Question: Do you have recommendations for sectioning skin for Xenium?
Answer: The Xenium Human Gene Expression panel was designed to cover both healthy skin and cancer conditions. The following cell types are prioritized: keratinocytes (3 layers), melanocytes, fibroblast, Langerhan's cells, and vascular endothelial cells. Additional panel metadata can be found here.
Skin can be difficult tissue to work with as it can be prone to detachment depending on which region of the skin you are interested in and also the disease state. We have found that the ability for skin to adhere to a slide may potentially decrease when moving into deeper layers of the specimen (i.e., hypodermis/subcutis). Generally speaking, the Xenium FFPE Tissue Preparation Guide and Xenium FFPE Deparaffinization/Decrosslinking Protocols have appropriate guidance for working with skin. While we always recommend following Demonstrated Protocols for Tissue Preparation on the Support Webpage, we have additional tips and tricks for working with skin for Xenium In Situ Gene Expression listed here.
- Blocks containing skin may require longer chilling times. Monitor block in 15 minute increments to identify optimal chilling time.
- Consider using a transfer system (if available) and sectioning directly into room temperature water and then transfer to a water bath at ~37°C.
- While we recommend ~42°C for most FFPE tissues, a low temperature water bath of ~37°C is usually better for skin. The temperature may need to be optimized for each block.
- After sectioning, gently flick the slide to remove excess water and place the slide in a drying rack. While we recommend ~30 min dry time for most samples (or until dry upon visual inspection), skin may benefit from extended drying times.
- Follow the instructions in the Xenium FFPE Deparaffinization/Decrosslinking Protocol. Slow immersion during deparaffinization steps (especially the first immersion in xylene and subsequent ethanol steps) is critical for minimizing detachment.
- If significant detachment is observed during 80°C decrosslinking, reduce decrosslinking temperature from 80°C in Demonstrated Protocol to 37°C for 30 minutes.
While this protocol modification has minimal impact on gene expression data, it is likely to compromise antigen retrieval and is not likely suitable for samples destined for post-Xenium Analyzer run IF staining.
Overall conclusions: While skin is tricky to work with, it is possible to obtain good Xenium data from skin.
10x Genomics Support does not have additional information on generating blocks, sectioning, and placing sections beyond what is provided in this article and will not be able to provide additional details from internal experiments or guidance on troubleshooting skin experiments at this time.
Products: Xenium In Situ Gene Expression