GEO series

Distinct Mammary Stem Cells Orchestrate the Long-term Homeostasis of Adult Mammary Gland

GSE251933 Mus musculus (mouse) Single-cell RNA-seq 16 samples Submitted 2025/04/18 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 16 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Mus musculus (mouse)
Samples: 16 samples: 6 × D vs 6 × T vs 4 × NGroups 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: Distinct mammary stem cells orchestrate long-term homeostasis of adult mammary glandCell discovery · 2025

Summary (written by the submitters)

The murine mammary gland is sustained by distinct pools of stem cells that are limited in space and time, exhibiting diverse multipotency and activity. However, the specific identities of these stem cells and their contributions to mammary gland homeostasis are not well understood. In this study, we investigated the spatial heterogeneity of the mammary gland at the single-cell transcription level.

Read the full summary ↓

Our findings reveal that mammary basal cells exhibit spatially distinct populations and characteristics, which can be further divided based on the expression of Cd34 and Cd200 markers. Notably, Cd34-Cd200+ basal cells demonstrate strong long-term self-renewal ability and possess the highest stem cell frequency, while Cd34+Cd200- basal cells show reduced stem cell potency. Through lineage tracing experiments using their signature genes, we discovered that Bcl11b+ cells were enriched in the Cd34-Cd200+ population and exhibited bipotency even in the postnatal mammary gland, with an increasing contribution to mammary epithelia observed during long-term tracing and after multiple rounds of pregnancies. Conversely, lineage tracing of Sema3a+ cells, enriched in the Cd34+Cd200- population, predominantly revealed their unipotent nature and significant contribution during alveologenesis. Notably, the Bcl11b+ cells displayed a slow response to pregnancy but contributed to long-term mammary homeostasis, in contrast to the rapid response observed in Sema3a+ cells. Importantly, depletion of Bcl11b in Krt14+ mammary basal cells resulted in reduced bipotency of mammary stem cells and impaired their long-term contribution to the mammary gland. Overall, our study identifies distinct bipotent and unipotent populations of mammary basal cells with different dynamic properties that play critical roles in maintaining postnatal mammary homeostasis. These findings are crucial for advancing our understanding of breast health and breast cancer research.

Published in

Distinct mammary stem cells orchestrate long-term homeostasis of adult mammary gland

Lin Z, Guo Y, Bai H et al. · Cell discovery 2025 · PMID 40234382 · doi:10.1038/s41421-025-00794-0

This dataset

Open GSE251933 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 GSE251933_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 PRJNA1055945 and SRA study SRP479720. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40234382) ↗

Study design

6 × D vs 6 × T vs 4 × N

Supports a between-group comparison across 16 samples.

How we read this: 3 replicated groups read from 16 sample titles; they account for 16 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

GSM7990250 D31 D
GSM7990251 D32 D
GSM7990252 D51 D
GSM7990253 D52 D
GSM7990254 D61 D
GSM7990255 D62 D
GSM7990256 N21 N
GSM7990257 N22 N
GSM7990258 N23 N
GSM7990259 N24 N
GSM7990260 T31 T
GSM7990261 T32 T
GSM7990262 T33 T
GSM7990263 T34 T
GSM7990264 T42 T
GSM7990265 T43 T

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