UTHSC BXD Hippocampus ILM v6.1 RSS Balanced (Feb17) RankInv

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This is untreated control "Base" group gene expression data for the hippocampus of BXD strains of mice (n = 27 strains and n = 35 animals). These data NON data are useful as baseline for comparison with NOS, NOE, RSS, and RSE data sets. NON = NON = No stress and no saline control injection; NOS = No restraint stress and given only saline injections prior to sacrifice; NOE = No restraint stress and given an ethanol injection prior to sacrifice; RSS = short restraint stress (1 episode) followed by a saline injection; and finally, RSE = Restraint stress followed by an ethanol injection.

For more details on the precise experimental paradigm, please see Ziebarth et al 2010 or the original paper that used this paradigm by Kerns RT, Ravindranathan A, Hassan S, Cage MP, York T, Williams RW, Miles MF (2005) Ethanol-responsive brain region expression networks: implications for behavioral responses to acute ethanol in DBA/2J versus C57BL/6J mice. Journal of Neuroscience 25: 2255-2266.

Restraint Stress Protocol

  1. Weigh animals all animals to be tested and record body weight.
  2. Bring animals into testing area at least one hour prior to testing. 9 a.m. The following steps will be done for three animals (in parallel) because we have three zero-mazes.
  3. Place animals in immobilization tubes for 15 minutes.
  4. Inject animals IP with saline OR ethanol* and return to home cages for 5 minutes. (Remember to counterbalance groups. All animals in one cage should not be assigned to same group).
  5. Place each animal into zero-maze for 10 minutes.
  6. Return animal to home cage.
  7. Exactly 4 hours after injection, kill animals and remove brains to RNAlater solution. Animals should be killed by rapid decapitation with scissors so that trunk blood can be collected at the same time for corticosteroid analysis.

Ethanol and saline injections
Ethanol will be mixed with saline : 12.5% v/v. 100 ml of solution = 87.5 ml of saline and 12.5 ml of ethanol. Animals receive an injection of 1.8 g/kg. Multiply animals’ body weight by 0.018 to get injection volume (i.e. 25 g mouse X .018 mL/g = 0.45mL injection volume).

"Adult mice were housed three to five to a cage with ad libitum access to standard rodent chow (Harlan Teklad, Madison, WI) and water in a 12 h dark/light cycle. All injections were intraperitoneal. Mice were given a saline injection once daily for 5 d to habituate them to the injection process. On day 6, mice received either an injection of saline or 20% ethanol in saline."

Data Quality: All five data have been error checked. Strain and sex assignments were verified and are correct. This was determined by analysis of approximately 20 "test Mendelian" probes such as that for Thumpd1 (ILM751048). These probes have very high LRS values and the expected strain distribution pattern given their chromosomal location. Expression of genes on X and Y chromosomes (such as Xist) were used to confirm sex.

Quality Control Data
Total cis eQTLs with LRS > 23 within 5 Mb, maximum cis eQTL LRS value and probe

  1. NON: 669 (n=27 BXDs), 86.5 for B3galt6 (ILM50195)
  2. NOS: 844 (n=28 BXDs), 100.2 for Telo2 (ILM4850047)
  3. NOE: 1186 (n=35 BXDs), 101.9 for Mela-associated pseudogene (ILM4850047)
  4. RSS: 725 (n=27 BXDs), 82.8 for Gpr116 (ILM105390524)
  5. RSE: 915 (n=29 BXDs), 100.6 for Casp9 (ILM60577)

Entered by Arthur Centeno, September 20, 2010.

Array data sets all generated by Dr. Lu Lu (2008 - 2009) at the University of Tennessee Health Science Center, Memphis.

Corresponding anxiety and ethanol response phenotypes generated by Dr. Melloni Cook and colleagues at the University of Memphis.


Hippocampus 5 Conditions
Illumina Rank Invariant Normalized; Log2 Transformed and Z-Scored
Batch and Outlier Analysis on Partek Genomic Suite 6.6
ANOVA Done with batch (BATCH 1 AND 2); Batch effect removed
Outliers removed are: 4060001003_A, 4060001010_D, 4060001012_A, 4060001012_C, 4060001012_E, AND 4060001078_A
Number of samples = 284
Number of probes = 46643

  1. UTHSC Hippocampus Illumina v6.1 5Trt (Nov12) RankInv LRS=(46 999)-> 1331
    ProbeSetID:ILM3440048 Gene:Cdkl2 Max LRS=192
  2. UTHSC Hippocampus Illumina v6.1 NON (Nov12) RankInv LRS=(46 999)-> 219
    ProbeSetID:ILM6350725 Gene:C14orf119 Max LRS=97.8
  3. UTHSC Hippocampus Illumina v6.1 NOS (Nov12) RankInv LRS=(46 999)-> 404
    ProbeSetID:ILM3440048 Gene:Cdkl2 Max LRS=106.6
  4. UTHSC Hippocampus Illumina v6.1 NOE (Nov12) RankInv LRS=(46 999)-> 509
    ProbeSetID:ILM5270066 Gene:MGC67181 Max LRS=151
  5. UTHSC Hippocampus Illumina v6.1 RSS (Nov12) RankInv LRS=(46 999)-> 415
    ProbeSetID:ILM5720687 Gene:Abhd16a Max LRS=121.7
  6. UTHSC Hippocampus Illumina v6.1 RSE (Nov12) RankInv LRS=(46 999)-> 421
    ProbeSetID:ILM6350725 Gene:C14orf119 Max LRS=144.1

Specifics of this data set

RSS = short restraint stress (1 episode) followed by a saline injection.

Index Array ID Condition Strain Sex Age
1 4207851045_D RSS BXD34 M 71
2 4060001083_B RSS BXD43 M 72
3 4068846017_C RSS BXD43 F 73
4 4060001083_F RSS BXD45 F 67
5 4256265070_D RSS BXD45 M 79
6 4060001096_F RSS BXD51 M 75
7 4256265045_E RSS BXD51 F 88
8 4256265043_B RSS BXD55 F 67
9 4256265024_D RSS BXD60 M 76
10 4256265045_F RSS BXD60 F 72
11 4207851058_D RSS BXD61 F 70
12 4256265083_B RSS BXD61 M 82
13 4068846017_E RSS BXD62 F 61
14 4256265080_F RSS BXD62 M 67
15 4207851052_A RSS BXD66 M 74
16 4256265044_B RSS BXD66 F 69
17 4060001003_E RSS BXD68 F 77
18 4060001075_C RSS BXD68 M 64
19 4068846021_E RSS BXD70 M 68
20 4207851038_C RSS BXD70 F 69
21 4060001003_F RSS BXD71 M 78
22 4060001011_E RSS BXD71 F 76
23 4207851014_A RSS BXD73 F 68
24 4207851014_D RSS BXD73 M 67
25 4051964017_A RSS BXD75 F 73
26 4256265058_B RSS BXD75 F 69
27 4256265058_C RSS BXD83 F 75
28 4256265074_F RSS BXD83 M 69
29 4256265062_B RSS BXD84 F 73
30 4256265086_B RSS BXD84 M 69
31 4207851051_F RSS BXD87 M 69
32 4256265083_A RSS BXD89 F 59
33 4256265073_A RSS BXD90 F 68
34 4256265087_F RSS BXD90 M 68
35 4207851051_B RSS BXD96 M 69
36 4256265085_C RSS BXD96 F 76
37 4060001079_F RSS BXD97 F 65
38 4256265080_A RSS BXD97 M 70
39 4060001011_F RSS BXD98 M 72
40 4256265086_A RSS BXD98 F 72
41 4207851014_C RSS BXD99 M 73
42 4256265086_C RSS BXD99 F 86
43 4060001068_F RSS BXD100 M 79
44 4207851051_D RSS BXD100 F 68
45 4207851045_C RSS BXD101 F 66
46 4060001012_F RSS DBA/2J F 70
47 4060001031_D RSS DBA/2J F 70