Table 1.
Overview of spatially resolved transcriptomics samples and filtering settings used in pre-processing steps
| Dataset | # RRST replicates | # Standard visium replicates | # Biological replicates | Filter |
|---|---|---|---|---|
| Mouse brain | 4 | 4 | 1 | No filter |
| Human prostate cancer | 2 | 2 | 1 | No filter |
| Adult human lung | 2 | 4 | 2 | Keep spots with > 300 unique genes |
| Adult human colon | 4 | 2 | 2 | Keep spots annotated as “mucosa”, “submucosa” or “muscularis” |
| Adult human small intestine | 2 | 12 | 1 | Keep spots annotated as “mucosa”, “TLS”, “submucosa”, “muscularis” or “serosa” and spots with > 100 unique genes |
| Mouse bone | 2 | 4 | 2 | Keep spots with > 500 unique genes |
| Pediatric brain tumor | 4 | 4 | 2 | No filter |