GEO series

Single cell RNAseq dataset of MDA-MB-231 xenograft and matched metastasis

GSE299393 Homo sapiens (human) Single-cell RNA-seq 17 samples Submitted 2025/06/23 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 17 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Homo sapiens (human)
Samples: 17 samples: 4 × Primary tumour, MDA-MB-231 xenograft model, Mouse vs 3 × Liver metastasis, MDA-MB-231 xenograft model, Mouse vs 3 × Lymph node metastasis, MDA-MB-231 xenograft model, Mouse vs 3 × Lung metastasis, MDA-MB-231 xenograft model, MouseGroups 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: AAnet Resolves a Continuum of Spatially Localized Cell States to Unveil Intratumoral HeterogeneityCancer discovery · 2025

Summary (written by the submitters)

Identifying functionally important cell states and structure within heterogeneous tumors remains a significant biological and computational challenge. Current clustering or trajectory-based models are ill-equipped to address the notion that cancer cells reside along a phenotypic continuum. We present Archetypal Analysis network (AAnet), a neural network that learns archetypal states within a phenotypic continuum in single-cell data.

Read the full summary ↓

Unlike traditional archetypal analysis, AAnet learns archetypes in simplex-shaped neural network latent space. Using pre-clinical models and clinical breast cancers, AAnet resolves distinct cell states and processes, including cell proliferation, hypoxia, metabolism and immune interactions. Primary tumor archetypes are recapitulated in matched liver, lung and lymph node metastases. This dataset comprises of the 10X genomics based single cell RNAseq on MDA-MB-231 xenografts and matched metastasis used to perform archetypal analysis to understand tumour hetegeneity as a phenotypic continuum.

Published in

AAnet Resolves a Continuum of Spatially Localized Cell States to Unveil Intratumoral Heterogeneity

Venkat A, Youlten SE, San Juan BP et al. · Cancer discovery 2025 · PMID 40552975 · doi:10.1158/2159-8290.CD-24-0684

This dataset

Open GSE299393 in finder → Find more human 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 GSE299393_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 PRJNA1274250 and SRA study SRP591205. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40552975) ↗

Study design

4 × Primary tumour, MDA-MB-231 xenograft model, Mouse vs 3 × Liver metastasis, MDA-MB-231 xenograft model, Mouse vs 3 × Lymph node metastasis, MDA-MB-231 xenograft model, Mouse vs 3 × Lung metastasis, MDA-MB-231 xenograft model, Mouse

Supports a between-group comparison across 13 samples.

How we read this: 4 replicated groups read from 17 sample titles; they account for 13 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

GSM9038574 Liver metastasis, MDA-MB-231 xenograft model, Mouse 43973 Liver metastasis, MDA-M…
GSM9038575 Lymph node metastasis, MDA-MB-231 xenograft model, Mouse 43973 Lymph node metastasis, …
GSM9038576 Lung metastasis, MDA-MB-231 xenograft model, Mouse 43973 Lung metastasis, MDA-MB…
GSM9038577 Primary tumour, MDA-MB-231 xenograft model, Mouse 43973 Primary tumour, MDA-MB-…
GSM9038578 Liver metastasis, MDA-MB-231 xenograft model, Mouse 43975 Liver metastasis, MDA-M…
GSM9038579 Lung metastasis, MDA-MB-231 xenograft model, Mouse 43975 Lung metastasis, MDA-MB…
GSM9038580 Lymph node metastasis, MDA-MB-231 xenograft model, Mouse 43975 Lymph node metastasis, …
GSM9038581 Primary tumour, MDA-MB-231 xenograft model, Mouse 43975 Primary tumour, MDA-MB-…
GSM9038582 Liver metastasis_1, MDA-MB-231 xenograft model, Mouse 43978
GSM9038583 Liver metastasis_2, MDA-MB-231 xenograft model, Mouse 43978
GSM9038584 Lymph node metastasis_1, MDA-MB-231 xenograft model, Mouse 43978
GSM9038585 Lymph node metastasis_2, MDA-MB-231 xenograft model, Mouse 43978
GSM9038586 Primary tumour, MDA-MB-231 xenograft model, Mouse 43978 Primary tumour, MDA-MB-…
GSM9038587 Liver metastasis, MDA-MB-231 xenograft model, Mouse 43979 Liver metastasis, MDA-M…
GSM9038588 Lung metastasis, MDA-MB-231 xenograft model, Mouse 43979 Lung metastasis, MDA-MB…
GSM9038589 Lymph node metastasis, MDA-MB-231 xenograft model, Mouse 43979 Lymph node metastasis, …
GSM9038590 Primary tumour, MDA-MB-231 xenograft model, Mouse 43979 Primary tumour, MDA-MB-…

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GSE271120 TRAIL-induced cytokine production via NFKB2 pathway promotes neutrophil chemotaxis and immune suppression in triple negative breast cancers [MDA-MB-231] 17 samples shares mda-mb-231
GSE223499 Non-small Cell Lung Cancer Brain Metastasis Atlas [single nuclei RNAseq] 42 samples shares metastasis

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