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Summary
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
- Weigh animals all animals to be tested and record body weight.
- 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.
- Place animals in immobilization tubes for 15 minutes.
- 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).
- Place each animal into zero-maze for 10 minutes.
- Return animal to home cage.
- 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
- NON: 669 (n=27 BXDs), 86.5 for B3galt6 (ILM50195)
- NOS: 844 (n=28 BXDs), 100.2 for Telo2 (ILM4850047)
- NOE: 1186 (n=35 BXDs), 101.9 for Mela-associated pseudogene (ILM4850047)
- RSS: 725 (n=27 BXDs), 82.8 for Gpr116 (ILM105390524)
- 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.
Notes
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
K MOZHUI (KMOZHUI@UTHSC.EDU) 12-Nov-12
Outliers removed are: 4060001003_A, 4060001010_D, 4060001012_A, 4060001012_C, 4060001012_E, AND 4060001078_A
Number of samples = 284
Number of probes = 46643
- UTHSC Hippocampus Illumina v6.1 5Trt (Nov12) RankInv LRS=(46 999)-> 1331
ProbeSetID:ILM3440048 Gene:Cdkl2 Max LRS=192 - UTHSC Hippocampus Illumina v6.1 NON (Nov12) RankInv LRS=(46 999)-> 219
ProbeSetID:ILM6350725 Gene:C14orf119 Max LRS=97.8 - UTHSC Hippocampus Illumina v6.1 NOS (Nov12) RankInv LRS=(46 999)-> 404
ProbeSetID:ILM3440048 Gene:Cdkl2 Max LRS=106.6 - UTHSC Hippocampus Illumina v6.1 NOE (Nov12) RankInv LRS=(46 999)-> 509
ProbeSetID:ILM5270066 Gene:MGC67181 Max LRS=151 - UTHSC Hippocampus Illumina v6.1 RSS (Nov12) RankInv LRS=(46 999)-> 415
ProbeSetID:ILM5720687 Gene:Abhd16a Max LRS=121.7 - 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
NOS = No restraint stress and given only saline injections prior to sacrifice.
Index Array ID Condition Strain Sex Age 1 4207851040_B NOS BXD34 M 67 2 4207851045_E NOS BXD43 F 75 3 4256265009_D NOS BXD43 M 64 4 4060001010_A NOS BXD45 F 81 5 4068846016_E NOS BXD45 M 65 6 4060001011_A NOS BXD51 F 85 7 4060001082_B NOS BXD51 M 75 8 4060001082_F NOS BXD55 F 62 9 4256265070_B NOS BXD55 M 76 10 4207851041_F NOS BXD60 F 76 11 4256265071_B NOS BXD60 M 77 12 4060001069_A NOS BXD61 F 78 13 4207851051_C NOS BXD61 M 78 14 4207851053_D NOS BXD62 F 67 15 4256265043_A NOS BXD62 M 68 16 4207851051_E NOS BXD66 M 63 17 4256265074_C NOS BXD66 F 69 18 4207851038_B NOS BXD68 F 69 19 4256265044_C NOS BXD68 M 66 20 4256265070_A NOS BXD70 F 61 21 4256265083_D NOS BXD70 M 67 22 4060001096_B NOS BXD71 M 83 23 4256265071_A NOS BXD71 F 0 24 4256265057_E NOS BXD73 F 66 25 4256265074_A NOS BXD73 M 69 26 4060001078_B NOS BXD75 M 70 27 4207851058_E NOS BXD75 F 68 28 4207851051_A NOS BXD83 M 67 29 4256265023_B NOS BXD83 F 70 30 4256265083_C NOS BXD84 M 69 31 4256265085_F NOS BXD84 M 67 32 4207851045_F NOS BXD87 M 68 33 4068846021_B NOS BXD89 F 69 34 4256265073_F NOS BXD89 M 69 35 4256265080_E NOS BXD90 M 73 36 4256265085_E NOS BXD90 F 73 37 4060001010_B NOS BXD96 M 68 38 4060001071_D NOS BXD96 F 69 39 4207851052_C NOS BXD96 M 69 40 4060001011_B NOS BXD97 M 68 41 4060001082_A NOS BXD98 F 72 42 4256265058_F NOS BXD98 M 70 43 4256265051_F NOS BXD99 M 70 44 4060001075_E NOS BXD100 F 63 45 4207851035_E NOS BXD100 M 72 46 4060001075_D NOS BXD101 M 78 47 4060001030_F NOS DBA/2J M 63 48 4060001012_B NOS DBA/2J F 81