GEO series

Defining the Regulatory Logic of Breast Cancer Using Single-Cell Epigenetic and Transcriptome Profiling

GSE243526 Homo sapiens (human) Single-cell RNA-seq 40 samples Submitted 2024/12/31 Platform GPL18573

At a glance

Single-cell RNA-seq · human · 40 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)
Topic: Breast cancerThis series is part of our curated briefing on it.
Samples: 40 samples: 40 samples, each with a distinct title — no replicated groupsGroups 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: Defining the regulatory logic of breast cancer using single-cell epigenetic and transcriptome profilingCell genomics · 2025

Summary (written by the submitters)

Annotation of the cis-regulatory elements mediating oncogenic transcription is essential to understanding breast cancer biology. In this work, we quantitatively linked variation in chromatin accessibility to gene expression within human breast tumors, normal mammary reduction tissue samples, and breast cancer cell lines using single-cell chromatin accessibility sequencing (scATAC-seq) and single-cell transcriptomic sequencing (scRNA-seq).

Read the full summary ↓

Our analysis resolved the underlying cellular heterogeneity in chromatin accessibility and transcriptional output for each patient sample. We also showed that our findings were recapitulated in the breast cancer cell line samples. These data will serve as an important resource for the single-cell genomics and breast cancer research communities.

Published in

Defining the regulatory logic of breast cancer using single-cell epigenetic and transcriptome profiling

Regner MJ, Garcia-Recio S, Thennavan A et al. · Cell genomics 2025 · PMID 39914387 · doi:10.1016/j.xgen.2025.100765

This dataset

Open GSE243526 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 GSE243526_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 PRJNA1018859. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39914387) ↗

Study design

40 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 40 sample titles: 40 distinct titles with little repetition. 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

GSM7789963 Primary breast tumor, scATAC-seq, Patient_5_35A4AL_ATAC
GSM7789964 Primary breast tumor, scRNA-seq, Patient_5_35A4AL_RNA
GSM7789965 Primary breast tumor, scATAC-seq, Patient_7_35EE8L_ATAC
GSM7789966 Primary breast tumor, scRNA-seq, Patient_7_35EE8L_RNA
GSM7789967 Primary breast tumor, scATAC-seq, Patient_8_3821AL_ATAC
GSM7789968 Primary breast tumor, scRNA-seq, Patient_8_3821AL_RNA
GSM7789969 Primary breast tumor, scATAC-seq, Patient_9_3B3E9L_ATAC
GSM7789970 Primary breast tumor, scRNA-seq, Patient_9_3B3E9L_RNA
GSM7789971 Primary breast tumor, scATAC-seq, Patient_10_3C7D1L_ATAC
GSM7789972 Primary breast tumor, scRNA-seq, Patient_10_3C7D1L_RNA
GSM7789973 Primary breast tumor, scATAC-seq, Patient_13_3D388L_ATAC
GSM7789974 Primary breast tumor, scRNA-seq, Patient_13_3D388L_RNA
GSM7789975 Primary breast tumor, scATAC-seq, Patient_11_3FCDEL_ATAC
GSM7789976 Primary breast tumor, scRNA-seq, Patient_11_3FCDEL_RNA
GSM7789977 Primary breast tumor, scATAC-seq, Patient_14_43E7BL_ATAC
GSM7789978 Primary breast tumor, scRNA-seq, Patient_14_43E7BL_RNA
GSM7789979 Primary breast tumor, scATAC-seq, Patient_14_43E7CL_ATAC
GSM7789980 Primary breast tumor, scRNA-seq, Patient_14_43E7CL_RNA
GSM7789981 Primary breast tumor, scATAC-seq, Patient_12_44F0AL_ATAC
GSM7789982 Primary breast tumor, scRNA-seq, Patient_12_44F0AL_RNA
GSM7789983 Primary breast tumor, scATAC-seq, Patient_15_45CB0L_ATAC
GSM7789984 Primary breast tumor, scRNA-seq, Patient_15_45CB0L_RNA
GSM7789985 Normal breast tissue, scATAC-seq, Patient_1_49758L_ATAC
GSM7789986 Normal breast tissue, scRNA-seq, Patient_1_49758L_RNA
GSM7789987 Normal breast tissue, scATAC-seq, Patient_2_49CFCL_ATAC
GSM7789988 Normal breast tissue, scRNA-seq, Patient_2_49CFCL_RNA
GSM7789989 Normal breast tissue, scATAC-seq, Patient_3_4AF75L_ATAC
GSM7789990 Normal breast tissue, scRNA-seq, Patient_3_4AF75L_RNA
GSM7789991 Normal breast tissue, scATAC-seq, Patient_4_4B146L_ATAC
GSM7789992 Normal breast tissue, scRNA-seq, Patient_4_4B146L_RNA
GSM7789993 Primary breast tumor, scATAC-seq, Patient_6_4C2E5L_ATAC
GSM7789994 Primary breast tumor, scRNA-seq, Patient_6_4C2E5L_RNA
GSM7789995 Breast cancer cell line, scRNA-seq, HCC1143_RNA
GSM7789996 Breast cancer cell line, scATAC-seq, HCC1143_ATAC
GSM7789997 Breast cancer cell line, scATAC-seq, MCF7_ATAC
GSM7789998 Breast cancer cell line, scRNA-seq, MCF7_RNA
GSM7789999 Breast cancer cell line, scRNA-seq, SUM149PT_RNA
GSM7790000 Breast cancer cell line, scATAC-seq, SUM149PT_ATAC
GSM7790001 Breast cancer cell line, scATAC-seq, T47D_ATAC
GSM7790002 Breast cancer cell line, scRNA-seq, T47D_RNA

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