CosMx Spatial Transcriptomics Protocol v1

This is a protocol for performing spatial transcriptomics (ST) using Bruker Nanostring’s CosMx technology. Here we are using their 1K panel where we have substituted 50 custom genes to target cell types in the healthy and disease kidneys and discover their spatial relationships. The protocol has many steps involving selecting tissue, tissue sectioning and mounting on slides, processing to prepare for hybridization with custom panel and in situ imaging. Post imaging, there are several types of analyses that can be performed and these will depend on the biological questions. Note that the ST methods and analytical tools are still evolving and there are several choices. Based on our roles in the HuBMAP and KPMP consortia, we have focused on key QC parameters to evaluate assay performance. Each of the steps from sectioning to data generation have quality assurance and control steps. Post CosMx assay, slides are stained with hematoxylin and eosin for bright-field microscopy and flanking tissue sections are typically also used for light microscopy evaluation or other technologies.