Cell type mapping reveals tissue niches and interactions in subcortical multiple sclerosis lesions [spatial transcriptomics]

We generated a paired snRNA-seq (n= 15) and spatial transcriptomics (n=19) dataset from subcortical chronic active and chronic inactive MS lesions, identifying spatial niches and key cell interactions driving inflammation and disease progression at the lesion rim. This repository offers access to all the trancriptomics data that was used in the paper. It includes, all FASTQ files for both transcriptomics, along with the necessary files for running spatial transcriptomic samples (H&E images and JSON files), as well as the curated atlas, all derived cell subtype atlases from the main atlas and all curated ST slides. Overall design: Paired single-nuclei RNA-sequencing and spatial transcriptomics data from multiple sclerosis (MS) subcortical white matter lesions from 7 controls and 12 MS human donors.