Spatially resolved integrative analysis of transcriptomic and metabolomic changes in tissue injury studies

This Zenodo record provides all processed datasets, MAGPIE inputs, and analysis scripts associated with the MAGPIE manuscript (Williams et al). AbstractRecent developments in spatially resolved -omics have enabled the joint study of gene expression, metabolite levels and tissue morphology, offering greater insights into biological pathways. Integrating these modalities from matched tissue sections to probe spatially-coordinated processes, however, remains challenging.Here we introduce MAGPIE, a framework for co-registering spatially resolved transcriptomics, metabolomics, and tissue morphology from the same or consecutive sections.We show MAGPIE’s generalisability and scalability on spatial multi-omics data from multiple tissues, combining Visium with MALDI and DESI mass spectrometry imaging. MAGPIE was also applied to new multimodal datasets generated with a specialised sampling strategy to characterise the metabolic and transcriptomic landscape in an in vivo model of drug-induced pulmonary fibrosis and to link small-molecule co-detection with endogenous lung responses.MAGPIE demonstrates the refined resolution and enhanced interpretability that spatial multimodal analyses provide for studying tissue injury especially in pharmacological contexts, and delivers a modular, accessible workflow for data integration The repository is designed to enable reproducibility of integrative multi-omics analyses performed in the manuscript and facilitate extended analysis of the new and previously published datasets. 1. MAGPIE Inputs The file magpie_inputs.zip contains separate folders for each dataset used in the manuscript. Each folder includes: MSI data in a peak-by-pixel table (MSI_intensities) along with (x,y)-coordinates and other metadata (MSI_metadata) and (if available) an MSI H&E image (MSI_HE) Visium Space Ranger outputs (from outs/ folder) These inputs are ready to be used directly with the MAGPIE pipeline (see the MAGPIE GitHub repository). 2. Analysis scripts and processed data The figure_notebooks.zip file contains qmd files and rendered htmls showing how the manuscript figures were generated and data/ which contains processed semla objects and other saved outputs used by these scripts. For more details on the contents of this record, see README.md