rep 2 MuSC RNA-seq III contro…
GSM9897988 MuSC RNA-seq III BMP6 1h biol rep 2 MuSC RNA-seq III BMP6 1…
GSM9897989 MuSC RNA-seq III BMP6+DAPT 1h biol rep 2 MuSC RNA-seq III BMP6+D…
GSM9897990 MuSC RNA-seq III BMP6+CHX 1h biol rep 2 MuSC RNA-seq III BMP6+C…
GSM9897991 MuSC RNA-seq III control 1h biol rep 3 MuSC RNA-seq III contro…
GSM9897992 MuSC RNA-seq III BMP6 1h biol rep 3 MuSC RNA-seq III BMP6 1…
GSM9897993 MuSC RNA-seq III BMP6+DAPT 1h biol rep 3 MuSC RNA-seq III BMP6+D…
GSM9897994 MuSC RNA-seq III BMP6+CHX 1h biol rep 3 MuSC RNA-seq III BMP6+C…
GSM9897995 MuSC RNA-seq III control 3h biol rep 1 MuSC RNA-seq III contro…
GSM9897996 MuSC RNA-seq III BMP6 3h biol rep 1 MuSC RNA-seq III BMP6 3…
GSM9897997 MuSC RNA-seq III BMP6+DAPT 3h biol rep 1 MuSC RNA-seq III BMP6+D…
GSM9897998 MuSC RNA-seq III BMP6+CHX 3h biol rep 1 MuSC RNA-seq III BMP6+C…
GSM9897999 MuSC RNA-seq III control 3h biol rep 2 MuSC RNA-seq III contro…
GSM9898000 MuSC RNA-seq III BMP6 3h biol rep 2 MuSC RNA-seq III BMP6 3…
GSM9898001 MuSC RNA-seq III BMP6+DAPT 3h biol rep 2 MuSC RNA-seq III BMP6+D…
GSM9898002 MuSC RNA-seq III BMP6+CHX 3h biol rep 2 MuSC RNA-seq III BMP6+C…
GSM9898003 MuSC RNA-seq III control 3h biol rep 3 MuSC RNA-seq III contro…
GSM9898004 MuSC RNA-seq III BMP6 3h biol rep 3 MuSC RNA-seq III BMP6 3…
GSM9898005 MuSC RNA-seq III BMP6+DAPT 3h biol rep 3 MuSC RNA-seq III BMP6+D…
GSM9898006 MuSC RNA-seq III BMP6+CHX 3h biol rep 3 MuSC RNA-seq III BMP6+C…

Datasets on a similar topic

GSE305745 Extensive Crosstalk between BMP and Notch Signaling Pathways in Activated Adult Muscle Stem Cells [CUT&Tag] 14 samples shares bmp, extensive, crosstalk, activated, muscle, notch
GSE306430 Stimulation of Adult Muscle Stem Cells with BMPs Results in Direct Activation of Notch Pathway Genes 56 samples shares bmp, muscle, notch
GSE250202 Yin Yang 1 Deficiency in Skeletal Muscle Stem Cell Aggravates Muscle Fibrosis in Duchenne Muscular Dystrophy Mouse by Disrupting Muscle Stem Cell/Macrophage/Fibro-adipogenic Progenitor Crosstalk [RNA-Seq] 12 samples shares crosstalk, rna-seq, muscle
GSE297833 ChAHP Silences SINE Retrotransposons by Inhibiting TFIIIB Recruitment [RNA-seq] 54 samples shares iii, rna-seq
GSE232166 Dual AAV gene therapy in combination with rapamycin rescues muscle and liver impairment in a mouse model of GSDIII. 36 samples shares iii, muscle
GSE313351 Intestinal BMP SMADs impart the mid-villus pattern via direct targeting of villus zonation genes and by controlling a transcription factor hierarchy [RNA-seq] 26 samples shares bmp, rna-seq
GSE244429 BMP9 and BMP10 coordinate liver cellular crosstalk to maintain liver health 24 samples shares bmp, crosstalk
GSE247252 H3K36 methylation regulates cell plasticity and regeneration in the intestinal epithelium (RNA-seq III) 20 samples shares iii, rna-seq

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.