Data Set Group2: UTHSC Affy MoGene 1.0 ST Spleen (Dec10)

Contact Information 
Robert Williams
University of Tennessee Health Science Center
71 S Manassas St, Room 405 TSRB
Memphis, TN 38163 USA
Tel. 901 4487050
rwilliams@uthsc.edu
Website

Download datasets and supplementary data files 



Specifics of this Data Set: 
None

Summary: 
This is a near final release of a spleen gene expression data set generated by a DODfunded 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 noncoding RNAs and even miRNA precursors (search "ncrna").

About the cases used to generate this set of data: 
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 strainone 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 noncoding 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 the tissue used to generate this set of data: 

About the array platform: 

About data values and 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 confounderlike factors that should be considered:
 Sex imbalance in the sample: use probe sets for Xist as correction in partial correlation
 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:
 BXD8, e.g., Probe set 10450161, 1036098. 10338684
 BXD13, e.g., Probe set 10450161, 1036098, 10402390, 10592493, 10342568,
 BXD21 (may be ok, only one probe set 10338684 is problematic)
 BXD23 (may be ok, only two probe sets 10421128, 10419465 is problematic)
 BXD36 (may be ok, only one probe set 10421128 is problematic)
 BXD40, e.g., Probe set 10341070
 BXD43, e.g., Probe set 10450161, 1036098, 10338684
 BXD48, e.g., Probe set 1036098, 10402390, 10514896, 10592493, 10357381, 10342568, 10571444, 10419465
 BXD62, e.g., Probe set 1036098, 1036098, 10402390, 10514896, 10592493, 10421128, 10571444
 BXD68 (may be ok, only one probe set 10338684 is problematic)
 BXD69, e.g., Probe set 10450161
 BXD73, e.g., Probe set 10341070, 1036098, 10402390, 10514896, 10587633, 10342568, 10421128
 BXD74, e.g., Probe set 10402390
 BXD80, e.g., Probe set 10341070, 1036098, 10592493, 10400109, 10338684, 10342568, 10421128, 10419465
 BXD83, e.g., Probe set 10450161, 10338684
 BXD87 (may be ok, only one probe set 10421128 is problematic)
 BXD89, e.g., Probe set 10450161, 1036098, 10402390, 10592493, 10357381, 10419465
 BXD93, e.g., Probe set 10402390, 10357381
 BALB/cByJ, e.g., Probe set 10388042, 1036098, 10587633, 10357381, 10342568, 10421128
 LP/J, e.g., Probe set 10592493
 DBA/2J, e.g., Probe set 10592493
Data Evaluation Summary
 Before correction: eQLTs with LOD >10 (LRS>46.1): n = 638
 After strain assignment correction: eQLTs with LOD >10 (LRS>46.1): n = 820
 Before correction: eQTL with high LOD and LRS: Trait ID 10450161 (H2Eaps) LOD = 51.6, LRS = 237.9
 After correction: eQTL with high LOD and LRS: Trait ID 10450161 (H2Eaps) LOD = 51.6, LRS = 278.1
 Lowest mean value: Trait ID 10344361, mean = 3.998
 Highest mean value: Trait ID 10598025, mean = 14.475 (MTND1)
 Greatest sex difference: Trait ID: 10606178 (Xist)
 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.

Experiment Type: 
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.

Contributor: 

Citation: 

Data source acknowledgment: 

Study Id: 
96




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 NIDA, NIMH, and NIAAA (P20DA 21131, 20012012)
 NCI MMHCC (U01CA105417), NCRR, BIRN, (U24 RR021760)

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