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 “Molecular Remodeling of Cancer-Associated Fibroblasts in Breast Cancer Patients Receiving Anti–PD-1 Immunotherapy” (Do et al., 2025).All data included here were reprocessed and analyzed from publicly available sources. No raw sequencing reads are redistributed.Source of Original DataThe dataset is derived from the BioKey study, whose raw scRNA-seq, scTCR-seq, and CITE-seq reads are deposited under restricted access in the European Genome-phenome Archive (EGA):Study: EGAS00001004809Raw single-cell reads: EGAD00001006608Processed per-patient count matrices available at: http://biokey.lambrechtslab.orgAccess to raw reads requires approval from the UZ Leuven–VIB Data Access Committee according to GDPR regulations.This Figshare deposit does not include any raw sequencing files, in compliance with the restrictions of the original study.Content of the Deposited Files1. cohort1.h5ad (AnnData object)This file contains the processed, normalized, and annotated gene expression matrix for fibroblast and stromal cells from 31 treatment-naive breast cancer patients receiving a single dose of pembrolizumab.2. cohort1_metadata.csvThis file contains the complete cell-level metadata corresponding to the .h5ad object.Intended UseThis 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.CitationIf using this dataset, please cite:Khanh Van Do, An Van Tran, Anh Duc Pham, Trang Thu Mac, Thang Luong Pham and Han Ngoc Do. Molecular Remodeling of Cancer-Associated Fibroblasts in Breast Cancer Patients Receiving Anti–PD-1 Immunotherapy. (2025).And acknowledge the original BioKey study that generated the raw sequencing data.