INIA Amygdala Affy MoGene 1.0 ST (Nov10) RMA

Summary

This is a final error-checked release of an amygdala gene expression data set generated by Khyobeni Mozhui, Lu Lu, and Robert W. Williams and colleagues with funding support from the NIH NIAAA. The basolateral complex of the amygdala 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

Data Evaluation Summary

1. eQLTs with LOD >10 (LRS>46.1): n = 525
2. eQTL with high LOD and LRS: Trait ID 10513604 (Hdhd3) LOD = 39.8, LRS = 183.5
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

   Index Array ID Tissue Strain Age Sex Date sacrifice Time sacrifice 1 R6853BL BLA C57BL/6J 77 F 8/18/10 8:45AM to 12:30 PM 2 R6861BL BLA C57BL/6J 77 M 8/18/10 8:45AM to 12:30 PM 3 R6851BL BLA D2B6F1 77 F 8/18/10 8:45AM to 12:30 PM 4 R6859BL BLA D2B6F1 77 M 8/18/10 8:45AM to 12:30 PM 5 R6863BL BLA DBA/2J 77 F 8/18/10 8:45AM to 12:30 PM 6 R6865BL BLA DBA/2J 68 M 8/18/10 8:45AM to 12:30 PM 7 R6857BL BLA B6D2F1 69 F 8/18/10 8:45AM to 12:30 PM 8 R6855BL BLA B6D2F1 69 M 8/18/10 8:45AM to 12:30 PM 9 R6799BL BLA BXD1 71 F 8/17/10 1:15 PM to 5 PM 10 R6795BL BLA BXD1 85 M 8/17/10 1:15 PM to 5 PM 11 R6787BL BLA BXD11 87 F 8/17/10 1:15 PM to 5 PM 12 R6785BL BLA BXD11 76 M 8/17/10 1:15 PM to 5 PM 13 R6819BL BLA BXD12 78 F 8/18/10 8:45AM to 12:30 PM 14 R6789BL BLA BXD12 73 M 8/17/10 1:15 PM to 5 PM 15 R6805BL BLA BXD12 77 M 8/17/10 1:15 PM to 5 PM 16 R6291BL BLA BXD13 N/A M 6/11/09 N/A 17 R6811BL BLA BXD14 81 F 8/18/10 8:45AM to 12:30 PM 18 R6825BL BLA BXD14 81 M 8/18/10 8:45AM to 12:30 PM 19 R6657BL BLA BXD16 N/A M 1/8/08 N/A 20 R6054BL BLA BXD19 N/A F 2/26/08 N/A 21 R6052BL BLA BXD19 N/A M 2/26/08 N/A 22 R6803BL BLA BXD24 85 F 8/17/10 1:15 PM to 5 PM 23 R6817BL BLA BXD24 86 M 8/18/10 8:45AM to 12:30 PM 24 R6063BL BLA BXD25 N/A F 3/12/08 N/A 25 R6062BL BLA BXD25 N/A M 3/12/08 N/A 26 R6659BL BLA BXD27 N/A F 1/8/08 N/A 27 R6791BL BLA BXD27 75 F 8/17/10 1:15 PM to 5 PM 28 R6797BL BLA BXD29 71 F 8/17/10 1:15 PM to 5 PM 29 R6793BL BLA BXD29 71 M 8/17/10 1:15 PM to 5 PM 30 R6815BL BLA BXD31 74 F 8/18/10 8:45AM to 12:30 PM 31 R6801BL BLA BXD31 73 M 8/17/10 1:15 PM to 5 PM 32 R6915BL BLA BXD32 81 F 8/18/10 1 PM to 6:45 PM 33 R6845BL BLA BXD32 81 M 8/18/10 8:45AM to 12:30 PM 34 R6821BL BLA BXD34 77 F 8/18/10 8:45AM to 12:30 PM 35 R6807BL BLA BXD34 77 M 8/18/10 8:45AM to 12:30 PM 36 R6057BL BLA BXD38 N/A F 2/26/08 N/A 37 R6056BL BLA BXD38 N/A M 2/26/08 N/A 38 R6827BL BLA BXD39 79 F 8/18/10 8:45AM to 12:30 PM 39 R6813BL BLA BXD39 79 M 8/18/10 8:45AM to 12:30 PM 40 R6847BL BLA BXD40 85 F 8/18/10 8:45AM to 12:30 PM 41 R6849BL BLA BXD40 85 M 8/18/10 8:45AM to 12:30 PM 42 R6809BL BLA BXD42 87 F 8/18/10 8:45AM to 12:30 PM 43 R6823BL BLA BXD42 87 M 8/18/10 8:45AM to 12:30 PM 44 R6759BL BLA BXD43 81 F 8/17/10 9:30 AM to 12:30AM 45 R6757BL BLA BXD43 81 M 8/17/10 9:30 AM to 12:30AM 46 R6745BL BLA BXD44 83 F 8/17/10 9:30 AM to 12:30AM 47 R6763BL BLA BXD45 77 F 8/17/10 9:30 AM to 12:30AM 48 R6761BL BLA BXD45 77 M 8/17/10 9:30 AM to 12:30AM 49 R6879BL BLA BXD48 76 F 8/18/10 1 PM to 6:45 PM 50 R6881BL BLA BXD48 76 M 8/18/10 1 PM to 6:45 PM 51 R6751BL BLA BXD49 84 F 8/17/10 9:30 AM to 12:30AM 52 R6747BL BLA BXD49 84 M 8/17/10 9:30 AM to 12:30AM 53 R6104BL BLA BXD5 N/A f 10/23/09 N/A 54 R6103BL BLA BXD5 N/A M 10/23/09 N/A 55 R6889BL BLA BXD50 77 F 8/18/10 1 PM to 6:45 PM 56 R6891BL BLA BXD50 77 M 8/18/10 1 PM to 6:45 PM 57 R6074BL BLA BXD51 N/A F 3/12/08 N/A 58 R6699BL BLA BXD51 N/A M 4/30/09 N/A 59 R6917BL BLA BXD56 84 F 8/18/10 1 PM to 6:45 PM 60 R6893BL BLA BXD56 77 M 8/18/10 1 PM to 6:45 PM 61 R6769BL BLA BXD60 70 F 8/17/10 9:30 AM to 12:30AM 62 R6771BL BLA BXD60 70 M 8/17/10 1:15 PM to 5 PM 63 R6655BL BLA BXD61 N/A F 1/29/08 N/A 64 R6653BL BLA BXD61 N/A M 1/29/08 N/A 65 R6835BL BLA BXD62 83 F 8/18/10 8:45AM to 12:30 PM 66 R6843BL BLA BXD62 83 M 8/18/10 8:45AM to 12:30 PM 67 R6887BL BLA BXD63 77 F 8/18/10 1 PM to 6:45 PM 68 R6885BL BLA BXD63 77 M 8/18/10 1 PM to 6:45 PM 69 R6877BL BLA BXD65 84 F 8/18/10 1 PM to 6:45 PM 70 R6873BL BLA BXD65 84 M 8/18/10 1 PM to 6:45 PM 71 R6929BL BLA BXD68 76 F 8/18/10 1 PM to 6:45 PM 72 R6931BL BLA BXD68 76 M 8/18/10 1 PM to 6:45 PM 73 R6775BL BLA BXD69 69 F 8/17/10 1:15 PM to 5 PM 74 R6773BL BLA BXD69 80 M 8/17/10 1:15 PM to 5 PM 75 R6925BL BLA BXD70 76 F 8/18/10 1 PM to 6:45 PM 76 R6921BL BLA BXD70 76 M 8/17/06 1 PM to 6:45 PM 77 R6869BL BLA BXD71 76 F 8/18/10 1 PM to 6:45 PM 78 R6871BL BLA BXD71 76 M 8/18/10 1 PM to 6:45 PM 79 R6777BL BLA BXD73 83 F 8/17/10 1:15 PM to 5 PM 80 R6779BL BLA BXD73 83 M 8/17/10 1:15 PM to 5 PM 81 R6837BL BLA BXD75 76 F 8/18/10 8:45AM to 12:30 PM 82 R6829BL BLA BXD75 76 M 8/18/10 8:45AM to 12:30 PM 83 R6933BL BLA BXD79 87 F 8/18/10 1 PM to 6:45 PM 84 R6935BL BLA BXD79 87 M 8/18/10 1 PM to 6:45 PM 85 R6781BL BLA BXD80 73 F 8/17/10 1:15 PM to 5 PM 86 R6783BL BLA BXD80 73 M 8/17/10 1:15 PM to 5 PM 87 R6913BL BLA BXD83 81 F 8/18/10 1 PM to 6:45 PM 88 R6911BL BLA BXD83 81 M 8/18/10 1 PM to 6:45 PM 89 R6841BL BLA BXD84 76 F 8/18/10 8:45AM to 12:30 PM 90 R6833BL BLA BXD84 76 M 8/18/10 8:45AM to 12:30 PM 91 R6937BL BLA BXD85 74 F 8/18/10 1 PM to 6:45 PM 92 R6939BL BLA BXD85 74 M 8/18/10 1 PM to 6:45 PM 93 R6909BL BLA BXD87 83 F 8/18/10 1 PM to 6:45 PM 94 R6895BL BLA BXD89 82 F 8/18/10 1 PM to 6:45 PM 95 R6897BL BLA BXD89 82 M 8/18/10 1 PM to 6:45 PM 96 R6903BL BLA BXD90 82 F 8/18/10 1 PM to 6:45 PM 97 R6905BL BLA BXD90 82 M 8/18/10 1 PM to 6:45 PM 98 R6923BL BLA BXD92 86 F 8/18/10 1 PM to 6:45 PM 99 R6927BL BLA BXD92 89 M 8/18/10 1 PM to 6:45 PM 100 R6919BL BLA BXD95 76 F 8/18/10 1 PM to 6:45 PM 101 R6867BL BLA BXD95 76 M 8/18/10 8:45AM to 12:30 PM 102 R6899BL BLA BXD97 71 F 8/18/10 1 PM to 6:45 PM 103 R6901BL BLA BXD97 71 M 8/18/10 1 PM to 6:45 PM 104 R6875BL BLA BXD99 77 F 8/18/10 1 PM to 6:45 PM 105 R6883BL BLA BXD99 77 M 8/18/10 1 PM to 6:45 PM 106 R6831BL BLA BXD100 83 M 8/18/10 8:45AM to 12:30 PM 107 R6943BL BLA BXD101 89 F 8/18/10 1 PM to 6:45 PM 108 R6941BL BLA BXD101 89 M 8/18/10 1 PM to 6:45 PM 109 R6753BL BLA BXD102 88 F 8/17/10 9:30 AM to 12:30AM 110 R6755BL BLA BXD102 88 M 8/17/10 9:30 AM to 12:30AM 111 R6765BL BLA BXD103 78 M 8/17/10 9:30 AM to 12:30AM

    

About cases

Cases. A total of 58 strains, including 54 BXD strains, both parental strains (C57BL/6J and DBA/2J) and both reciprocal F1 hybrids (B6D2F1 and D2B6F1) were analyzed. In most cases, two arrays were processed per strain--one for males and one for females. All tissue and RNA was extracted by K. Mozhui. Samples were pooled by sex and usually include at least two cases per sex and strain.

Sex Balance. Fifty strains have matched male and female samples. Five strains have male only samples (BXD5, 13, 16, 100 and 103). Three strains have only female samples (BXD44, 70, and 87.) 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 tissue

Dissection Protocol

1. Animals were sacrificed by cervical dislocation and brains were immediately dissected from the head and stored in RNAlater (www.ambion.com) for 2 to 3 days at 4 deg C in a refrigerator.
2. Brains were placed with ventral side up on a cutting surface and a partial coronal cut was made with a surgical blade at a level that corresponds approximately to the -2.5 mm behind the stereotaxic Bregma point (this cut is just a little rostral from the pontine fibres when viewed from the ventral side).
3. Brains were placed in a coronal matrix (egg-style slicer) and a 2-mm thick coronal slab was taken just rostral to the initial cut.
4. The 2-mm thick slab was placed on a clean glass slide and the hypothalamus was cut out and placed in a tube on dry ice.
5. To dissect the BLA, the temporal lobes were detached by placing a scalpel in the lateral ventricles and teasing it apart. The cortical amygdala was removed and the BLA was then cut out and placed in a tube on dry ice.
6. Tissue from two mice (right and left sides) and from the same strain and sex (an usually the same litter) were pooled. The only exceptions are BLA samples from strains BXD5, BXD13, BXD16, BXD19, BXD25, BXD38, BXD51, and BXD61 (tissue was obtained from only one animal per array).

 

About platform

[MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version] (GPL6246)

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 no initial correction for batch effects and the data in this initial release do not incorporate any additional corrections. However, there are several confounder-like factors that should be considered:

1. Sex imbalance in the sample: use probe sets for Xist as correction in partial correlation
2. Dissection variation: examine and use probe sets for Ttr as a correction for the inclusion of choroid plexus and non-parenchmymal tissue in samples. Transthyretin is only expressed in the choroid plexus (PMID 16698124
3. Background noise factors: examine and use probe sets with very low expression using the search "mean=(3.900 4.135)". This will extract the 54 probe sets with the lowest expression. (Note that the number 54 is less than the total number of cases (58) 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 54 probe sets in this amygdala data set accounts of 42% 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 amygdala data set can be map as a trait. It is not associated with any QLTs that are even suggestive, and the highest LRS is about 10 on chromosomes 18 and 19. The second principal component trait, which accounts for only 5% of the "noise" variance, has a suggestive QTL (LRS of 12, high B allele) on chromosome 4 at about 90 Mb. We therefore do not think that there is significant risk of major false trans eQTL bands in this data set.

Data Release. This data set was first uploaded into GeneNetwork November 25, 2010 and made accessible without a password to all users on December 1, 2010. The data set was orginally entered with two strain identification errors that were fixed Dec 10, 2010 by KM Mozhui and A Centeno (array R6659BL was originally listed as BXD16 but is BXD27; R6789BL was original listed as BXD27 is BXD12). The current data release has no known errors of sex or strain assignment.

Data Status and Use. The 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.

Contributors

Mozhui K, Williams RW

Specifics of this data set

Gene Level