Question: What is the capture rate/efficiency of Visium?
Answer: The sensitivity of the Visium Spatial Gene Expression solution is dependent on a large number of factors, such as tissue type, species, permeabilization time, and sequencing depth. For example, with one of our public Visium datasets using the mouse brain hippocampus region, we saw an average of 4.5k genes and 20k UMIs per spot. In this experiment, tissue thickness was 10um, and sequencing depth was 50k paired-end reads per spot covered with tissue. Sequencing saturation was not achieved at 50k paired-end reads per spot covered with tissue, indicating that additional sequencing will result in more unique genes and UMIs. Thus it is challenging to say what sensitivity a given experiment will yield beforehand, but a successful Tissue Optimization experiment with a good fluorescent signature will help guide for optimal gene expression data and experimental outcome.