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RNA-seq datasets of the mTOR signalling pathway and the estrogen-dependent regulation of the transcriptome in mouse mammary gland epithelial organoids

GSE298518 Mus musculus (mouse) Single-cell RNA-seq 18 samples Submitted 2025/08/05 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 18 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
18 samples: 6 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
RNA-seq dataset of the estrogen-dependent regulation of the transcriptome in mouse mammary gland organoidsData in brief · 2025
Summary (written by the submitters)
This GSE covered two different but complementary works on mouse mammary epithelial organoids. The first one is a publication from 2025 in Data in Brief entitled "RNA-seq dataset of the estrogen-dependent regulation of the transcriptome in mouse mammary gland epithelial organoids”. The second one is a publication from 2026 in Scientific Reports entitled “The mTOR signalling pathway regulates key steps of mammary gland organoid genesis in a temporal manner”.
Read the full summary ↓
The mammary gland development in utero and during life is strongly regulated by hormones. We first studied the impact of estradiol during 11 days in culture and performed bulk mRNA sequencing to better understand the impact of estrogen signalling on the mammary epithelial cell transcriptome. Besides, the development of the gland is also a complex process that evolves throughout life. In developmental assays, the mechanistic target of rapamycin (mTOR) was shown to be a regulator of cellular lineage determination and branching morphogenesis, acting in a time-dependent manner to control these processes. We treated our organoids with Torin 1 at two different growing points and used bulk mRNA sequencing to demonstrate the regulatory functions of mTOR in controlling mammary epithelial cells’ capacity to generate organoids. Altogether, these two datasets help understand the function of the mammary gland. They can be reanalyzed and combined with recent single-cell RNA-seq data to better understand the role of the estrogen receptor and the mTOR signalling pathway in the functions of the gland in physiological conditions, such as lactation or pathological conditions, such as breast cancer.
Published in
RNA-seq dataset of the estrogen-dependent regulation of the transcriptome in mouse mammary gland organoids
Lacouture A, Sylla MS, Germain L et al. · Data in brief 2025 · PMID 40896136 · doi:10.1016/j.dib.2025.111984
This dataset
Open GSE298518 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 GSE298518_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 PRJNA1269599 and SRA study SRP588659. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40896136) ↗
Study design
6 conditions, mostly in triplicate
Mammary gland epithelial organoids, Estradiol… ×3 Mammary gland epithelial organoids, DMSO 6 da… ×3 Mammary gland epithelial organoids, DMSO 12 d… ×3 Mammary gland epithelial organoids, Torin 6 d… ×3 Mammary gland epithelial organoids, Torin 12 … ×3 Mammary gland epithelial organoids, Control 1… ×2 Mammary gland epithelial organoids,Control 11… ×1

Supports a between-group comparison across 17 samples.

How we read this: 6 replicated groups read from 18 sample titles; they account for 17 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
Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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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.