This is a project which is currently making use of HPC facilities at Newcastle University. It is active.
For further information about this project, please contact:
This project aims to create the first integrated single-cell and spatial transcriptomic atlas of paediatric and adult cutaneous mastocytosis, a skin disorder marked by mast cell accumulation. By comparing lesional, non-lesional, and healthy skin samples, the study will investigate how mast cell states, genetic drivers, immune and stromal environments, and tissue niches differ between paediatric disease, which often regresses, and adult disease, which usually persists. The findings will help explain why these disease forms follow different clinical courses and may identify new therapeutic targets.
We will use the HPC facility to process and analyse large single-cell RNA-seq and spatial transcriptomics datasets from cutaneous mastocytosis skin samples. Analyses will include read alignment, transcript quantification, quality control, normalisation, batch correction, clustering, cell-type annotation, differential expression, dataset integration, spatial domain detection, cellular neighbourhood analysis, and ligand–receptor interaction inference. Software will include tools such as Cell Ranger, Space Ranger, Xenium pipelines, Seurat, Scanpy, scVI/scANVI, Harmony, Squidpy, Giotto, Cell2location, and Python/R-based workflows, managed using reproducible environments.