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Data Set Group: UTHSC Hippocampus Illumina v6.1 NOS, NOE, RSS, and RSE data sets modify this page

Data Set: UTHSC BXD Hippocampus ILM v6.1 RSS Balanced (Feb16) RankInv modify this page
GN Accession: GN782
GEO Series: No Geo series yet
Title:
Organism: Mouse (mm10)
Group: BXD
Tissue: Hippocampus mRNA
Dataset Status: Public
Platforms: Illumina Mouse WG-6 v1, v1.1 (GPL6105)
Normalization: RankInv
Contact Information
Robert Williams
University of Tennessee Health Science Center
855 Monroe Ave Room 501
Memphis, TN 38103 USA
Tel. 901 448-7050
rwilliams@uthsc.edu
Website
Download datasets and supplementary data files

Specifics of this Data Set:
None

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

  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.



About the cases used to generate this set of data:


About the tissue used to generate this set of data:


About the array platform:


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

  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


Experiment Type:


Contributor:


Citation:


Data source acknowledgment:


Study Id:
82

CITG WWW service initiated January, 1994 as The Portable Dictionary of the Mouse Genome and June 15, 2001 as WebQTL. This site is currently operated by Rob Williams, Lei Yan, Pjotr Prins, Zachary Sloan, Arthur Centeno. Design and code by Lei Yan, Zach Sloan, Kenneth Manly, Jintao Wang, Danny Arends, Pjotr Prins, Sam Ockman, Xiaodong Zhou, Christian Fernandez, Ning Liu, Rudi Alberts, Elissa Chesler, Evan G. Williams, Alexander G. Williams, Robert W. Williams, and colleagues. Python Powered Registered with Nif
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