Matched primary-metastasis single-nucleus and spatial profiling of leiomyosarcoma

This repository contains single-nucleus RNA sequencing (snRNA-seq) data and spatial transcriptomics data from matched primary and metastatic leiomyosarcoma (LMS) samples. snRNA-seq data The snRNA-seq dataset comprises four matched primary–metastasis pairs (eight archival formalin-fixed paraffin-embedded [FFPE] tumor samples), including two lung and two liver metastases. Following quality control, approximately 49,000 nuclei were retained. Data Processing and Annotation:snRNA-seq data were quality controlled and annotated to resolve malignant, stromal, immune, and organ-resident cell populations. Malignant cells were identified using inferred copy-number variation profiles, supported by matched DNA methylation array data. Repository Contents:- Quality-controlled and annotated Seurat object (`.rds`)- Per-sample HDF5 expression matrices for all eight samples (`.h5`)- Sample and cell-level metadata (`.csv`) Spatial transcriptomics data The spatial transcriptomics (ST) dataset was generated using the Xenium platform (10x Genomics) and comprises a tissue microarray (TMA) containing primary and metastatic LMS samples. The dataset includes spatially resolved gene expression data together with corresponding hematoxylin and eosin (H&E)-stained tissue images. Data Processing and Annotation:ST data were quality controlled and annotated using a combined strategy integrating Seurat anchor-based label transfer with SingleR predictions, reviewed by a pathologist with reference to the histomorphology of matched H&E-stained sections. Repository Contents:- Quality-controlled and annotated Seurat object (`.rds`)- Complete Xenium output directory containing the ST data and associated files- corresponding H&E stained TMA image (`.ome.tif`) These datasets provide complementary single-nucleus and spatially resolved molecular profiles of LMS, and enable investigation of malignant, stromal, and immune cell states during metastatic progression.