GEO series

A single cell and spatial atlas of preinvasive breast cancer

GSE348584 Homo sapiens (human) Single-cell RNA-seq 15 samples Submitted 2026/09/25 Platform GPL33762

At a glance

Single-cell RNA-seq · human · 15 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: 15 samples
Data you can get: A processed table (series matrix) and supplementary files from NCBI.

Summary (written by the submitters)

Ductal carcinoma in situ (DCIS) is the most common preinvasive breast cancer, however our knowledge of the DCIS tumor microenvironment (TME) remains limited. We constructed a comprehensive atlas of the TME in estrogen-receptor positive DCIS using fresh samples collected from normal breast tissues, DCIS and invasive breast cancers. This Series only contains the Xenium samples, for the Visium samples see GSE348919.

This dataset

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Download · which file do I need?

Direct links to NCBI, 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.

All supplementary files ↗

3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE348584_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

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 PRJNA1534928. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Samples in this study

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+ 15 more — browse all 15 samples with per-sample file links →

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