UCHSC BXD Whole Brain M430 2.0 (Nov06) RMA

Summary

A PhenoGen Informatics data set. Please cite: Saba L, Bhave SV, Grahame N, Bice P, Lapadat R, Belknap J, Hoffman PL, Tabakoff B (2006) Candidate genes and their regulatory elements: alcohol preference and tolerance. Mammalian Genome 17:669-688 Full Text PDF Version, Full Text HTML Version

This November 2006 data freeze provides estimates of mRNA expression in whole brains of BXD recombinant inbred mice measured using Affymetrix MOE 430 version 2 micorarrays. Data were generated at the University of Colorado at Denver and Health Science Center (UCDHSC). Single whole brain samples were hybridized to 248 individual arrays. Data were processed using the RMA protocol followed by a secondary quantile normalization at the probe set level and a scale and location adjustment to ensure an average expression level of 8 units and a standard deviation of 2 units for easy comparison to other transforms.

The PhenoGen Informatics web site provides additional analytic tools and transforms associated with these data.

About cases

This data set includes estimates of gene expression for 50 genetically uniform lines of mice: C57BL/6J (B6 or simply B), DBA/2J (D2 or D), 30 BXD recombinant inbred (RI) strain derived by crossing female B6 mice with male D2 mice and then inbreeding progeny for over 21 generations, and 18 other inbred strains of mice available from the Jackson Laboratory. All mice used were naïve males from 70-90 days old. This set of RI strains is a remarkable resource because many of these strains have been extensively phenotyped for hundreds of interesting traits over a 25-year period. Another significant advantage of this RI set is that the two parental strains (B6 and D2) have both been extensively sequenced and are known to differ at approximately 1.8 million SNPs. Coding variants (mostly single nucleotide polymorphisms and insertion-deletions) that may produce interesting phenotypes can be rapidly identified in this particular RI set.

In this mRNA expression database we generally used stock obtained directly from The Jackson Laboratory between 2003 and 2005.

About tissue

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

About platform

Affymetrix MOE430v2 GeneChip: The expression data were generated using 248 MOE430v2 arrays. The chromosomal locations of MOE430v2 probe sets were determined by BLAT analysis of concatenated probe sequences using the Mouse Genome Sequencing Consortium Mar 2005 (mm6). This BLAT analysis is performed periodically by Yanhua Qu as each new build of the mouse genome is released (see http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=mouse). We thank Yan Cui (UTHSC) for allowing us to use his Linux cluster to perform this analysis. It is possible to confirm the BLAT alignment results yourself simply by clicking on the Verify link in the Trait Data and Editing Form (right side of the Location line).

About data processing

Probe set data: The expression data were processed by Laura Saba (UCDHSC). The original CEL files were read into the R environment (Ihaka and Gentleman 1996). Data were processed using the Robust Multichip Average (RMA) method (Irrizary et al. 2003). Values were log2 transformed within the rma function in R. This data set includes further normalization to produce final estimates of expression that can be compared directly to the other transforms.

This includes an initial quantile normalization on the RMA normalized probe set data followed by a transformation to force an array average of 8 units and stabilized standard deviation of 2 units within each array. Please see Bolstad and colleagues (2003) for a helpful comparison of RMA and two other methods of processing Affymetrix array data sets.

Expression estimates (strain averages) range from a low of about 3.8 for probe set 1457109_x_at to a high of 15 for Gapdh (probe set 1418625_s_at). The mean expression of 8.0 actually represents a relatively low value of expression (roughly 250 on the original scale) because it is the average of all transcripts on the array, including those that are not expressed. Nonetheless, it is possible to obtain good signal down to very low values. For example, probe set 1437432_a_at (Trim12) has an average expression of 4.56 (extremely low), but it still is associated with a strong QTL (LRS of 45) precisely at the location of the parent gene (Chr 7 at 104 Mb). This demonstrates unequivocally that the small strain differences in expression of Trim12 measured by probe set 1437432_a_at is not noise but is generated by true allelic differences in Trim12 mRNA binding to the arrays.

Contributors

Saba L, Bhave SV, Grahame N, Bice P, Lapadat R, Belknap J, Hoffman PL, Tabakoff B.

Acknowledgment

Data was generated with funds from NIAAA for Gene Array Technology Center (AA013162) and from the NIAAA Integrated Neuroinformatics Resource for Alcoholism (AA013524).

Notes

This text file originally generated by RWW, YHQ, August for UTHSC Brain mRNA U74Av2 (Aug05) RMA. Updated for UC Denver Whole Brain M430v2 BXD (Nov06) RMA Data by LMS, November 2006. Updated by RWW, Feb 2008.