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
NOS = No restraint stress and given only saline injections prior to sacrifice.
+ ++diff --git a/general/datasets/UTHSC_ILM_BXD_hipp_NOSb_0217/summary.rtf b/general/datasets/UTHSC_ILM_BXD_hipp_NOSb_0217/summary.rtf new file mode 100644 index 0000000..5aeb69c --- /dev/null +++ b/general/datasets/UTHSC_ILM_BXD_hipp_NOSb_0217/summary.rtf @@ -0,0 +1,39 @@ ++ +
++ + ++ ++ +
++ +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 +
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
+ +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
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.
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