(a) Comparison of FPKM- vs. CPM-based enrichment for CA2 marker genes in Figure 3b. (b,c) As in Figure 3c,d, but for CPM-based analysis. (d) As in a, but for mossy cell marker genes of Figure 4b. (e,f) as in Figure 5b,c, but for CPM-based analysis. Insert: comparison of the number of differentially expressed genes for FPKM- vs. CPM-based approaches. (g) As in Figure 6c, but for CPM-based analysis. (h) Representative example of FPKM values for datasets obtained with TopHat and STAR alignment (dorsal CA1 correlation r = 0.98; all datasets r = 0.98 ± 0.00, Pearson correlation, mean ± SD, n = 8 datasets). (i) Representative example of differential expression results obtained from Tophat and STAR alignment (dorsal vs. ventral CA1: 1015 genes identified using Tophat alignment, 1072 genes identified using STAR alignment). Colored points denote differentially expressed genes, with green color used here to better visualize data points. (j) Overlap in differentially expressed genes from the representative example in i. Here, 955/1015 = 94.1% of genes found using TopHat alignment were also identified with STAR. Across entire dataset, 95.0 ± 1.3% of differentially expressed genes found by TopHat approach were shared with STAR, with STAR identifying 6.8 ± 1.3% more genes than TopHat on average (mean ± SD, n = 28 pairwise comparisons for each).