Protocol for Xenium spatial transcriptomics studies using fixed frozen mouse brain sections

Here, we present a protocol for Xenium spatial transcriptomics studies using fixed frozen mouse brain sections. We describe steps for intracardiac perfusion, cryosectioning, and floating section mounting of brain sections, which enable runs on the Xenium analyzer and data delivery. We demonstrate that, in addition to the 10× Genomics-validated formalin-fixed paraffin-embedded (FFPE) and fresh frozen sections, fixed frozen thin brain sections are compatible with the Xenium platform and provide excellent imaging and quantification results for spatially resolved gene expression. For complete details on the use and execution of this protocol, please refer to Ma et al.1 [Display omitted] •Steps for intracardial perfusion, brain collection, cryoprotection, and OCT embedding•Instructions for mounting fixed frozen mouse brain thin sections on Xenium slides•Fixed frozen sections allow for better sample preparation and usage of the imaging area•Fixed frozen sections provide excellent results in spatially resolved gene expressions Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. Here, we present a protocol for Xenium spatial transcriptomics studies using fixed frozen mouse brain sections. We describe steps for intracardiac perfusion, cryosectioning, and floating section mounting of brain sections, which enable runs on the Xenium analyzer and data delivery. We demonstrate that, in addition to the 10× Genomics-validated formalin-fixed paraffin-embedded (FFPE) and fresh frozen sections, fixed frozen thin brain sections are compatible with the Xenium platform and provide excellent imaging and quantification results for spatially resolved gene expression.