Question: Should I select FFPE, Fresh Frozen, or Fixed Frozen for my Visium HD Spatial Gene Expression experiment?
Answer: If you have the flexibility of well-preserved tissue for multiple sample types that will address your research question, below are some considerations for sample selection:
Preservation of Tissue Morphology - Typically we see that well preserved FFPE tissues have the most well-preserved tissue morphology and therefore result in the highest quality H&E images for downstream analysis like cell segmentation.
Sensitivity - Typically we see that processing well-preserved Fresh Frozen tissues with Visium HD generates the highest UMIs per tissue area compared to similar samples that are FFPE or Fixed Frozen. This trend is not unexpected as well preserved Fresh Frozen tissues have the highest RNA quality. However, as Fresh Frozen tissue is more susceptible to RNA degradation it is important to store Fresh Frozen tissue properly and extended storage may impact RNA quality.
Tissue Handling / Sample Storage - Typically FFPE is the optimal tissue for ease of handling and sample input flexibility. Archived FFPE slides (sectioned, H&E stained, hardset coverslipped and stored) can be profiled using Visium HD. Sectioning and sample placement is typically the easiest with FFPE. In addition, FFPE samples are more robust to RNA degradation. FFPE blocks that have been stored for months or years have been successfully profiled using Visium HD.
Visium HD also works robustly with Fixed Frozen tissue and delivers high quality results. However, Fixed Frozen is a more challenging tissue compared to FFPE and Fresh Frozen due to higher rates of tissue detachment. Fixed Frozen tissue blocks are more prone to tears and folds when the blade cuts through the OCT block which can lead to non-uniform adhesion to the slide surface. Fixed Frozen tissue sections tend to hold more water content and require longer thawing to fully dry the tissue. Additional details including tips and best practices when working with Fixed Frozen tissues can be found in the Visium HD Fixed Frozen Tissue Preparation Handbook (CG000764).
Products: Visium HD