Gene set enrichment analysis

No statistical methods were used to predetermine sample sizes, but our sample sizes for TRAP analyses surpass those reported in previous publications^23,28,87 and our sample sizes for Stereo-seq samples are comparable with or exceed those of similar spatial transcriptomic datasets¹¹. All statistical analyses were performed with R (v4.2.1) and Python (v3.9). All P values were modified to an FDR of 1, 5 or 10 % as described in the text with the Benjamini & Hochberg method.