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Data Set Group: VCU BXD VTA consisting of Ethanol, Saline and Ethanol vs Saline Datasets AffyM430 2.0 (Jun09) modify this page

Data Set: VCU BXD VTA Sal M430 2.0 (Jun09) RMA modify this page
GN Accession: GN228
GEO Series: No Geo series yet
Title:
Organism: Mouse (mm10)
Group: BXD
Tissue: Ventral Tegmental Area mRNA
Dataset Status: Public
Platforms: Affy Mouse Genome 430 2.0 (GPL1261)
Normalization: RMA
Contact Information
Michael Miles
Virginia Commonwealth University
901 West Franklin Street
Richmond, VA 23284 USA
Tel. 804 827-4054
mfmiles@vcu.edu
Website
Download datasets and supplementary data files

Specifics of this Data Set:

Expression analysis was conducted by estimating the relative abundance of over 45,000 transcripts in the VTA in response to saline.



Summary:

This BXD data set provides estimates of ventral tegmental area (VTA) mRNA expression in response to ethanol (1.8 g/kg x 4 hours) across 35 BXD recombinant inbred strains and their B6 and D2 progenitor strains. All samples are from a total of 596 adult male animals obtained from Jackson Laboratory (27 classical BXD strains) or Oak Ridge National Laboratory (extended BXD series) and raised in a standard laboratory environment. An average of 8 males per strain was used to measure anxiety-like behavior in response to restraint and ethanol (IP) treatment in the light-dark transition model of anxiety.

All RNA isolation and subsequent probe generation and hybridization to microarrays were completed using a supervised randomization procedure to minimize batch effects. Affymetrix M430 type 2.0 microarrays were used for hybridization using standard procedures. Expression analysis was conducted by estimating the relative abundance of over 45,000 transcripts in the VTA in response to ethanol or saline and transforming these data using the S-score method to compare ethanol vs. saline expression from pairs of arrays for each strain (Kerns et al., Methods 31:274, 2003). The S-score is a method developed for Affymetrix oligonucleotide arrays that is particularly suited to comparing expression on 2 or a small number of chips. The S-score output for each probeset is not an indication of expression magnitude but rather, the change in expression between compared arrays. The S-score is essentially a z-score centered around zero with positive S-scores reflecting increased gene expression with ethanol and negative scores reflecting ethanol-induced decreases in expression. Larger magnitude S-scores show more significant changes in expression and are generally correlated with the fold-change.



About the cases used to generate this set of data:


About the tissue used to generate this set of data:


About the array platform:

GEO: GPL1261 Affymetrix GeneChip Mouse Genome 430 2.0 Array



About data values and data processing:


Notes:

All samples were processed by Nate Bruce at VCU between April and May 2009. The BioRad Experion RNA analyzer and used to assess total RNA integrity and verify equal molar ratios of 18S and 28S ribosomal RNA. All RNA Quality Index (RQI) calculations were > 8. Standard Affymetrix reagents and protocols were used for generation of cDNA and biotinylated cRNA from total RNA samples. Integrity of cRNA was checked by Experion analysis prior to microarray hybridizations. All probes exceeded a maximum size of 3000 nt for the upper border of the cRNA size distribution.



Experiment Type:


Contributor:


Citation:


Data source acknowledgment:


Study Id:
75

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GeneNetwork support from:
  • 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)
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  • NCI MMHCC (U01CA105417), NCRR, BIRN, (U24 RR021760)
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