BIDMC TMC / STU - Methodological compendium for Singular Genomics G4X spatial multiomics platform v1

This protocol describes the application of the Singular Genomics G4X Spatial Sequencer for high-resolution, in situ spatial multiomics on formalin-fixed, paraffin-embedded (FFPE) tissue sections within the HuBMAP consortium. Tissue sections are transferred using a hydrogel-pad based mechanism that separates sectioning from slide assembly, enabling profiling of up to 128 millimeter-scale regions of interest per run across approximately 40cm² of imageable area. The platform integrates spatial transcriptomics (up to 500-plex), multiplexed proteomics (up to 18-plex), and automated fluorescent Hematoxylin and Eosin (fH&E) imaging, with molecular and histological data registered at subcellular resolution. This workflow allows tissue cutting, storage, and transfer to occur independently, with gel-mounted sections storable at 4°C and transportable between locations. This modular approach supports multi-institutional studies in which tissue collection centers and analytical sequencing sites are geographically separate, facilitating the generation of high-density spatial datasets across distributed research networks.