UTHSC Affy MoGene 1.0 ST Spleen (Oct10) RMA
Accession number: GN271

Summary Description of Data Set:

Summary:

This is a preliminary release WITH KNOWN ERRORS 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.

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").

Animals and Tissue 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 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.

Sample Processing:

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.

Experimental Design and Batch Structure:

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 data set still is provisional and contains numerous strain identification errors that have NOT YET BEEN FIXED. Based on an analysis of the top 20 Mendelian loci, the following 21 strains are 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 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.

Data Evaluation Summary

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

   Table 1