← BioTransfer GEO Dataset Finder
GEO series

Lineage Tracing Reveals Clone-Specific Responses to Doxorubicin in Triple-Negative Breast Cancer

GSE291679 Homo sapiens (human) Single-cell RNA-seq 36 samples Submitted 2025/03/18 Platform GPL18573Platform GPL24676
At a glance

Single-cell RNA-seq · human · 36 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
Homo sapiens (human)
Topic
Breast cancerThis series is part of our curated briefing on it.
Samples
36 samples: 7 conditions, mostly with about 5 replicates eachGroups 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
Lineage Tracing Reveals Clone-Specific Responses to Doxorubicin in Triple-Negative Breast CancerbioRxiv : the preprint server for biology · 2025
Summary (written by the submitters)
Triple-negative breast cancer, characterized by aggressive growth and high intratumor heterogeneity, presents a significant clinical challenge. Here, we use a lineage-tracing system, ClonMapper, which couples heritable clonal identifying tags with single-cell RNA-sequencing (scRNA-seq), to better elucidate the response to doxorubicin in a model of TNBC.
Read the full summary ↓
We demonstrate that, while there is a dose-dependent reduction in overall clonal diversity, there is no pre-existing resistance signature among surviving clones. Separately, we found the existence of two transcriptomically distinct clonal subpopulations that remain through the course of treatment. Among clones persisting across multiple samples we identified divergent phenotypes, suggesting a response to treatment independent of clonal identity. Finally, a subset of clones harbor novel changes in expression following treatment. The clone and sample specific responses to treatment identified herein highlight the need for better personalized treatment strategies to overcome tumor heterogeneity.
Published in
Lineage Tracing Reveals Clone-Specific Responses to Doxorubicin in Triple-Negative Breast Cancer
Morgan D, Gardner AL, Brock A · bioRxiv : the preprint server for biology 2025 · PMID 40166195 · doi:10.1101/2025.03.18.643980
This dataset
Open GSE291679 in finder → Find more human RNA-seq datasets → Breast cancer landscape →
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 GSE291679_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 PRJNA1234648 and SRA study SRP569684. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40166195) ↗
Study design
7 conditions, mostly with about 5 replicates each
MDA-MB-231 Cell Library 1KB3-P ×8 MDA-MB-231 Cell Library 1KB3 Dox-250 ×6 MDA-MB-231 Cell Library 1KB3 Dox-400 ×5 MDA-MB-231 Cell Library 1KB3 Dox-550 ×5 MDA-MB-231 Cell Library 1KB3 ×4 MDA-MB-231 Cell Library 1KB3 ESAM ×2 MDA-MB-231 Cell Library 1KB3 ESAM+ ×2 MDA-MB-231 Cell Library 1KB ×1 +3 more

Supports a between-group comparison across 32 samples.

How we read this: 7 replicated groups read from 36 sample titles; they account for 32 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
More Breast cancer datasets

Search all human 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.