Sample Processing: : Samples were processed at the Mount Sinai School of Medicine in the laboratory of Dr. Erwin Bottinger. All processing steps were performed Kremena Star. Total RNA was extracted with TRIZOL, followed by Rneasy Mini Kit purification (QUAGEN) by Kremena Star at MSSM. RNA purity was evaluated using the 260/280 nm (protein contamination) and the 260/230 nm (TRIZOL contamination) absorbance ratios, and values had to be greater than 1.9 and 0.8 respectively. Most of the samples 260/280 nm values fell between 1.9 and 2.1 and the majority of the 260/230 nm measurements were in the range 1.8 to 2.3. RNA integrity was assessed with the Agilent Bioanalyzer 2100. We set a quality threshold at 28s/18s rRNA greater than 0.9 or RNA integrity number (RIN) of greater than 6.9. When the two metrics were in disagreement we gave priority on the RIN value as recommended by the Agilent Bioanalyzer 2100 technical support representative. Synthesis of cDNA template from total RNA was performed using the one-cyclecDNA synthesis kit from Affymetrix (Affymetrix, P/N 900431). The Affymetrix IVT-labeling kit ((Affymetrix, P/N 900449)) was used to synthesize labeled cRNA. The cRNA was evaluated using both the 260/280 ratio (values of 1.9 to 2.1). The cRNA is then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup (Affymetrix, P/N 900371). Fragmented cRNA samples were accessed with Agilent Bioanalyzer 2100 (cRNA frgments between 25 and 200 nucleotides are required for optimal hybridization and immediately injected onto the array. The arrays were hybridized and washed following standard Affymetrix protocols.
Replication and Sample Balance: We obtained a male sample pool and female sample pool from each isogenic group. Initially all strains were represented by male and female samples, however, not all data sets passed the quality control steps. Forty-two (thirty-one BXD, D2B6F1 and ten inbred strains) are represented by male and female samples.
Experimental Design and Batch Structure: The data set consists of arrays processed in twenty-three groups over a six month period (March 2006 to July 2006). Each group consists of 4 to 12 arrays. All arrays were processed using the Affymetrix Eukaryotic Sample and Array Processing protocol (701024 Rev. 3), by a single operator, Kremena Star. All samples in a group were labeled on the same. The hybridization station accommodates up to 4 samples, and since most of the groups had 12 samples, processed in 3 batches on the same day. Samples were washed in groups of four and kept at 4° C until all 12 (or 4-12) arrays were ready to scan. Samples were scanned in sets of four.
This table lists all arrays ordered by strain and includes Microarray ID, number of mice per pool, Microarray date, GAPDH 3`/5`Signal Ratio, Percent of transcripts present on the microarray chip, Strain, Generation, Sex, Age and Source of mice.
Microarray_ID # mice Microarray Date GAPDH (3`/5`) % present strains generation sex age Mice Source GKHI-KS-050603.07-051706 3 05/14/02 0.73 37.6 C57BL/6J M 56 UTM RW GKHI-KS-070803.01-051706 3 05/14/02 0.75 41.6 C57BL/6J F 69 UTM RW GKHI-KS-DBA-Male-070706 2 07/06/02 0.71 37.3 DBA/2J M 56 JAX GKHI_KS_121404.75-042106 4 04/18/02 DBA/2J F 59 UTM RW GKHI_KS_121404.75-033006 4 03/19/02 0.73 48.5 DBA/2J F 59 UTM RW GKHI_KS_121404.78-042006 4 04/17/02 0.83 40.6 DBA/2J F 59 UTM RW GKHI_KS_070804.39-042006 4 04/17/02 0.82 39.0 D2B6F1 M 59 UTM RW GKHI_KS_030904.01-042006 4 04/17/02 0.82 35.9 D2B6F1 M 57 UTM RW GKHI-KS-121404.73-070706 2 07/06/02 0.76 36.3 D2B6F1 F 69 UTM RW GKHI-KS-010705.38-051206 5 05/09/02 0.81 39.9 BXD1 M 59 Harvard/BIDMC GKHI-KS-060905.19 5 06/05/02 0.75 42.3 BXD1 M 68 UTM RW GKHI-KS-051206.13-070706 3 07/06/02 0.71 36.3 BXD1 F 57 UTM RW GKHI-KS-021304.10-051206 4 05/09/02 0.81 39.1 BXD2 M 61 Harvard/BIDMC GKHI-KS-040303-04-050406 3 05/01/02 0.80 37.6 BXD5 F 56 UMemphis GKHI-KS-010705-53-050306 5 05/01/02 0.76 37.1 BXD5 F 58 Harvard/BIDMC GKHI-KS-031103.01-062206 3 06/21/02 0.75 37.1 BXD5 M 71 UMemphis GKHI-KS-040505-51-050306 5 05/01/02 0.71 35.5 BXD6 M 58 UTM RW GKHI-KS-092705-29--050406 5 05/02/02 0.75 36.1 BXD6 160 F 64 UTM RW GKHI_KS_092404.01-042106 4 04/18/02 0.71 36.3 BXD8 M 59 Harvard/BIDMC GKHI-KS-051205-25-042706 5 04/23/02 0.92 37.9 BXD8 F 77 UTM RW KS-021605-17-042606 5 04/22/02 0.85 40.8 BXD9 F 67 UTM RW KS-032905-32-042606 5 04/22/02 0.91 36.8 BXD9 F 60 UTM RW GKHI-KS-062006.08-070706 3 07/06/02 0.74 36.3 BXD9 M 78 UTM RW GKHI-KS-031505.22-051206 5 05/09/02 0.74 39.5 BXD11 F 65 UTM RW GKHI-KS-031605.01 5 06/05/02 0.74 43.4 BXD11 F 69 UTM RW GKHI_KS_102104.40-042106 4 04/18/02 0.72 38.5 BXD12 M 60 Harvard/BIDMC GKHI-KS-112002.07-051106 2 05/08/02 0.77 42.0 BXD12 F 64 UMemphis GKHI-KS-120904.33-051206 4 05/09/02 0.71 38.4 BXD13 F 60 Harvard/BIDMC GKHI-KS-042304.01 4 06/05/02 0.71 44.1 BXD13 F 58 Harvard/BIDMC GKHI-KS-020905.34-051106 5 05/08/02 0.75 40.7 BXD14 F 68 UTM RW GKHI-KS-022405.46-051106 5 05/08/02 0.71 40.2 BXD14 F 60 Harvard/BIDMC GKHI-KS-091704.09-062206 4 06/21/02 0.73 39.0 BXD14 M 59 Harvard/BIDMC GKHI-KS-013004.45-062206 4 06/21/02 0.76 38.5 BXD15 M 61 Harvard/BIDMC GKHI-KS-022405.43-051106 5 05/08/02 0.73 40.5 BXD15 F 60 Harvard/BIDMC GKHI-KS-041604.10-051106 4 05/08/02 0.73 42.6 BXD15 F 60 Harvard/BIDMC GKHI-KS-031805.01-051106 5 05/08/02 0.79 42.4 BXD16 F 59 Harvard/BIDMC GKHI-KS-031805.04-051106 5 05/08/02 0.77 39.9 BXD16 M 60 Harvard/BIDMC GKHI-KS-040805.10-051006 5 05/05/02 0.93 38.7 BXD18 F 59 Harvard/BIDMC GKHI-KS-052804.09-051106 4 05/05/02 0.67 37.6 BXD19 F 60 Harvard/BIDMC GKHI-KS-010705.47-051106 5 05/05/02 0.73 42.3 BXD19 F 60 Harvard/BIDMC GKHI-KS-010705.44-070706 3 07/06/02 0.73 36.1 BXD19 M 60 Harvard/BIDMC GKHI-KS-062905.07-051106 5 05/05/02 0.72 37.9 BXD20 M 60 Harvard/BIDMC GKHI-KS-072104.58-051106 4 05/05/02 0.73 37.0 BXD20 F 59 Harvard/BIDMC GKHI-KS-050405.21-051206 4 05/09/02 0.81 35.1 BXD21 F 60 Harvard/BIDMC GKHI-KS-040705.24 5 06/05/02 0.80 40.2 BXD21 F 99 UAB GKHI-KS-110405.01-051006 5 05/05/02 0.71 42.1 BXD22 F 60 Harvard/BIDMC GKHI-KS-110405.04-051006 5 05/05/02 0.76 40.6 BXD22 M 60 Harvard/BIDMC GKHI-KS-040805.01-051206 5 05/09/02 0.74 36.4 BXD23 F 60 Harvard/BIDMC GKHI-KS-040805.04-051006 5 05/05/02 0.73 39.3 BXD23 M 60 Harvard/BIDMC GKHI_KS_091704.13-042106 4 04/18/02 0.73 37.7 BXD24 M 59 Harvard/BIDMC GKHI-KS-040303-20-050206 3 04/30/02 0.77 36.3 BXD24 F 71 UMemphis GKHI-KS-021805.20-051006 5 05/05/02 0.83 40.5 BXD25 F 67 UAB GKHI-KS-090705.05-062206 5 06/21/02 0.76 38.4 BXD25 M 58 UTM RW GKHI-KS-090705.03-051006 5 05/05/02 0.81 40.1 BXD25 F 58 UTM RW GKHI-KS-022105.42-051006 5 05/05/02 0.81 41.8 BXD27 M 70 UAB GKHI-KS-032205.31-051006 5 05/05/02 0.74 39.0 BXD27 M 60 UTM RW GKHI-KS-060706.10-070706 3 07/06/02 0.69 37.8 BXD27 F 85 UTM RW GKHI-KS-012805-41-050506 5 05/04/02 0.81 34.2 BXD28 F 60 Harvard/BIDMC GKHI-KS-012805-44-050506 5 05/04/02 0.81 35.8 BXD28 M 60 Harvard/BIDMC GKHI-KS-012805-38-050506 5 05/04/02 0.77 42.7 BXD29 F 60 Harvard/BIDMC GKHI-KS-012805-35-050506 5 05/04/02 0.84 35.8 BXD29 F 60 Harvard/BIDMC GKHI-KS-012805-32-050506 5 05/04/02 0.74 39.9 BXD31 F 60 Harvard/BIDMC GKHI-KS-100604-07-050506 4 05/04/02 0.79 40.2 BXD31 M 60 Harvard/BIDMC GKHI-KS-021605.26-051706 5 05/14/02 1.11 39.0 BXD32 F 63 UTM RW GKHI-KS-112002.01-051206 2 05/09/02 0.76 38.1 BXD32 F 60 UMemphis GKHI-KS-072605-01-050506 5 05/04/02 0.79 41.3 BXD33 50 F 63 UTM RW GKHI-KS-091405-23-050506 5 05/04/02 0.84 38.4 BXD33 50 M 76 UTM RW GKHI-KS-111104-18-050506 4 05/04/02 0.79 42.2 BXD36 F 61 Harvard/BIDMC GKHI-KS-031804-07-050506 4 05/04/02 0.85 42.5 BXD36 F 58 Harvard/BIDMC GKHI-KS-092005.16-051206 5 05/09/02 0.72 37.2 BXD38 46 F 65 UTM RW GKHI-KS-031403.01-060806 1 06/07/02 0.69 39.6 BXD38 M 69 UMemphis GKHI-KS-090104.21-051106 4 05/08/02 0.72 36.3 BXD39 F 60 Harvard/BIDMC GKHI-KS-040204.30 4 06/05/02 0.77 43.9 BXD39 F 59 Harvard/BIDMC GKHI-KS-051805-16-050506 5 05/04/02 2.16 43.8 BXD40 F 61 UTM RW GKHI-KS-111902-04-050506 2 05/04/02 0.84 41.0 BXD40 F 56 UMemphis GKHI-KS-050604-01-050406 4 05/01/02 0.85 35.6 BXD43 23 F 61 UTM RW GKHI-KS-080905-43-050406 5 05/01/02 0.78 33.7 BXD43 28 F 62 UTM RW GKHI-KS-031004-01-050406 4 05/01/02 0.75 36.2 BXD44 21 F 57 UTM RW GKHI-KS-020504-01-050406 4 05/01/02 0.75 30.8 BXD44 20 M 66 UTM RW GKHI-KS-071504-01-050406 4 05/01/02 0.74 37.7 BXD45 20 F 58 UTM RW GKHI-KS-081104-05-050406 4 05/01/02 0.78 34.2 BXD45 20 M 93 UTM RW GKHI-KS-031204-01-050406 4 05/01/02 0.75 35.6 BXD48 22 M 60 UTM RW GKHI-KS-021104.06-051706 4 05/14/02 0.75 41.1 BXD48 21 F 58 UTM RW GKHI-KS-033005-21-050306 5 05/01/02 0.78 34.9 BXD51 27 M 64 UTM RW GKHI-KS-090204-01-050306 4 05/01/02 0.72 38.3 BXD51 24 F 63 UTM RW GKHI_KS-010704.01-040606 4 04/03/02 0.75 37.5 BXD60 21 M 64 UTM RW GKHI_KS_013004.38-042006 4 04/17/02 0.78 40.1 BXD60 21 F 60 UTM RW GKHI-KS-030905-28-050206 5 04/30/02 0.73 36.6 BXD61 20 F 63 UTM RW GKHI-KS-050305-18-050206 5 04/30/02 0.83 35.8 BXD61 21 F 70 UTM RW GKHI_KS-121803.01-040706 3 04/03/02 0.80 40.0 BXD62 20 M 54 UTM RW GKHI_KS_021204.01-042006 4 04/17/02 0.85 39.8 BXD62 21 F 59 UTM RW GKHI-KS-020905-25-050206 5 04/30/02 0.84 35.2 BXD63 21 M 70 UTM RW GKHI-KS-040705.49-060806 2 06/07/02 0.85 39.4 BXD65 20 F 55 UTM RW GKHI-KS-040406.12-060806 2 06/07/02 0.73 40.4 BXD65 23 F 60 UTM RW GKHI-KS-052405-36-050406 5 05/02/02 0.84 36.8 BXD67 20 F 65 UTM RW GKHI-KS-041205-01-050206 5 04/30/02 0.77 39.7 BXD67 20 F 54 UTM RW GKHI-KS-062305-01-050206 5 04/30/02 0.76 36.0 BXD68 20 F 59 UTM RW GKHI-KS-062305-09-050206 5 04/30/02 0.93 37.4 BXD68 20 F 64 UTM RW GKHI_KS_110105.30-042006 5 04/17/02 0.80 39.0 BXD69 26 F 66 UTM RW GKHI-KS-061504.64-062206 4 06/21/02 0.72 39.3 BXD69 20 M 55 UTM RW GKHI_KS-050404.04-040606 4 04/03/02 0.77 38.3 BXD69 20 F 63 UTM RW GKHI-KS-042705-01-042706 5 04/23/02 0.83 38.6 BXD70 21 F 64 UTM RW GKHI-KS-051705-59-042706 5 04/23/02 0.89 38.5 BXD70 22 F 61 UTM RW GKHI-KS-030805-40-042706 5 04/23/02 0.86 38.5 BXD73 23 F 61 UTM RW GKHI-KS-041905.172-062206 5 06/21/02 0.79 37.6 BXD73 24 M 64 UTM RW GKHI-KS-072605-03-042706 5 04/23/02 0.87 38.2 BXD73 25 F 72 UTM RW GKHI-KS-041205-04-050406 5 05/02/02 0.83 41.4 BXD75 22 F 60 UTM RW GKHI-KS-041205.07 5 06/05/02 0.79 45.8 BXD75 22 F 60 UTM RW GKHI-KS-101805-35-050406 5 05/02/02 0.79 38.4 BXD77 24 F 60 UTM RW GKHI-KS-070605.43 5 06/05/02 0.77 42.8 BXD77 23 F 62 UTM RW GKHI-KS-071205-31-042706 5 04/23/02 0.91 37.7 BXD80 20 F 65 UTM RW GKHI-KS-071205-2-042706 5 04/23/02 0.90 38.1 BXD80 20 F 65 UTM RW KS-011305-11-042606 5 04/22/02 0.82 39.0 BXD85 22 M 91 UTM RW KS-110805-27-042606 5 04/22/02 0.91 35.2 BXD85 25 F 63 UTM RW KS-080404-28-042606 4 04/22/02 0.84 36.8 BXD86 21 F 58 UTM RW KS-080504-04-042606 4 04/22/02 0.81 33.4 BXD86 20 M 77 UTM RW KS-051705-57-042606 5 04/22/02 1.11 35.6 BXD87 20 M 63 UTM RW KS-032905-46-042606 5 04/22/02 0.85 36.1 BXD87 20 M 57 UTM RW GKHI-KS-080905-49-042706 5 04/23/02 0.89 37.6 BXD90 23 F 71 UTM RW GKHI-KS-101105.26 5 06/05/02 0.84 43.6 BXD90 25 F 70 UTM RW GKHI_KS-062304.02-040606 4 04/03/02 0.85 40.9 BXD92 21 M 55 UTM RW GKHI_KS_071404.01-042006 4 04/17/02 0.77 39.5 BXD92 21 F 62 UTM RW GKHI_KS_031005.17-042006 5 04/17/02 0.77 38.1 BXD96 20 M 65 UTM RW GKHI-KS-111505.12 5 06/05/02 0.77 44.1 BXD96 23 M 66 UTM RW GKHI-KS-012406.21-060806 3 06/07/02 0.73 36.6 BTBR T+tf/J F 60 Harvard/BIDMC GKHI-KS-012406.24-060806 3 06/07/02 1.28 39.2 BTBR T+tf/J F 60 Harvard/BIDMC GKHI-KS-030206.13-060806 3 06/07/02 0.71 41.2 BXSB/MpJ F 61 Harvard/BIDMC GKHI-KS-030206.16-060806 3 06/07/02 0.66 37.2 BXSB/MpJ F 61 Harvard/BIDMC GKHI-KS-011906.31-060806 3 06/07/02 0.80 37.2 C3H/HeJ M 60 Harvard/BIDMC GKHI-KS-011906.34-060806 3 06/07/02 0.76 38.5 C3H/HeJ M 60 Harvard/BIDMC GKHI-KS-060806.04-070706 3 07/06/02 0.68 37.3 C3H/HeJ F 76 Harvard/BIDMC GKHI-KS-071505.08-060806 3 06/07/02 0.71 37.4 C57BL/6ByJ F 51 JAX GKHI-KS-071505.11-060806 2 06/07/02 0.73 39.2 C57BL/6ByJ F 51 JAX GKHI-KS-030305.15-060806 3 06/07/02 0.71 37.4 CAST/Ei F 64 JAX GKHI-KS-031005.35-060906 3 06/08/02 0.70 35.7 CAST/Ei M 64 JAX GKHI-KS-022206.16-060906 3 06/08/02 0.71 37.9 KK/HlJ F 61 Harvard/BIDMC GKHI-KS-022206.07-060906 3 06/08/02 0.72 35.5 KK/HlJ M 61 Harvard/BIDMC GKHI-KS-031606.01-060906 3 06/08/02 0.86 35.9 MOLF/Ei M 60 Harvard/BIDMC GKHI-KS-022206.16-060906 3 06/08/02 0.87 37.4 MOLF/Ei F 60 Harvard/BIDMC GKHI-KS-012006.25-060906 3 06/08/02 0.75 38.3 NOD/LtJ F 58 Harvard/BIDMC GKHI-KS-012006.28-061306 3 06/11/02 0.82 37.1 NOD/LtJ F 58 Harvard/BIDMC GKHI-KS-032306.04.060906 3 06/08/02 0.73 40.2 NZB/BlNJ F 61 Harvard/BIDMC GKHI-KS-032306.07-060906 3 06/08/02 0.74 39.4 NZB/BlNJ F 61 Harvard/BIDMC GKHI-KS-020706.04-060906 3 06/08/02 0.71 41.6 NZW/LacJ F 65 Harvard/BIDMC GKHI-KS-020206.19-060906 3 06/08/02 0.77 36.7 NZW/LacJ M 60 Harvard/BIDMC GKHI-KS-012406.33-061306 3 06/11/02 0.95 35.3 PWD/PhJ F 60 Harvard/BIDMC GKHI-KS-012406.30-062006 3 06/18/02 0.88 36.3 PWD/PhJ M 60 Harvard/BIDMC GKHI-KS-020206.01-062206 3 06/21/02 1.02 35.9 PWK/PhJ F 60 Harvard/BIDMC GKHI-KS-020206.04-062206 3 06/21/02 0.96 38.7 PWK/PhJ F 60 Harvard/BIDMC GKHI-KS-020206.07-062206 3 06/21/02 0.98 36.6 PWK/PhJ M 60 Harvard/BIDMC GKHI-KS-020206.10-062206 3 06/21/02 0.87 35.2 PWK/PhJ M 60 Harvard/BIDMC GKHI-KS-052705.01-061306 2 06/11/02 0.72 38.3 WSB/EiJ F 52 UTM RW GKHI-KS-051005.07-061306 3 06/11/02 0.77 38.0 WSB/EiJ M 58 JAX