UTHSC BXD Hippocampus ILM v6.1 NOE 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

NOE = No restraint stress and given an ethanol injection prior to sacrifice.

Index Array ID Condition Strain Sex Age
1 4060001078_D NOE BXD34 F 75
2 4060001088_A NOE BXD43 F 67
3 4207851040_C NOE BXD43 F 65
4 4207851040_D NOE BXD45 F 71
5 4207851041_C NOE BXD45 M 68
6 4068846016_D NOE BXD51 F 73
7 4207851035_D NOE BXD51 M 85
8 4060001003_C NOE BXD55 F 79
9 4068846016_C NOE BXD55 M 68
10 4060001071_A NOE BXD60 F 76
11 4068846016_A NOE BXD60 M 67
12 4060001003_D NOE BXD61 M 67
13 4207851041_A NOE BXD61 F 70
14 4060001075_F NOE BXD62 M 68
15 4207851041_B NOE BXD62 F 67
16 4207851035_A NOE BXD66 F 73
17 4256265071_C NOE BXD66 M 63
18 4207851035_B NOE BXD68 M 66
19 4256265026_E NOE BXD68 F 67
20 4060001010_F NOE BXD70 M 87
21 4207851045_B NOE BXD70 F 69
22 4256265057_A NOE BXD71 F 76
23 4256265087_C NOE BXD71 M 75
24 4256265042_B NOE BXD73 F 66
25 4060001010_E NOE BXD75 F 70
26 4256265042_C NOE BXD75 M 69
27 4060001083_A NOE BXD83 M 69
28 4256265071_D NOE BXD83 F 80
29 4256265045_C NOE BXD84 F 68
30 4207851058_A NOE BXD87 F 63
31 4256265080_C NOE BXD87 M 65
32 4207851058_B NOE BXD89 M 68
33 4256265024_A NOE BXD89 F 71
34 4256265024_B NOE BXD90 F 68
35 4256265052_A NOE BXD90 M 74
36 4256265023_A NOE BXD96 M 68
37 4256265023_F NOE BXD96 F 68
38 4256265044_A NOE BXD96 M 68
39 4068846017_B NOE BXD97 M 67
40 4068846017_A NOE BXD98 F 74
41 4207851052_F NOE BXD98 M 71
42 4068846021_F NOE BXD99 M 70
43 4060001088_E NOE BXD100 F 61
44 4060001088_D NOE BXD101 M 71
45 4060001030_D NOE DBA/2J F 79
46 4256265069_F NOE DBA/2J F 79