Question: What information is necessary to record while performing the Visium Spatial Gene Expression assay?
Answer: When performing the Visium Gene Expression experiment, it is important to record three key pieces of information, which will be utilized during data analysis. If these details aren't recorded, it can prove difficult or impossible to determine what sequencing data should be mapped back to which tissue image.
The following information should be recorded for each Visium Gene Expression slide:
- The tissue type or the lab-specific block identifier sectioned and placed into each of the four capture areas: A1, B1, C1, & D1.
- The slide serial number found on the sticker at the top of the Gene Expression slide. This information will be required when performing image alignment.
- The sample index plate well location that was used for each of the four samples when performing sample index PCR. The plate well locations are required when generating the sample sheet to demultiplex libraries during analysis.
It may be helpful to name the imaging files with the Slide Serial number, capture area, and tissue block ID for helpful record keeping. For example: VA99A99-999_A1_TissueX