Naïve male mice were euthanized by CO2 exposure, and whole brains were removed and frozen on dry ice. Brains were stored at -70 deg C until used. The RNeasy Midi kit for lipid-rich tissues (Qiagen, Valencia, CA) was used to extract total RNA, and the RNeasy Mini kit (Qiagen) was used for cleanup. Biotin-labeled cRNA was obtained by in vitro transcription of the double-stranded cDNA that was originally synthesized from the total RNA. Each whole brain sample of biotin-labeled cRNA was fragmented and hybridized to a separate oligonucleotide array. After hybridization, the chips were stained with streptavidin-phycoerythrin conjugate and scanned using an Affymetrix GeneArray scanner.

 

Strain	Sample Number	Scale factor	Average background	Absent	Marginal	Present	Affy-bActin	Affy-GAPH
BXD1	1	0.343	65.57	45.5%	4.1%	50.4%	1.33	0.74
BXD1	2	0.362	68.26	46.9%	4.5%	48.6%	1.30	0.76
BXD1	3	0.375	66.19	46.9%	4.2%	48.9%	1.27	0.77
BXD1	4	0.408	57.16	45.0%	4.0%	51.1%	1.27	0.80
BXD2	1	0.270	60.53	44.0%	4.1%	51.8%	1.52	0.87
BXD2	2	0.280	67.57	45.0%	4.2%	50.8%	1.31	0.75
BXD2	3	0.295	67.03	45.2%	4.1%	50.7%	1.34	0.76
BXD2	4	0.209	99.86	50.0%	4.7%	45.3%	1.24	0.73
BXD2	5	0.246	73.28	46.2%	4.3%	49.5%	1.34	0.73
BXD5	1	0.249	75.34	47.3%	4.4%	48.3%	1.34	0.73
BXD5	2	0.306	70.11	47.5%	4.5%	47.9%	1.31	0.77
BXD5	3	0.265	64.80	44.8%	4.3%	50.9%	1.33	0.74
BXD5	4	0.282	66.04	45.5%	4.2%	50.4%	1.41	0.76
BXD5	5	0.216	71.87	46.0%	3.9%	50.1%	3.07	1.01
BXD6	1	0.294	66.72	45.8%	4.3%	49.9%	1.38	0.75
BXD6	2	0.304	62.83	45.8%	4.2%	50.0%	1.25	0.72
BXD6	3	0.301	61.80	45.3%	4.3%	50.5%	1.27	0.76
BXD6	5	0.273	67.04	44.4%	4.2%	51.4%	1.32	0.76
BXD6	6	0.272	66.39	45.4%	4.3%	50.3%	1.32	0.75
BXD8	1	0.207	81.90	44.0%	3.9%	52.1%	1.33	0.74
BXD8	2	0.254	70.19	44.0%	3.9%	52.0%	1.32	0.72
BXD8	3	0.300	72.61	46.0%	4.0%	50.0%	1.30	0.74
BXD8	4	0.457	52.63	39.5%	3.3%	57.2%	1.14	0.79
BXD8	5	0.381	55.09	41.2%	3.4%	55.4%	1.12	0.79
BXD9	1	0.349	90.32	48.5%	4.1%	47.4%	1.38	0.78
BXD9	2	0.241	86.66	51.2%	4.8%	44.0%	1.38	0.75
BXD9	3	0.284	67.21	47.2%	4.3%	48.5%	1.33	0.78
BXD9	4	0.303	64.47	46.9%	4.5%	48.6%	1.32	0.77
BXD9	5	0.351	59.40	47.4%	4.4%	48.2%	1.41	0.80
BXD9	6	0.312	63.41	46.3%	4.4%	49.4%	1.39	0.76
BXD11	1	0.267	61.85	44.6%	4.3%	51.1%	1.36	0.75
BXD11	2	0.317	63.76	45.3%	4.3%	50.4%	1.29	0.79
BXD11	3	0.306	59.35	44.8%	4.2%	51.0%	1.33	0.79
BXD11	4	0.223	98.84	51.1%	4.6%	44.3%	1.32	0.73
BXD11	5	0.292	65.03	45.4%	4.0%	50.5%	1.38	0.78
BXD12	1	0.357	54.50	42.5%	3.7%	53.8%	1.15	0.76
BXD12	2	0.379	55.05	42.7%	3.7%	53.6%	1.15	0.76
BXD12	3	0.347	56.34	43.2%	3.9%	52.9%	1.17	0.74
BXD12	4	0.541	65.16	43.1%	3.4%	53.6%	1.08	0.79
BXD12	5	0.178	96.04	43.4%	4.0%	52.7%	1.29	0.74
BXD12	6	0.234	67.32	43.0%	3.9%	53.0%	1.31	0.75
BXD12	7	0.255	68.41	42.7%	4.2%	53.2%	1.50	0.76
BXD13	1	0.285	59.51	45.8%	4.2%	49.9%	1.22	0.75
BXD13	2	0.275	67.19	44.9%	4.2%	50.9%	1.29	0.76
BXD13	3	0.277	66.05	45.7%	4.2%	50.2%	1.38	0.79
BXD13	4	0.214	82.73	48.6%	4.5%	46.9%	1.40	0.78
BXD13	5	0.237	71.73	46.0%	4.3%	49.7%	1.29	0.77
BXD13	6	0.308	57.58	47.2%	4.2%	48.6%	1.33	0.74
BXD14	2	0.372	58.42	46.8%	4.4%	48.8%	1.19	0.74
BXD14	3	0.354	57.39	45.0%	4.2%	50.8%	1.20	0.72
BXD14	4	0.296	64.96	45.7%	4.4%	49.9%	1.20	0.69
BXD14	5	0.257	66.46	44.9%	4.4%	50.8%	1.24	0.72
BXD14	6	0.418	54.03	47.4%	4.1%	48.5%	1.10	0.74
BXD15	1	0.396	58.77	43.6%	3.9%	52.5%	1.33	0.78
BXD15	2	0.270	151.42	52.7%	4.7%	42.6%	1.36	0.73
BXD15	3	0.366	70.26	44.7%	3.9%	51.4%	1.29	0.79
BXD15	4	0.407	53.40	43.6%	4.1%	52.4%	1.38	0.79
BXD16	1	0.388	48.98	43.7%	4.1%	52.2%	1.41	0.79
BXD16	2	0.353	55.48	43.7%	4.0%	52.3%	1.44	0.82
BXD16	3	0.339	61.60	45.3%	4.2%	50.5%	1.42	0.80
BXD16	4	0.240	95.15	50.4%	4.7%	44.9%	1.39	0.73
BXD16	5	0.270	70.63	46.3%	4.3%	49.4%	1.45	0.75
BXD16	6	0.281	72.99	47.0%	4.2%	48.8%	1.40	0.77
BXD18	1	0.384	59.78	45.4%	4.0%	50.6%	1.12	0.71
BXD18	2	0.288	93.67	49.5%	4.4%	46.1%	1.15	0.70
BXD18	3	0.286	89.64	45.2%	4.1%	50.8%	1.27	0.71
BXD18	4	0.294	69.85	44.0%	4.1%	51.8%	1.26	0.70
BXD18	5	0.417	59.80	47.0%	4.3%	48.7%	1.15	0.72
BXD18	6	0.373	65.30	45.9%	4.3%	49.8%	1.18	0.74
BXD19	1	0.364	59.35	46.7%	4.2%	49.1%	1.27	0.73
BXD19	2	0.419	59.77	46.8%	4.1%	49.1%	1.23	0.74
BXD19	3	0.303	62.66	46.0%	4.4%	49.6%	1.30	0.74
BXD19	4	0.280	91.00	51.8%	4.5%	43.7%	1.32	0.68
BXD19	5	0.303	66.18	47.1%	4.5%	48.4%	1.33	0.72
BXD19	6	0.389	63.61	47.5%	4.4%	48.1%	1.28	0.73
BXD21	1	0.350	75.93	44.9%	3.9%	51.3%	1.29	0.77
BXD21	2	0.338	59.00	43.8%	4.0%	52.1%	1.29	0.77
BXD21	3	0.304	59.94	44.9%	4.0%	51.2%	1.44	0.77
BXD21	4	0.235	94.44	51.0%	4.8%	44.2%	1.35	0.73
BXD21	5	0.310	64.22	46.9%	4.2%	48.9%	1.42	0.77
BXD22	1	0.363	58.10	45.3%	3.9%	50.8%	1.24	0.80
BXD22	2	0.385	55.58	44.5%	4.0%	51.5%	1.28	0.80
BXD22	3	0.345	61.03	46.8%	4.3%	48.9%	1.35	0.81
BXD22	4	0.242	85.36	53.6%	4.8%	41.6%	1.35	0.75
BXD22	5	0.316	62.02	47.3%	4.5%	48.2%	1.40	0.77
BXD22	6	0.325	66.38	47.5%	4.3%	48.2%	1.29	0.78
BXD23	1	0.276	75.99	45.3%	4.1%	50.6%	1.27	0.75
BXD23	2	0.333	81.76	47.9%	4.0%	48.1%	1.28	0.78
BXD23	3	0.275	102.46	47.4%	3.9%	48.8%	1.30	0.77
BXD23	4	0.178	115.83	50.2%	4.7%	45.2%	1.38	0.73
BXD23	5	0.258	92.38	47.6%	4.2%	48.2%	1.32	0.77
BXD23	6	0.256	88.23	46.3%	4.1%	49.5%	1.31	0.74
BXD24	1	0.348	71.69	44.9%	4.1%	51.1%	1.25	0.74
BXD24	2	0.324	74.05	44.3%	4.0%	51.7%	1.23	0.80
BXD24	3	0.401	64.08	45.6%	4.0%	50.4%	1.08	0.74
BXD24	4	0.246	82.84	45.7%	4.3%	50.0%	1.20	0.75
BXD24	6	0.389	54.28	44.3%	4.2%	51.5%	1.20	0.67
BXD27	1	0.507	50.08	43.6%	3.9%	52.5%	1.48	0.81
BXD27	2	0.468	51.29	44.0%	3.7%	52.3%	1.44	0.90
BXD27	3	0.526	49.67	43.5%	3.9%	52.6%	1.29	0.94
BXD27	4	0.537	48.92	43.5%	3.8%	52.8%	1.46	0.91
BXD28	1	0.284	51.58	44.6%	4.2%	51.2%	1.26	0.80
BXD28	2	0.322	50.16	44.9%	4.3%	50.8%	1.21	0.76
BXD28	3	0.397	50.97	45.9%	4.2%	49.9%	1.14	0.78
BXD28	4	0.330	74.26	51.4%	4.6%	44.0%	1.26	0.72
BXD28	5	0.284	52.34	44.3%	4.4%	51.3%	1.32	0.73
BXD28	6	0.349	57.14	47.8%	4.5%	47.7%	1.30	0.79
BXD29	1	0.422	58.68	44.0%	3.7%	52.3%	1.42	0.86
BXD29	3	0.400	58.72	43.1%	3.8%	53.2%	1.31	0.89
BXD29	5	0.365	61.79	46.9%	4.3%	48.8%	1.38	0.91
BXD31	1	0.379	51.10	45.8%	4.3%	50.0%	1.13	0.75
BXD31	2	0.333	48.64	43.7%	4.1%	52.2%	1.22	0.71
BXD31	3	0.519	47.71	48.2%	4.3%	47.5%	1.13	0.72
BXD31	4	0.243	75.24	48.6%	4.8%	46.6%	1.23	0.71
BXD31	5	0.325	53.19	46.9%	4.6%	48.6%	1.22	0.75
BXD31	6	0.320	46.98	44.5%	4.3%	51.2%	1.24	0.74
BXD32	1	0.256	70.43	45.4%	3.9%	50.8%	1.83	0.87
BXD32	2	0.288	67.44	44.5%	4.1%	51.4%	1.34	0.77
BXD32	3	0.361	58.13	44.4%	4.0%	51.6%	1.36	0.77
BXD32	4	0.367	61.39	44.7%	4.1%	51.2%	1.40	0.78
BXD32	5	0.324	68.04	45.6%	4.3%	50.1%	1.39	0.75
BXD32	6	0.266	95.49	50.8%	4.5%	44.6%	1.41	0.73
BXD33	1	0.344	61.65	44.9%	3.9%	51.2%	1.38	0.82
BXD33	2	0.356	61.04	44.7%	4.1%	51.2%	1.44	0.79
BXD33	4	0.385	59.92	44.1%	3.9%	52.0%	1.38	0.82
BXD34	1	0.297	91.13	52.1%	4.6%	43.3%	1.34	0.70
BXD34	2	0.508	51.79	44.8%	3.9%	51.3%	1.42	0.76
BXD34	3	0.284	85.33	50.7%	4.6%	44.7%	1.51	0.72
BXD34	4	0.297	61.95	44.9%	4.1%	51.0%	1.36	0.77
BXD34	5	0.516	56.02	46.3%	4.0%	49.7%	1.33	0.74
BXD34	6	0.545	54.46	45.2%	3.8%	51.0%	1.49	0.87
BXD36	1	0.435	62.74	48.1%	4.0%	47.8%	1.36	0.73
BXD36	2	0.333	71.24	48.8%	4.3%	46.8%	1.44	0.72
BXD36	3	0.320	72.97	48.3%	4.3%	47.4%	1.38	0.74
BXD36	4	0.391	73.58	49.5%	4.2%	46.3%	1.25	0.75
BXD38	1	0.303	87.68	39.2%	3.3%	57.5%	1.08	0.82
BXD38	2	0.343	61.39	39.7%	3.2%	57.1%	1.12	0.82
BXD38	3	0.453	67.19	41.2%	3.4%	55.4%	1.11	0.83
BXD38	4	0.424	64.36	41.6%	3.5%	55.0%	1.11	0.82
BXD39	1	0.357	64.36	47.3%	4.3%	48.3%	1.33	0.78
BXD39	2	0.332	60.23	46.5%	4.2%	49.3%	1.41	0.80
BXD39	3	0.331	65.27	46.2%	4.2%	49.6%	1.32	0.75
BXD39	4	0.362	62.60	45.5%	4.0%	50.5%	1.28	0.80
BXD39	5	0.347	58.97	46.1%	4.3%	49.7%	1.29	0.79
BXD39	6	0.327	63.12	46.2%	4.3%	49.6%	1.29	0.77
BXD40	1	0.371	60.01	45.2%	4.1%	50.7%	1.32	0.77
BXD40	2	0.245	84.69	49.1%	4.5%	46.4%	1.33	0.72
BXD40	3	0.324	64.17	46.8%	4.3%	48.8%	1.34	0.73
BXD40	4	0.280	63.97	45.1%	4.2%	50.7%	1.48	0.74
BXD40	5	0.271	69.40	45.9%	4.3%	49.8%	1.33	0.74
BXD40	6	0.307	59.99	45.5%	4.2%	50.4%	1.37	0.76
BXD42	1	0.424	53.91	45.1%	4.1%	50.8%	1.54	0.83
BXD42	2	0.216	92.34	46.7%	4.3%	49.1%	1.44	0.76
BXD42	3	0.249	84.52	45.7%	4.1%	50.2%	1.52	0.80
BXD42	5	0.236	85.29	46.2%	4.0%	49.8%	1.38	0.77
DBA/2J	1	0.313	79.69	46.8%	4.2%	49.0%	1.24	0.72
DBA/2J	2	0.294	82.27	46.5%	4.2%	49.3%	1.27	0.73
DBA/2J	3	0.349	78.58	47.8%	4.3%	47.8%	1.31	0.73
DBA/2J	4	0.389	72.02	48.0%	4.3%	47.7%	1.21	0.77
DBA/2J	5	0.362	66.73	46.5%	4.4%	49.1%	1.23	0.75
DBA/2J	6	0.341	79.88	46.7%	4.0%	49.4%	1.33	0.74
C57BL/6J	1	0.294	82.84	46.7%	4.1%	49.2%	1.23	0.76
C57BL/6J	2	0.242	80.40	43.1%	4.1%	52.8%	1.29	0.76
C57BL/6J	3	0.250	110.90	47.8%	4.0%	48.2%	1.32	0.76
C57BL/6J	4	0.289	101.88	47.5%	4.1%	48.4%	1.18	0.75
C57BL/6J	5	0.299	114.59	48.7%	4.1%	47.3%	1.13	0.74
C57BL/6J	6	0.251	105.90	45.8%	3.8%	50.4%	1.30	0.76
129P3/J	1	0.496	59.26	41.9%	3.5%	54.5%	1.28	0.79
129P3/J	2	0.550	50.83	42.0%	3.7%	54.3%	1.16	0.78
129P3/J	3	0.443	56.08	43.0%	3.8%	53.3%	1.22	0.73
129P3/J	4	0.521	58.92	44.8%	3.8%	51.4%	1.30	0.74
129P3/J	5	0.503	58.26	44.9%	3.8%	51.3%	1.32	0.74
129S1/SvImJ	1	0.311	66.76	47.8%	3.9%	48.3%	2.04	0.97
129S1/SvImJ	2	0.262	57.63	44.5%	3.9%	51.6%	1.61	0.81
129S1/SvImJ	3	0.322	62.67	45.3%	3.8%	50.9%	1.70	0.83
129S1/SvImJ	4	0.185	119.02	50.2%	4.4%	45.5%	1.66	0.75
A/J	1	0.453	51.85	42.6%	3.6%	53.8%	1.20	0.73
A/J	2	0.396	56.61	45.9%	3.9%	50.2%	1.21	0.76
A/J	3	0.421	62.34	47.0%	4.1%	48.8%	1.29	0.72
A/J	4	0.508	61.52	48.2%	4.1%	47.7%	1.22	0.74
AKR/J	1	0.331	54.70	41.7%	3.9%	54.4%	1.22	0.74
AKR/J	2	0.464	55.46	44.1%	3.7%	52.1%	1.30	0.76
AKR/J	4	0.444	53.62	47.6%	4.0%	48.4%	1.23	0.71
AKR/J	5	0.439	58.62	47.4%	4.3%	48.3%	1.23	0.70
BALB/cByJ	1	0.336	75.49	50.0%	4.1%	45.9%	1.54	0.82
BALB/cByJ	2	0.280	67.93	47.1%	4.3%	48.7%	1.43	0.76
BALB/cByJ	3	0.312	73.77	47.7%	4.1%	48.2%	1.79	0.92
BALB/cByJ	4	0.262	79.97	46.1%	4.1%	49.8%	1.38	0.79
BALB/cByJ	5	0.276	81.32	46.3%	4.1%	49.6%	1.34	0.79
BALB/cJ	1	0.591	54.25	43.2%	3.5%	53.3%	1.15	0.80
BALB/cJ	2	0.346	50.36	39.9%	3.3%	56.8%	1.20	0.77
BALB/cJ	3	0.333	52.79	40.4%	3.7%	55.9%	1.25	0.77
BALB/cJ	5	0.495	54.78	45.0%	3.7%	51.3%	1.15	0.72
BTBR T+tf/J	3	0.315	62.83	46.4%	4.1%	49.5%	1.38	0.78
BTBR T+tf/J	4	0.243	90.12	51.6%	4.8%	43.6%	1.31	0.75
BTBR T+tf/J	5	0.294	71.21	46.6%	4.3%	49.0%	1.41	0.77
BTBR T+tf/J	6	0.268	67.53	46.6%	4.2%	49.2%	1.32	0.75
BTBR T+tf/J	1	0.370	55.40	45.7%	4.1%	50.2%	1.41	0.75
BTBR T+tf/J	2	0.488	50.89	47.2%	4.2%	48.6%	1.36	0.75
C3H/HeJ	1	0.511	59.20	43.3%	3.4%	53.3%	1.17	0.83
C3H/HeJ	2	0.405	79.49	41.3%	3.3%	55.5%	1.18	0.83
C3H/HeJ	3	0.454	59.47	41.7%	3.5%	54.9%	1.16	0.81
C3H/HeJ	4	0.448	56.28	41.5%	3.5%	55.0%	1.16	0.79
C3H/HeJ	5	0.389	50.17	41.1%	3.6%	55.2%	1.24	0.79
C58/J	1	0.336	56.66	46.0%	4.2%	49.8%	1.29	0.73
C58/J	2	0.372	58.61	46.7%	4.3%	49.0%	1.21	0.71
C58/J	3	0.366	64.58	46.8%	4.2%	49.0%	1.20	0.72
C58/J	4	0.371	52.72	45.3%	4.1%	50.6%	1.24	0.72
CAST/EiJ	1	0.467	55.74	47.1%	3.8%	49.1%	1.39	0.79
CAST/EiJ	2	0.545	50.29	46.8%	3.8%	49.4%	1.34	0.84
CAST/EiJ	3	0.469	55.08	47.4%	4.0%	48.5%	1.32	0.76
CAST/EiJ	4	0.390	83.05	53.0%	4.4%	42.6%	1.36	0.72
CBA/J	1	0.292	67.25	44.9%	4.0%	51.2%	1.22	0.76
CBA/J	2	0.347	61.99	46.4%	4.0%	49.7%	1.25	0.82
CBA/J	3	0.305	62.16	46.3%	4.3%	49.4%	1.31	0.75
CBA/J	4	0.303	64.82	46.5%	4.0%	49.5%	1.34	0.76
CBA/J	5	0.313	64.15	45.3%	4.1%	50.7%	1.37	0.78
CBA/J	6	0.365	56.84	45.6%	4.1%	50.4%	1.31	0.76
FVB/NJ	1	0.497	63.99	44.2%	3.5%	52.3%	1.33	0.79
FVB/NJ	2	0.475	55.24	44.8%	3.8%	51.4%	1.33	0.74
FVB/NJ	3	0.527	56.07	42.6%	3.5%	53.9%	1.31	0.86
FVB/NJ	4	0.447	62.56	41.7%	3.5%	54.8%	1.24	0.82
KK/HIJ	1	0.309	93.54	49.6%	4.3%	46.1%	1.57	0.74
KK/HIJ	2	0.298	63.24	48.0%	4.4%	47.6%	1.37	0.72
KK/HIJ	4	0.223	93.03	44.7%	4.0%	51.3%	1.39	0.74
KK/HIJ	5	0.153	136.67	51.9%	4.6%	43.5%	1.24	0.71
MOLF/EiJ	1	0.339	67.11	49.1%	4.3%	46.6%	1.55	0.83
MOLF/EiJ	2	0.319	80.73	49.1%	4.2%	46.7%	1.52	0.78
MOLF/EiJ	3	0.380	69.03	49.1%	4.2%	46.7%	1.29	0.82
MOLF/EiJ	4	0.238	95.19	48.7%	4.1%	47.2%	1.35	0.79
NOD/LtJ	1	0.356	78.42	49.1%	4.2%	46.7%	1.35	0.76
NOD/LtJ	2	0.422	59.71	47.4%	4.0%	48.5%	1.25	0.73
NOD/LtJ	3	0.377	77.84	49.8%	4.0%	46.2%	1.24	0.75
NOD/LtJ	4	0.535	60.86	50.6%	4.4%	45.0%	1.28	0.74
NOD/LtJ	5	0.336	74.58	46.6%	3.9%	49.5%	1.32	0.72
NZW/LacJ	2	0.442	50.31	44.6%	4.1%	51.3%	1.33	0.82
NZW/LacJ	3	0.331	56.86	44.2%	4.0%	51.7%	1.60	0.78
NZW/LacJ	4	0.338	55.23	44.1%	4.0%	51.9%	1.31	0.78
NZW/LacJ	5	0.351	56.90	49.3%	4.3%	46.5%	1.30	0.75
PWD/PhJ	1	0.444	57.65	47.2%	3.9%	48.9%	1.62	0.78
PWD/PhJ	2	0.328	67.58	47.3%	4.2%	48.5%	1.36	0.76
PWD/PhJ	3	0.322	73.90	47.5%	4.0%	48.5%	1.46	0.81
PWD/PhJ	4	0.271	75.79	46.1%	4.0%	50.0%	1.39	0.79
PWD/PhJ	5	0.191	144.73	57.7%	5.0%	37.3%	1.36	0.67
SJL/J	1	0.528	54.58	41.1%	3.4%	55.4%	1.16	0.80
SJL/J	3	0.663	56.21	41.8%	3.3%	55.0%	1.22	0.75
SJL/J	4	0.646	52.96	40.5%	3.2%	56.3%	1.13	0.81
SJL/J	5	0.639	61.91	44.8%	3.4%	51.9%	1.37	0.79