Processed single-cell RNA-seq dataset of cancer-associated fibroblasts in breast cancer patients receiving anti–PD-1 therapy

This dataset contains the processed single-cell RNA sequencing (scRNA-seq) data used in the study <b>“Molecular Remodeling of Cancer-Associated Fibroblasts in Breast Cancer Patients Receiving Anti–PD-1 Immunotherapy”</b> (Do et al., 2025).<br>All data included here were <b>reprocessed and analyzed from publicly available sources</b>. No raw sequencing reads are redistributed.<b>Source of Original Data</b>The dataset is derived from the <b>BioKey study</b>, whose raw scRNA-seq, scTCR-seq, and CITE-seq reads are deposited under <b>restricted access</b> in the European Genome-phenome Archive (EGA):Study: <b>EGAS00001004809</b>Raw single-cell reads: <b>EGAD00001006608</b>Processed per-patient count matrices available at: <i>http://biokey.lambrechtslab.org</i>Access to raw reads requires approval from the UZ Leuven–VIB Data Access Committee according to GDPR regulations.<br>This Figshare deposit <b>does not include any raw sequencing files</b>, in compliance with the restrictions of the original study.<b>Content of the Deposited Files</b><b>1. </b><code><strong>cohort1.h5ad</strong></code><b> (AnnData object)</b>This file contains the <b>processed, normalized, and annotated gene expression matrix</b> for fibroblast and stromal cells from <b>31 treatment-naive breast cancer patients</b> receiving a single dose of pembrolizumab.<b>2. </b><code><strong>cohort1_metadata.csv</strong></code>This file contains the <b>complete cell-level metadata</b> corresponding to the <code>.h5ad</code> object.<b>Intended Use</b>This dataset is shared to support transparency and reproducibility of the analyses performed in our study, specifically:identification of CAF subtypesdifferential expression analysispathway enrichmentcell–cell interaction inferencecross-dataset validationThe data may be freely reused for research and educational purposes, provided proper citation.<b>Citation</b>If using this dataset, please cite:<b>Khanh Van Do, An Van Tran, Anh Duc Pham, Trang Thu Mac, Thang </b><b>Luong Pham and Han Ngoc Do. Molecular Remodeling of Cancer-Associated Fibroblasts in Breast Cancer Patients Receiving Anti–PD-1 Immunotherapy. (2025).</b>And acknowledge the <b>original BioKey study</b> that generated the raw sequencing data.