Question: How do I study a large tissue specimen (greater than 6.5 mm x 6.5 mm) using Visium for FFPE?
Answer: Depending upon the tissue type, scoring of the tissue and placing sections across different capture areas of the slide may be employed if the tissue is too large to fit within a single capture area. Each scored tissue could be placed into a separate capture area to obtain spatial information for a different tissue section.
Once you expose the block and get closer to the region of interest, you can glide a razor blade over the surface of the tissue to introduce a shallow cut (score). As you section the block, you will generate separate sections containing the separated tissue. As sectioning proceeds, you may need to repeat scoring the block to achieve sections of the appropriate and desired size. It is recommended to try out this strategy on a paraffin block without tissue before using actual tissue to gain experience with performing this.
If you’re interested in multiple scored regions of the same block, they can be placed on separate capture areas and you may be able to combine the data later using the Space Ranger aggr pipeline. Please refer to this Q&A article for some additional considerations of using Space Ranger aggr: Can I aggregate data from different samples or staining protocols using Space Ranger aggr?
Products: Visium for FFPE