Loading Spatial Data Answer Key

Exercise 1

1. Given the information that we know from the metadata, what might be some questions that we are interested in interrogating using our data?

• Identify and characterize tumor cells in CRC
• Construct cell-communication networks, using spatial locations to constrain our results
• What are unique subtypes/cell states that are found in CRC vs. NAT
• Associate cell states with spatial locations
• Establish domains and niches of cell populations in quadrants of the slides
• etc.

Exercise 2

2. What differences do you see between 8um and 16um bins?

There are more cells in the 8um compared to the 16um. The number of features/genes remain the same.

This is why the bin value matters, it determines how many “cells” are ultimately generated. A smaller bin size results in more spots. This is because we are taking smaller sections of the same data, meaning we use more bins to cover the same area as a large bin size.

Exercise 3

3. What function can we use to double check that we have a singular counts layer?

Layers(seurat_merged)