Question: Are plant samples compatible with Visium for Fresh Frozen Assay?
Answer: Plant samples have not been validated for the Visium assay (optimized tissue list). Working with plant samples may require workflow modifications. The guidance provided here is not officially supported and only provides general recommendations based on literature searches and lessons learned. 10x Genomics cannot provide additional information outside what is stated in this article, and the information provided here should be considered as a starting point for further optimization depending on the experimental design and the tissue type.
Customers should consider the below challenges when working with plant samples.
- The enzymatic permeabilization and tissue removal (for Tissue Optimization) protocol steps were not designed for the plant samples. Workflow modifications might be needed in those steps. Customers should consider separate workflow optimization efforts for each specific tissue type used (root, stem, seed, leaf, etc.) as tissue morphology can vary significantly in different plant parts. Tissue Optimization Assay should be performed for each tissue type. It is more likely to have good Gene Expression data when a good cDNA footprint can be generated from the Tissue Optimization Assay.
- Some common dyes used in plant staining (e.g., Toluidine Blue O) are not validated for the Visium Assay. Visium for Fresh Frozen Assay only supports H&E or Immunofluorescence staining. 10xGenomics has not tested the impact on the assay performance if alternative staining methods are used.
- Some chemicals such as phenolics from plant tissues may impact downstream biochemistry. Customers should always perform a Tissue Optimization Assay before carrying out the Gene Expression Assay and start with a pilot Gene Expression Assay before working with large batches of samples.
Some customers had success applying the Visium for Fresh Frozen Assay with plant samples (example of publications summarized in table 1). Please note that 10x Genomics does not directly support or endorse the customer developed protocols cited in this article. For more details on the protocols, we recommend reaching out to the authors.
Product: Visium for fresh-frozen