Bone-derived osterix+ osteolineage cells are a source of tumor-promoting myofibroblastic cancer-associated fibroblasts in breast cancer
Year: 2026
Type: book
Abstract: The codes are consolidated from RMarkdown files used for analyzing and visualizing data. Note: Publicly available data are retrieved from data availability section of the original publications. Patient metadata was retrived and organized into separate excel sheets from the supplementary data provided by the publication. The finalized codes for processing CAF subset from Wu 2021 dataset is no longer available due to untimely code backup and loss of cluster access. In principle, the integrated human CAF dataset can be reproduced by integrating the entire Wu 2021 and Cords 2023 datasets, removing low-quality cells, re-clustering, and isolating the PDGFRA+ PDGFRB+/- clusters. Clusters were annotated using canonical markers, which are shown in the publication but may not be included in the codes for preliminary processing of the datasets. Files required for performing ssGSEA over the TCGA datasets were generated from the bulk RNA and signature genesets manually and via command-line. The codes and procedurals are not included, but the files should be reproducible given the documentations on the file format. The sequences and codes for creating the customized reference genome with TdtTomato are available at https://github.com/aulezko/MouseChoroidPlexus/releases/tag/MouseChoroidPlexus. The raw and processed data of the mouse scRNA-seq generated for this paper are available at GSE292888. See Data Availability section of the publication for descriptions of retrieving publicly available human data. Version notes: V1: the codes used for data analysis V2: Some codes were updated for correction during the revision V3: codes for visualization were updated for editorial revision. Specifically, statistical tests were added to some of the plots.
Institution: Washington University in St. Louis
Topic: Cancer Cells and Metastasis
Subfield: Oncology
Field: Medicine
Domain: Health Sciences
Open Access status: green
OpenAlex ID: W7119983729
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