Spatial Transcriptomics Identifies Immune-Stromal Niches Associated with Cancer in Adult Dermatomyositis

This dataset contains R data objects from our study on adult-onset dermatomyositis (DM) and cutaneous lupus erythematosus (CLE). Files are named using the convention _sp_ = spatial transcriptomics and _sc_ = single-cell RNA-seq. All objects are Seurat objects and can be loaded into R via readRDS(). Spatial transcriptomics (*_sp_data.RDS) — Xenium Prime 5K, 10x Genomics High-resolution spatial transcriptomics data from 19 skin biopsies: 12 DM lesional samples, 4 CLE lesional samples, 3 healthy control samples Files: main_object_sp_data.RDS — main spatial Seurat object with all cells across the 19 biopsies Lymphoid_sp_data.RDS — T and NK cell fine-typing Myeloid_sp_data.RDS — myeloid fine-typing (macrophages, dendritic cells, monocytes, Langerhans cells) CXCL10_myeloid_sp_data.RDS — CXCL10⁺ inflammatory myeloid subsets B_Plasma_sp_data.RDS — B and plasma cells cyclic_immune_sp_data.RDS — proliferating / cycling immune cells Ep_Keratinocytes_sp_data.RDS — interfollicular epidermal keratinocytes Sweat_glands_Fol_Keratinocytes_sp_data.RDS — eccrine, apocrine, and sebaceous gland cells together with follicular keratinocytes Fibroblasts_sp_data.RDS — fibroblast subsets Vascular_sp_data.RDS — endothelial cells Smooth_Pericytes_sp_data.RDS — smooth muscle cells, pericytes, and Schwann cells Single-cell RNA sequencing (*_sc_data.RDS) — Chromium Single Cell Gene Expression Flex, 10x Genomics Single-cell RNA-seq data from 44 skin biopsies: 22 DM patients (lesional), 9 CLE patients (lesional), 8 non-lesional samples from a subset of patients, 6 healthy controls Files: main_object_sc_data.RDS — main single-cell Seurat object with all cells across the 44 biopsies Lymphoid_sc_data.RDS — T and NK cell fine-typing Myeloid_sc_data.RDS — myeloid fine-typing (macrophages, dendritic cells, monocytes, Langerhans cells) B_Plasma_pDC_sc_data.RDS — B cells, plasma cells, and plasmacytoid dendritic cells Ep_Keratinocytes_sc_data.RDS — interfollicular epidermal keratinocytes Fol_Keratinocytes_sc_data.RDS — follicular keratinocytes Sweat_glands_sc_data.RDS — eccrine, apocrine, and sebaceous gland cells Fibroblasts_sc_data.RDS — fibroblast subsets Vascular_sc_data.RDS — endothelial cells Smooth_Pericytes_sc_data.RDS — smooth muscle cells, pericytes, and Schwann cells Each fine-typing object is a subset of the corresponding main_object_* and contains the curated cluster annotations (sp_type / type and sp_annotation / annotation) used in the paper, together with sample-level metadata (patient ID, condition, anatomical site, sex, age, subtype).