Source Data for Figures in Spatial colocalization and molecular crosstalk of myofibroblastic CAFs and tumor cells shape lymph node metastasis in oral squamous cell carcinoma

This Figshare deposit contains the source data underlying the figures presented in our manuscript: "Spatial colocalization and molecular crosstalk of myofibroblastic CAFs and tumor cells shape lymph node metastasis in oral squamous cell carcinoma" (submitted to PLOS Genetics, Manuscript ID: PGENETICS-D-25-00169R1).

The source data files within this deposit are organized into folders corresponding to each figure number (e.g., a folder named Source Data Fig. 1 for Figure 1, Source Data Supporting Fig. 1 for Supporting Figure S1, and so on, covering Figures 1-9 and Supporting Figures S1-S6). Within each figure-specific folder, users will find the relevant data files used to generate that figure or its panels.

These files may include, but are not limited to:

csv files containing numerical data for plots, graphs, tables, and statistical values presented in the figures.

Original image files (e.g., .tif, .png) for microscopy, immunohistochemistry (IHC), or other visual data, where applicable.

Specific data formats for certain analyses, such as NetCDF (.nc) files for trace plot data (e.g., Supporting Figure S4R).

Please refer to the filenames within each figure-specific folder for more details on their content. This deposit provides the specific data subsets or processed values used to generate the final figures presented in our study.

The raw sequencing reads for the primary spatial transcriptomics experiments are available at DDBJ under BioProject accession PRJDB13905 (https://ddbj.nig.ac.jp/search/entry/bioproject/PRJDB13905). A processed and integrated AnnData object (.h5ad) combining four of these samples is available at GEA under accession E-GEAD-511 (https://ddbj.nig.ac.jp/public/ddbj_database/gea/experiment/E-GEAD-000/E-GEAD-511/). Supplementary spatial metadata components (pickled Python objects) for use with this integrated AnnData object are available at Figshare (https://doi.org/10.6084/m9.figshare.20408067). For the complete 10x Genomics Space Ranger output files for each of the four individual samples (including filtered_feature_bc_matrix.h5 files, full spatial image folders, and patho_annot folders), please refer to our separate Figshare deposit:https://doi.org/10.6084/m9.figshare.29237660.

All patient-derived images or data included in this specific Figshare deposit have been appropriately de-identified prior to deposition.