UTHSC Affy MoGene 1.0 ST Spleen (Oct10) RMA

Summary

This is a near final release of a spleen gene expression data set generated by a DOD-funded consortium (Byrne, Kotb, Williams, and Lu). Please contact Lu Lu or Robert Williams regarding status of this data set. The initial data enterted in 2010 had many errors described below. The data set is much improved and has no known errors of strain assignment.

Animals were generated at UTHSC by Lu Lu and colleagues. The spleen of untreated young adult mice was profiled using the Affymetrix GeneChip Mouse Gene 1.0 ST array that contains approximately 34,728 probe sets that target approximately 29,000 well defined transcripts (RefSeq mRNA isoforms) and essentially all known protein coding genes in mouse. This array is an "exon style" array with multiple probes in all known exons of each gene (an average of about 27 per gene) and is an abridged version of the Affymetrix Exon 1.0 ST array. However, it also does contain some probes that target non-coding RNAs and even miRNA precursors (search "ncrna").

Experiment design

RNA Processing. Total RNA was purified using the RNAeasy micro kit on the QIAcube system (www.qiagen.com). RNA purity and concentration was checked using 260/280 nm absorbance ratio and RNA integrity was analyzed using the Agilent Bioanalyzer 2100 (Agilent Technologies).

Array Processing: All arrays were processed by Lorne Rose in the UTHSC Molecular Resources Center (MRC), Memphis TN. The table below provides a summary of cases, sex, and age. The spleen was dissected by both Dr. Lu Lu and colleagues and Dr. Abdeltawab and colleagues. All arrays were run together (interleaved) as a single large batch.

About cases

Cases. A total of 111 strains, including 81 BXD strains, both parental strains (C57BL/6J and DBA/2J) and both reciprocal F1 hybrids (B6D2F1 and D2B6F1), and 26 other common inbred strains were quantified. In most cases, two arrays were processed per strain--one for males and one for females. All tissue and RNA was extracted by Lu Lu and colleagues. Samples were pooled by sex and usually include at least two cases per sex and strain.

Sex Balance. XX strains have matched male and female samples. XX strains have male only samples (BXDX, XX, XX, XXX and XXX). XX strains have only female samples (BXDXX, XX, and XX.) Please review the expression data for Xist probe set 10606178. This non-coding RNA is expressed highly only in females and can be used to check the sex of a sample or pool of tissue. Ddx3y probe set 10608138 can also be used. This is a Y chromosome gene that is expressed abundantly in male samples and at background levels in female samples.

About data processing

Data Processing. Array data sets were generated by the vendors GCOS system. Expression values were logged and then were further normalized and rescaled so that the mean value for each array data set is 8 units with a standard deviation of 2 units. Data were processed by Arthur Centeno.

Batch Effects. This data set required some correction for batch effects and the data in this initial release incorporate any additional corrections. There are several additional confounder-like factors that should be considered:

1. Sex imbalance in the sample: use probe sets for Xist as correction in partial correlation
2. Background noise factors: examine and use probe sets with very low expression using the search "mean=(3.900 4.135)". This will extract the probe sets with the lowest expression. (Note that the number 54 is less than the total number of cases in this data set; important in computing principal components.) Add these probe sets to your collection window and then compute the correlation matrix. Use the first few principal components as surrogates for nuisance factors in partial correlation analysis. The first principal component of the lowest probe sets in this spleen data set accounts of XX% of the the variance. Mapping of this noise trait can be used to evaluate the effects of shared noise on QTL results. The first principal component in the spleen data set can be mapped as a trait.

Data Release. This data set was first uploaded into GeneNetwork by Arthur Centeno, October 11, 2010 and made accessible without a password to all users on November 1, 2010. The initial data release had numerous strain identification errors that have now largely been fixed. Based on an analysis of the top 20 Mendelian loci, the following 21 strains were likely to have been incorrectly identified or assigned in the current release:

1. BXD8, e.g., Probe set 10450161, 1036098. 10338684
2. BXD13, e.g., Probe set 10450161, 1036098, 10402390, 10592493, 10342568,
3. BXD21 (may be ok, only one probe set 10338684 is problematic)
4. BXD23 (may be ok, only two probe sets 10421128, 10419465 is problematic)
5. BXD36 (may be ok, only one probe set 10421128 is problematic)
6. BXD40, e.g., Probe set 10341070
7. BXD43, e.g., Probe set 10450161, 1036098, 10338684
8. BXD48, e.g., Probe set 1036098, 10402390, 10514896, 10592493, 10357381, 10342568, 10571444, 10419465
9. BXD62, e.g., Probe set 1036098, 1036098, 10402390, 10514896, 10592493, 10421128, 10571444
10. BXD68 (may be ok, only one probe set 10338684 is problematic)
11. BXD69, e.g., Probe set 10450161
12. BXD73, e.g., Probe set 10341070, 1036098, 10402390, 10514896, 10587633, 10342568, 10421128
13. BXD74, e.g., Probe set 10402390
14. BXD80, e.g., Probe set 10341070, 1036098, 10592493, 10400109, 10338684, 10342568, 10421128, 10419465
15. BXD83, e.g., Probe set 10450161, 10338684
16. BXD87 (may be ok, only one probe set 10421128 is problematic)
17. BXD89, e.g., Probe set 10450161, 1036098, 10402390, 10592493, 10357381, 10419465
18. BXD93, e.g., Probe set 10402390, 10357381
19. BALB/cByJ, e.g., Probe set 10388042, 1036098, 10587633, 10357381, 10342568, 10421128
20. LP/J, e.g., Probe set 10592493
21. DBA/2J, e.g., Probe set 10592493

Data Evaluation Summary

1. Before correction: eQLTs with LOD >10 (LRS>46.1): n = 638
2. After strain assignment correction: eQLTs with LOD >10 (LRS>46.1): n = 820
3. Before correction: eQTL with high LOD and LRS: Trait ID 10450161 (H2-Ea-ps) LOD = 51.6, LRS = 237.9
4. After correction: eQTL with high LOD and LRS: Trait ID 10450161 (H2-Ea-ps) LOD = 51.6, LRS = 278.1
5. Lowest mean value: Trait ID 10344361, mean = 3.998
6. Highest mean value: Trait ID 10598025, mean = 14.475 (MT-ND1)
7. Greatest sex difference: Trait ID: 10606178 (Xist)
8. Great variation within and among strains: Trait ID 10454192 (Ttr

   Table 1 (please confirm that these assignments are after correction)

   Index Array ID Phase Strain Age Sex 1 R5583S 1 129P3/J 65 F 2 R5584S 1 129P3/J 66 M 3 R5585S 1 129S1/SvImJ 66 F 4 R5586S 1 129S1/SvImJ 66 M 5 R5587S 1 129X1/SvJ 65 F 6 R5588S 1 129X1/SvJ 66 M 7 R6348S 3 B6D2F1 67 F 8 R6347S 3 B6D2F1 62 F 9 R5590S 1 B6D2F1 79 M 10 R5662S 1 BALB/cByJ 59 F 11 R5664S 1 BALB/cByJ 59 M 12 R5591S 1 BALB/cJ 51 F 13 R5592S 1 BALB/cJ 51 M 14 R6154S 2 BTBR T+ tf/J 60 F 15 R6516S 3 BXD1 82 F 16 R6584S 3 BXD1 95 M 17 R5759S 1 BXD2 N/A F 18 R5837S 1 BXD2 106 M 19 R5874S 2 BXD5 86 F 20 R6554S 3 BXD5 60 M 21 R6359S 3 BXD6 72 F 22 R5777S 1 BXD6 149 M 23 R6364S 3 BXD8 76 F 24 R5637S 1 BXD8 71 F 25 R6365S 3 BXD8 76 M 26 R5746S 1 BXD9 70 F 27 R5981S 2 BXD9 67 M 28 R5980S 2 BXD9 67 M 29 R6182S 2 BXD11 84 F 30 R6486S 3 BXD11 58 M 31 R6711S2 4 BXD12 71 F 32 R6608S 3 BXD12 48 F 33 R5885S 2 BXD12 44 M 34 R5755S 1 BXD13 160 F 35 R5887S 2 BXD13 53 M 36 R6180S 2 BXD14 70 F 37 R5669S 1 BXD14 91 M 38 R6456S 3 BXD15 60 F 39 R6622S 3 BXD15 60 F 40 R6626S 3 BXD15 60 M 41 R6181S 2 BXD16 74 F 42 R6515S 3 BXD16 64 M 43 R5673S 1 BXD18 80 F 44 R5674S 1 BXD18 65 M 45 R6553S 3 BXD19 158 F 46 R6551S 3 BXD19 60 M 47 R6643S4 4 BXD20 59 F 48 R6595S 3 BXD20 60 M 49 R5735S 1 BXD21 64 F 50 R5892S 2 BXD21 99 M 51 R5896S 2 BXD22 60 F 52 R6414S 3 BXD22 73 M 53 R6550S 3 BXD23 74 F 54 R6586S 3 BXD23 102 F 55 R5630S 1 BXD24 71 F 56 R6356S 3 BXD24 57 M 57 R6162S 2 BXD25 67 F 58 R6625S 3 BXD25 67 F 59 R6642S4 4 BXD25 58 M 60 R5761S 1 BXD27 N/A F 61 R5763S 1 BXD27 90 M 62 R6621S 3 BXD28 113 F 63 R6548S 3 BXD28 60 M 64 R6547S 3 BXD29 60 F 65 R6453S 3 BXD31 48 F 66 R6452S 3 BXD31 48 M 67 R6583S 3 BXD32 60 F 68 R5765S 1 BXD32 71 M 69 R5689S 1 BXD33 65 F 70 R6450S 3 BXD33 55 M 71 R5767S 1 BXD34 72 F 72 R5900S 2 BXD34 70 M 73 R6588S 3 BXD36 61 F 74 R6490S 3 BXD36 63 M 75 R6417S 3 BXD38 64 F 76 R6439S 3 BXD38 72 M 77 R5769S 1 BXD39 N/A F 78 R5771S 1 BXD39 74 M 79 R5773S 1 BXD40 N/A F 80 R5775S 1 BXD40 N/A M 81 R6494S 3 BXD41 72 F 82 R5910S 2 BXD42 79 F 83 R6493S 3 BXD42 69 M 84 R6341S 3 BXD43 59 F 85 R6401S 3 BXD43 99 M 86 R5916S 2 BXD43 79 M 87 R5839S 1 BXD44 141 F 88 R5779S 1 BXD44 124 M 89 R6405S 3 BXD45 58 F 90 R6610S 3 BXD45 55 M 91 R5922S 2 BXD48 64 F 92 R5925S 2 BXD48 60 M 93 R6719S1 4 BXD49 58 F 94 R6485S 3 BXD49 79 M 95 R5781S 1 BXD50 61 F 96 R6464S 3 BXD51 65 F 97 R6585S 3 BXD51 63 M 98 R6500S 3 BXD55 58 F 99 R5938S 2 BXD55 93 M 100 R6504S 3 BXD56 58 F 101 R6503S 3 BXD56 58 M 102 R5783S 1 BXD60 111 F 103 R5784S 1 BXD60 85 M 104 R5786S 1 BXD61 86 F 105 R6449S 3 BXD61 65 M 106 R6716S1 4 BXD62 54 F 107 R5790S 1 BXD62 115 M 108 R6519S 3 BXD63 54 F 109 R6717S1 4 BXD63 70 M 110 R5792S 1 BXD64 167 F 111 R6641S4 4 BXD64 68 M 112 R6630S 3 BXD64 68 M 113 R6477S 3 BXD65 58 F 114 R6628S 3 BXD65 70 M 115 R6511S 3 BXD66 70 F 116 R6448S 3 BXD66 61 M 117 R5794S 1 BXD66 144 M 118 R6502S 3 BXD67 66 F 119 R6545S 3 BXD67 61 M 120 R6337S 3 BXD68 56 F 121 R6594S 3 BXD68 64 M 122 R5796S 1 BXD69 85 F 123 R5798S 1 BXD69 98 M 124 R6402S 3 BXD70 93 F 125 R5841S 1 BXD70 121 F 126 R6592S 3 BXD70 59 M 127 R6328S 3 BXD71 87 F 128 R5967S 2 BXD71 64 M 129 R5969S 2 BXD73 64 F 130 R5800S 1 BXD73 120 M 131 R6646S 3 BXD74 40 F 132 R6524S 3 BXD74 72 M 133 R6445S 3 BXD75 85 F 134 R5843S 1 BXD75 103 F 135 R5845S 1 BXD75 103 M 136 R6604S 3 BXD77 64 F 137 R6513S 3 BXD77 72 M 138 R6582S 3 BXD78 144 F 139 R6563S 3 BXD78 95 M 140 R6645S4 4 BXD79 66 F 141 R5806S 1 BXD79 78 M 142 R5847S 1 BXD80 89 F 143 R5852S 1 BXD80 79 M 144 R6562S 3 BXD81 99 F 145 R6468S 3 BXD81 65 M 146 R6560S 3 BXD82 85 F 147 R6512S 3 BXD83 68 F 148 R5810S 1 BXD83 139 M 149 R6510S 3 BXD84 87 F 150 R5970S 2 BXD84 107 F 151 R6603S 3 BXD84 99 M 152 R6517S 3 BXD85 58 F 153 R6718S1 4 BXD85 86 M 154 R5812S 1 BXD86 61 F 155 R5814S 1 BXD86 59 M 156 R5816S 1 BXD87 112 F 157 R6488S 3 BXD87 137 M 158 R6580S 3 BXD88 125 F 159 R5977S 2 BXD89 68 F 160 R5979S 2 BXD89 79 M 161 R5978S 2 BXD89 79 M 162 R5818S 1 BXD90 106 F 163 R5820S 1 BXD90 131 M 164 R6343S 3 BXD92 62 F 165 R5984S 2 BXD92 55 M 166 R6581S 3 BXD93 173 M 167 R6557S 3 BXD93 126 M 168 R6509S 3 BXD95 59 F 169 R5822S 1 BXD95 89 M 170 R6640S4 4 BXD96 70 F 171 R6514S 3 BXD96 64 M 172 R6506S 3 BXD97 78 F 173 R5849S 1 BXD97 130 F 174 R6591S 3 BXD97 122 M 175 R5990S 2 BXD98 65 F 176 R6596S 3 BXD98 67 M 177 R5993S 2 BXD99 74 F 178 R5995S 2 BXD99 50 M 179 R6607S 3 BXD100 75 F 180 R6411S 3 BXD100 104 M 181 R6508S 3 BXD101 59 F 182 R5593S 1 BXD101 59 M 183 R6523S 3 BXD102 60 F 184 R6466S 3 BXD102 50 M 185 R6404S 3 BXD103 72 F 186 R6609S 3 BXD103 57 M 187 R6555S 3 C57BL/10J 73 M 188 R5596S 1 C57BL/10J 73 M 189 R5597S 1 C57BL/6ByJ 51 F 190 R5598S 1 C57BL/6ByJ 69 M 191 R5600S 1 C57BL/6J 79 F 192 R5599S 1 C57BL/6J 60 F 193 R6451S 3 C57BL/6J 77 M 194 R6410S 3 C57BL/6J 85 M 195 R5603S 1 C57BLKS/J 66 F 196 R5604S 1 C57BLKS/J 66 M 197 R5996S 2 CBA/CaJ 66 F 198 R6349S 3 CBA/CaJ 66 M 199 R6458S 3 D2B6F1 64 F 200 R6353S 3 D2B6F1 60 M 201 R5605S 1 DBA/2J 79 F 202 R6446S 3 DBA/2J 83 M 203 R6597S 3 FVB/NJ 60 F 204 R5643S 1 FVB/NJ 60 F 205 R6598S 3 FVB/NJ 60 M 206 R5606S 1 ILS 74 F 207 R5607S 1 ILS 74 M 208 R5610S 1 ISS 97 M 209 R6627S 3 KK/HlJ 64 F 210 R6444S 3 KK/HlJ 65 M 211 R5702S 1 KK/HlJ 61 M 212 R5613S 1 LG/J 63 F 213 R5704S 1 LG/J 65 M 214 R5614S 1 LP/J 65 F 215 R5615S 1 LP/J 65 M 216 R6599S 3 MOLF/EiJ 60 F 217 R6606S 3 MOLF/EiJ 60 M 218 R6544S 3 NOD/LtJ 77 F 219 R5709S 1 NOD/LtJ 58 M 220 R6601S 3 NZB/BlNJ 61 F 221 R5711S 1 NZB/BlNJ 61 F 222 R6427S 3 NZB/BlNJ 58 M 223 R6150S 2 NZO/HlLtJ 71 F 224 R6155S 2 NZW/LacJ 65 F 225 R5654S 1 NZW/LacJ 60 M 226 R5721S 1 PL/J 59 M 227 R5616S 1 PWD/PhJ 60 M 228 R5725S 1 PWK/PhJ 121 M 229 R6174S 2 SJL/J 63 F 230 R6350S 3 SJL/J 65 M 231 R6419S 3 WSB/EiJ 60 F 232 R5620S 1 WSB/EiJ 60 M

Notes

Data Status and Use. This is a provisional release that will soon be replaced by a final corrected data set. In the interim this data set is open for exploration and use for focused analysis of single genes. Please contact Robert W. Williams at rwilliams@uthsc.edu regarding use of these data regarding the best citation.
This data set is not yet freely available for global analysis. This data set has not yet been used or described in any publication. Please see the GeneNetwork data sharing policy for more background on data use.

Contact. Please contact Robert W. Williams at rwilliams@uthsc.edu regarding use of these data.