Adapting spatial transcriptomics to archival FFPE tissue samples prepared with routine clinical histology workflows

Processed data (https://doi.org/10.5281/zenodo.23558413) for the STAY study: "Adapting spatial transcriptomics to FFPE tissue sections prepared with routine histology workflows in clinical settings". Code: https://github.com/LeireAG/STAY Files One zip per data type. Each unzips to its own folder (e.g. spaceranger/), split into one subfolder per cohort and one per sample: <type>/<cohort>/<sample_id>/. The README.md in each cohort folder describes its contents. Sample IDs are listed in resources/sample_list.csv in the code repository. Zip Cohorts Contents spaceranger.zip paired, standard, STAY, lymph_node Space Ranger output per sample histopathology_annotation.zip paired, standard, STAY, lymph_node QuPath annotations and spot-level annotations (CSV) analysis.zip paired, STAY, standard Cropped H&E images and shifted spot coordinates (paired); per-spot detachment scores (STAY, standard) r_objects.zip paired, lymph_node Final Seurat/semla objects: paired_object.rds, lymph_node_object.rds Raw data (data/raw_data/) is deposited separately: RAW_DATA_ACCESSION The STAY cohort and lymph node data were obtained from: https://doi.org/10.6019/S-BIAD3080 and https://doi.org/10.5281/zenodo.18917100 How to use git clone https://github.com/LeireAG/STAY STAY cd STAY/data # download the zips into STAY/data, then: for f in *.zip; do unzip -n "$f"; done Each zip fills its matching folder in data/ (data/spaceranger/, data/r_objects/, ...). Then follow the repository README to set up the environments and run the analysis.