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Repair Windows errors before they cause bigger problemsFix Now →Fix the driver behind crashes, sound loss and screen glitchesFind Drivers →Clear out junk files and repair common Windows errorsFree Scan →First identify the spatial assay and tissue type: fresh-tissue preparation is platform- and specimen-specific, so there is no universal freezing, sectioning, or slide protocol. For a fresh-frozen workflow, the general priority is to preserve RNA and tissue morphology promptly, then follow the selected assay’s current handbook for embedding, sectioning, slide handling, storage, and downstream processing.
Choose the assay and tissue workflow before collection
Start with the target platform, assay, tissue type, and current protocol revision. Use the matching tissue-preparation handbook and compatible slide or kit documentation—not a procedure chosen only because it is also described as spatial RNA analysis.
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- 10x Genomics’ Visium HD documentation and Xenium documentation cover distinct workflows. Their instructions should not be treated as interchangeable.
- Bruker’s GeoMx knowledge base provides guidance for that platform’s tissue workflows, including fresh-frozen tissue.
Before collecting tissue, confirm which preservation format the assay accepts, what slide or preparation materials it requires, and which preparation steps apply to your specimen. A fresh-frozen method is not interchangeable with a workflow intended for FFPE tissue.
Preserve the specimen promptly
For fresh-frozen preparation, minimize delay between collection and freezing. The 10x Genomics Visium tissue guide recommends snap-freezing freshly obtained tissue to help prevent RNA degradation and ice-crystal-related morphological damage. Bruker also identifies cold and warm ischemic time, fixation, and storage as factors that matter for GeoMx tissue handling.
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There is no universal collection-to-freezing time threshold established across tissues and spatial assays. Do not apply a number from another tissue, platform, or study as a general limit; use the assay’s current instructions and tissue-specific validation.
Embed and freeze according to the selected protocol
OCT compound is used in the cited fresh-frozen guidance to preserve tissue structure and support cryosectioning. The Visium tissue guide describes OCT embedding, and Bruker advises storing fresh-frozen GeoMx tissue in OCT. Use the embedding medium and procedure specified for the assay; neither the timing nor the exact handling should be assumed universal.
Follow platform-specific instructions for sections and slides
Sectioning conditions, slide placement, and frozen-slide storage depend on the assay. Consult the relevant slide and tissue-preparation documentation for the exact workflow rather than borrowing values from a different platform or paper. A published spatial transcriptomics method is an example of a particular protocol, not a general specification for every spatial RNA assay.
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Before sectioning, verify the required slide type and any tissue-specific quality checks. Then follow the current protocol for section preparation and storage; the available guidance does not establish one section thickness or storage condition that applies to all platforms and tissues.
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Keep staining, fixation, and permeabilization within the assay workflow
Later processing is also assay-specific. Xenium’s handbook includes tissue quality assessment, fixation, and permeabilization guidance. Apply the steps and sequence in the current handbook for the selected assay; do not add a generic post-section treatment or substitute steps from an FFPE workflow for a fresh-frozen specimen.
Independent reader supportYour contribution helps us test, update, and keep practical guides available for everyone.Record pre-analytic handling for reproducibility
Keep a specimen record that lets the lab interpret how tissue was handled and reproduce the workflow. Useful details include:
- Collection date and time, and time to freezing
- Tissue identity and orientation
- Embedding medium
- Storage conditions
- Assay, platform, and protocol revision used
This is a practical recordkeeping recommendation, not a universal form prescribed by the cited sources.
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