Processed single-cell RNA-seq dataset of cancer-associated fibroblasts in breast cancer patients receiving anti–PD-1 therapy
<p dir="ltr">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 i...
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| _version_ | 1849927637188739072 |
|---|---|
| author | Thang Pham (19938126) |
| author2 | Khanh V. Do (22645458) An Van Tran (22645586) Anh Duc Pham (22645589) Trang Mac Thu (22645610) |
| author2_role | author author author author |
| author_facet | Thang Pham (19938126) Khanh V. Do (22645458) An Van Tran (22645586) Anh Duc Pham (22645589) Trang Mac Thu (22645610) |
| author_role | author |
| dc.creator.none.fl_str_mv | Thang Pham (19938126) Khanh V. Do (22645458) An Van Tran (22645586) Anh Duc Pham (22645589) Trang Mac Thu (22645610) |
| dc.date.none.fl_str_mv | 2025-11-25T01:40:00Z |
| dc.identifier.none.fl_str_mv | 10.6084/m9.figshare.30663536.v1 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/dataset/Processed_single-cell_RNA-seq_dataset_of_cancer-associated_fibroblasts_in_breast_cancer_patients_receiving_anti_PD-1_therapy/30663536 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Cancer cell biology cancer-associated fibroblasts (CAF) Breast Cancer 1000 immune checkpoint inhibitors (CPI) Anti-PD-1 therapy Tumor Microenvironment CD 90 CAF subtypes Immune resistance Single-cell RNA Sequencing (scRNA) |
| dc.title.none.fl_str_mv | Processed single-cell RNA-seq dataset of cancer-associated fibroblasts in breast cancer patients receiving anti–PD-1 therapy |
| dc.type.none.fl_str_mv | Dataset info:eu-repo/semantics/publishedVersion dataset |
| description | <p dir="ltr">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.</p><h3><b>Source of Original Data</b></h3><p dir="ltr">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):</p><ul><li>Study: <b>EGAS00001004809</b></li><li>Raw single-cell reads: <b>EGAD00001006608</b></li><li>Processed per-patient count matrices available at: <a href="http://biokey.lambrechtslab.org" rel="noopener" target="_new"><i>http://biokey.lambrechtslab.org</i></a></li></ul><p dir="ltr">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.</p><h3><b>Content of the Deposited Files</b></h3><h4><b>1. </b><code><strong>cohort1.h5ad</strong></code><b> (AnnData object)</b></h4><p dir="ltr">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.</p><h4><b>2. </b><code><strong>cohort1_metadata.csv</strong></code></h4><p dir="ltr">This file contains the <b>complete cell-level metadata</b> corresponding to the <code>.h5ad</code> object.</p><h3><b>Intended Use</b></h3><p dir="ltr">This dataset is shared to support transparency and reproducibility of the analyses performed in our study, specifically:</p><ul><li>identification of CAF subtypes</li><li>differential expression analysis</li><li>pathway enrichment</li><li>cell–cell interaction inference</li><li>cross-dataset validation</li></ul><p dir="ltr">The data may be freely reused for research and educational purposes, provided proper citation.</p><h3><b>Citation</b></h3><p dir="ltr">If using this dataset, please cite:</p><p dir="ltr"><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></p><p dir="ltr">And acknowledge the <b>original BioKey study</b> that generated the raw sequencing data.</p> |
| eu_rights_str_mv | openAccess |
| id | Manara_493316b9bd6a6cbac77b528a13e63866 |
| identifier_str_mv | 10.6084/m9.figshare.30663536.v1 |
| network_acronym_str | Manara |
| network_name_str | ManaraRepo |
| oai_identifier_str | oai:figshare.com:article/30663536 |
| publishDate | 2025 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | Processed single-cell RNA-seq dataset of cancer-associated fibroblasts in breast cancer patients receiving anti–PD-1 therapyThang Pham (19938126)Khanh V. Do (22645458)An Van Tran (22645586)Anh Duc Pham (22645589)Trang Mac Thu (22645610)Cancer cell biologycancer-associated fibroblasts (CAF)Breast Cancer 1000immune checkpoint inhibitors (CPI)Anti-PD-1 therapyTumor Microenvironment CD 90CAF subtypesImmune resistanceSingle-cell RNA Sequencing (scRNA)<p dir="ltr">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.</p><h3><b>Source of Original Data</b></h3><p dir="ltr">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):</p><ul><li>Study: <b>EGAS00001004809</b></li><li>Raw single-cell reads: <b>EGAD00001006608</b></li><li>Processed per-patient count matrices available at: <a href="http://biokey.lambrechtslab.org" rel="noopener" target="_new"><i>http://biokey.lambrechtslab.org</i></a></li></ul><p dir="ltr">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.</p><h3><b>Content of the Deposited Files</b></h3><h4><b>1. </b><code><strong>cohort1.h5ad</strong></code><b> (AnnData object)</b></h4><p dir="ltr">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.</p><h4><b>2. </b><code><strong>cohort1_metadata.csv</strong></code></h4><p dir="ltr">This file contains the <b>complete cell-level metadata</b> corresponding to the <code>.h5ad</code> object.</p><h3><b>Intended Use</b></h3><p dir="ltr">This dataset is shared to support transparency and reproducibility of the analyses performed in our study, specifically:</p><ul><li>identification of CAF subtypes</li><li>differential expression analysis</li><li>pathway enrichment</li><li>cell–cell interaction inference</li><li>cross-dataset validation</li></ul><p dir="ltr">The data may be freely reused for research and educational purposes, provided proper citation.</p><h3><b>Citation</b></h3><p dir="ltr">If using this dataset, please cite:</p><p dir="ltr"><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></p><p dir="ltr">And acknowledge the <b>original BioKey study</b> that generated the raw sequencing data.</p>2025-11-25T01:40:00ZDatasetinfo:eu-repo/semantics/publishedVersiondataset10.6084/m9.figshare.30663536.v1https://figshare.com/articles/dataset/Processed_single-cell_RNA-seq_dataset_of_cancer-associated_fibroblasts_in_breast_cancer_patients_receiving_anti_PD-1_therapy/30663536CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/306635362025-11-25T01:40:00Z |
| spellingShingle | Processed single-cell RNA-seq dataset of cancer-associated fibroblasts in breast cancer patients receiving anti–PD-1 therapy Thang Pham (19938126) Cancer cell biology cancer-associated fibroblasts (CAF) Breast Cancer 1000 immune checkpoint inhibitors (CPI) Anti-PD-1 therapy Tumor Microenvironment CD 90 CAF subtypes Immune resistance Single-cell RNA Sequencing (scRNA) |
| status_str | publishedVersion |
| title | Processed single-cell RNA-seq dataset of cancer-associated fibroblasts in breast cancer patients receiving anti–PD-1 therapy |
| title_full | Processed single-cell RNA-seq dataset of cancer-associated fibroblasts in breast cancer patients receiving anti–PD-1 therapy |
| title_fullStr | Processed single-cell RNA-seq dataset of cancer-associated fibroblasts in breast cancer patients receiving anti–PD-1 therapy |
| title_full_unstemmed | Processed single-cell RNA-seq dataset of cancer-associated fibroblasts in breast cancer patients receiving anti–PD-1 therapy |
| title_short | Processed single-cell RNA-seq dataset of cancer-associated fibroblasts in breast cancer patients receiving anti–PD-1 therapy |
| title_sort | Processed single-cell RNA-seq dataset of cancer-associated fibroblasts in breast cancer patients receiving anti–PD-1 therapy |
| topic | Cancer cell biology cancer-associated fibroblasts (CAF) Breast Cancer 1000 immune checkpoint inhibitors (CPI) Anti-PD-1 therapy Tumor Microenvironment CD 90 CAF subtypes Immune resistance Single-cell RNA Sequencing (scRNA) |