Data Set Group2: UTHSC Hippocampus Illumina v6.1 NOS, NOE, RSS, and RSE data sets

Data Set: UTHSC BXD Hippocampus ILM v6.1 RSS Balanced (Feb16) RankInv GN Accession: GN782 GEO Series: No Geo series yet Title: Organism: Mouse (Mus musculus, mm10) Group: BXD Tissue: Hippocampus mRNA Dataset Status: Public Platforms: Illumina Mouse WG-6 v1, v1.1 (GPL6105) Normalization: RankInv

Contact Information Lu Lu University of Tennessee Health Science Center 71 S. Manassas, Room 410K Memphis, TN 38163 USA Tel. 901 448-7557 lulu@uthsc.edu Website Download datasets and supplementary data files GN782_MeanDataAnnotated_rev050516.txt.zip (N/A)

Specifics of this Data Set:

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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.

About the cases used to generate this set of data:

About the tissue used to generate this set of data:

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About data values and data processing:

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

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Data source acknowledgment:

Study Id:

82

• The UT Center for Integrative and Translational Genomics
• NIGMS Systems Genetics and Precision Medicine project (R01 GM123489, 2017-2021)
• NIDA NIDA Core Center of Excellence in Transcriptomics, Systems Genetics, and the Addictome (P30 DA044223, 2017-2022)
• NIA Translational Systems Genetics of Mitochondria, Metabolism, and Aging (R01AG043930, 2013-2018)
• NIAAA Integrative Neuroscience Initiative on Alcoholism (U01 AA016662, U01 AA013499, U24 AA013513, U01 AA014425, 2006-2017)
• NIDA, NIMH, and NIAAA (P20-DA 21131, 2001-2012)
• NCI MMHCC (U01CA105417), NCRR, BIRN, (U24 RR021760)