Table 1.

Summary of statistical analyses

			Wild-type (WT)			Nhe6-null (MUT)
Figure, statistical test, and measure	Brain region	Time point, mo	Mean	SEM	n	Mean	SEM	n	Statistics
Fig. 1
Two-tailed Student’s t test
Area (cm²)
	Whole brain	0	0.376	0.021	9	0.394	0.011	12	p = 0.42
	Whole brain	1	1.015	0.012	11	1.030	0.030	7	p = 0.61
	Whole brain	2	1.257	0.033	8	1.112	0.042	6	p = 0.018
	Whole brain	6	1.326	0.011	7	1.243	0.011	6	p = 0.00025
	Whole brain	23	1.105	0.013	4	1.0068	0.0073	5	p = 0.00025
	Cortex	0	0.244	0.013	9	0.2499	0.0083	12	p = 0.67
	Cortex	1	0.7527	0.0074	11	0.766	0.020	7	p = 0.51
	Cortex	2	0.908	0.027	8	0.808	0.030	6	p = 0.029
	Cortex	6	0.949	0.011	7	0.907	0.012	6	p = 0.025
	Cortex	23	0.7723	0.0089	4	0.7501	0.0031	5	p = 0.035
	Cerebellum	0	0.0316	0.0024	9	0.0323	0.0016	12	p = 0.78
	Cerebellum	1	0.2188	0.0050	11	0.2210	0.0088	7	p = 0.83
	Cerebellum	2	0.2913	0.0056	8	0.254	0.011	6	p = 0.0067
	Cerebellum	6	0.3006	0.0037	7	0.2590	0.0059	6	p = 7.5 × 10^–5
	Cerebellum	23	0.2483	0.0078	4	0.1760	0.0057	5	p = 0.00012
	Cerebellum + midbrain	0	0.153	0.014	9	0.1441	0.0029	12	p = 0.49
	Cerebellum + midbrain	1	0.2619	0.0062	11	0.264	0.010	7	p = 0.85
	Cerebellum + midbrain	2	0.3484	0.0083	8	0.304	0.016	6	p = 0.021
	Cerebellum + midbrain	6	0.3776	0.0012	7	0.3365	0.0078	6	p = 0.00015
	Cerebellum + midbrain	23	0.3124	0.0064	4	0.2368	0.0068	5	p = 0.000096
Fig. 2
Two-tailed Student’s t test
Thickness (mm)	Cortex	22	1.210	0.029	3	1.090	0.018	3	p = 0.025
Area (mm²)
	Striatum	22	4.689	0.030	3	4.062	0.045	3	p = 0.00031
	Hippocampus	22	2.455	0.047	3	2.074	0.068	3	p = 0.0098
	Cerebellum	22	7.128	0.014	2	4.586	0.089	4	p = 4.6 × 10^–5
Width (mm)
	Spinal cord (Region 1)	22	1.890	0.073	2	1.491	0.073	2	p = 0.060
	Spinal cord (Region 2)	22	1.987	0.080	2	1.845	0.033	2	p = 0.24
Fig. 3
Two-way ANOVA followed by Tukey’s multiple comparison test
Thickness (mm)
	Cortex	2	1.154	0.018	3	1.126	0.029	3	p = 0.84
	Cortex	22	1.210	0.029	3	1.090	0.018	3	p = 0.035
Area (mm²)
	Striatum	2	4.060	0.077	3	3.83	0.12	3	p = 0.24
	Striatum	22	4.689	0.030	3	4.062	0.045	3	p = 0.0021
	Hippocampus	2	2.199	0.011	3	2.113	0.062	3	p = 0.66
	Hippocampus	22	2.455	0.047	3	2.074	0.068	3	p = 0.0036
	Cerebellum	2	6.53	0.15	3	5.91	0.16	3	p = 0.034
	Cerebellum	22	7.128	0.014	2	4.586	0.089	4	p < 0.0001
Slopes generated from linear regression
Thickness (mm)
	Cortex	2–22	0.0028	0.0017		–0.0018	0.0017		p = 0.10
Area (mm²)
	Striatum	2–22	0.0315	0.0041		0.0116	0.0066		p = 0.034
	Hippocampus	2–22	0.0128	0.0024		–0.0020	0.0046		p = 0.021
	Cerebellum	2–22	0.0300	0.0097		–0.0661	0.0085		p < 0.0001
Fig. 4
Two-tailed Student’s t test
PC density	Cerebellar vermis: Primary fissure	5	2.94	0.13	3	1.99	0.24	3	p = 0.03
Calbindin signal	Cerebellar vermis: Primary fissure	5	32.9	2.8	4	15.5	1.7	4	p = 0.002
PC density	Cerebellar vermis: Primary fissure	11–13	3.28	0.28	5	0.77	0.26	4	p < 0.001
Calbindin signal	Cerebellar vermis: Primary fissure	11–13	30.7	3.6	6	8.80	0.92	4	p = 0.001
PC density	Cerebellar vermis: Primary fissure	5 and 11–13	—	—	—	—	—	—	p = 0.006
Calbindin signal	Cerebellar vermis: Primary fissure	5 and 11–13	—	—	—	—	—	—	p = 0.01
Fig. 5
Two-tailed Student’s t test
PC density
	Cerebellar vermis: Anterior lobe	5	3.27	0.24	3	0.74	0.44	4	p = 0.006
	Cerebellar vermis: Flocculonodular lobe	5	3.49	0.36	3	2.42	0.52	3	p = 0.17
	Cerebellar vermis: Anterior lobe	11–13	3.22	0.30	4	0.21	0.13	3	p < 0.001
	Cerebellar vermis: Flocculonodular lobe	11–13	3.31	0.43	4	2.78	0.51	3	p = 0.46
One-way ANOVA followed by Tukey’s multiple comparison test
PC density	Cerebellar vermis: Primary fissure, Anterior lobe, Flocculonodular lobe	5 and 11–13	—	—	—	—	—	—	11–13 mo MUT F_(2,7) = 20.11 p = 0.001
Fig. 6
Two-tailed Student’s t test
PC density
	Periphery	5	4.86	0.45	3	3.95	0.27	3	WT vs. MUT p = 0.16
	Periphery	5							Periphery vs. Vermis in WT p = 0.02
	Periphery	5							Periphery vs. Vermis in MUT p = 0.006
Fig. 7
Two-tailed Student’s t test
PC density
	Cerebellar vermis: Primary fissure	6	3.25	0.07	2	1.02	0.38	3	p = 0.02
	Cerebellar vermis: Anterior lobe	6	3.80	0.12	2	0.84	0.58	3	p = 0.03
	Cerebellar vermis: Flocculonodular lobe	6	3.51	0.43	2	3.24	0.54	3	p = 0.75
One-way ANOVA followed by Tukey’s multiple comparison test
PC density	Cerebellar vermis: Primary fissure, Anterior lobe, Flocculonodular lobe	6	—	—	—	—	—	—	F_(2,6) = 6.94 p = 0.03
Fig. 8
Two-tailed Student’s t test
PC density	Cerebellar vermis: Primary fissure	5	3.05	0.35	3	0.83	0.45	4	p = 0.007
Calbindin signal	Cerebellar vermis: Primary fissure	5	32.1	2.5	3	13.3	1.4	4	p = 0.001
Fig. 10
Two-tailed Student’s t test
Microglia cell count
	Cortex	22	159	15	3	219	10	4	p = 0.019
	Striatum	22	398.7	5.6	3	568	30	4	p = 0.0054
	Hippocampus CA	22	74.0	4.4	3	100.0	3.4	4	p = 0.0048
	Hippocampus DG	22	56.0	6.7	3	67.3	3.9	4	p = 0.18
Fig. 13
Two-tailed Student’s t test
Size of CD68-positive puncta in Iba1-positive cells (μm²)
	Cortex	22	19.76	0.49	3	28.0	2.0	3	p = 0.015
	Striatum	22	20.5	2.0	3	29.9	4.0	3	p = 0.11
	Hippocampus DG	22	7.2	2.2	3	10.8	2.5	3	p = 0.34

CA, cornu Ammonis; CD68, cluster of differentiation 68; DG, dentate gyrus; Iba1, ionized calcium-binding adapter molecule 1; mo, month or months; MUT, Nhe6-null; PC, Purkinje cell; SEM, standard error of the mean; WT, wild-type.