Question: How do I study a large tissue specimen (greater than 6.5 mm x 6.5 mm) using Visium for FFPE v1?
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. Process each capture area's data with the spaceranger count software pipeline. Then combine the multiple samples with the spaceranger aggr pipeline to produce a Loupe file containing all of the samples. As of this writing (Loupe-v6.4.1), while the UMAP and t-SNE projection views include barcode data for all of the samples, Loupe limits the spatial view to per-sample. To view side-by-side samples in their spatial contexts, create and import a custom projection. We describe this Loupe interoperability at https://support.10xgenomics.com/single-cell-gene-expression/software/visualization/latest/tutorial-interoperability. Although this document is in the single-cell documentation, it can also be applied to Visium spatial samples. Batch effect correction is unsupported for spaceranger aggr as stated in the article Can I aggregate data from different samples or staining protocols using Space Ranger aggr?
Products: Visium for FFPE