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Series GSE18151 Query DataSets for GSE18151
Status Public on May 12, 2010
Title Age-related retinal degeneration study in mice
Organism Mus musculus
Experiment type Expression profiling by array
Summary The first goal of the study was to find the genes that explain the difference in progression of age-related retinal degeneration (ageRD) between the inbred strains C57BL/6J-c2J (B6a) and BALB/cByJ (C). The specific goal was to find the candidate genes that explain the chromosome 6 and chromosome 10 quantitative trait loci (QTL) found in a previous study. Genes differentially expressed in retina between both strains and that map to the QTL are candidate genes.
By integrating different approaches: microarray study, knowledge-based candidate gene search and screening of genetic variants, we found 35 candidate genes for chromosome 6 QTL and 14 candidate genes for chromosome 10 QTL. Five genes for each QTL were selected for sequencing and qPCR analysis. One gene, Tnfaip3 was selected for phenotypic testing and was excluded as the quantitative trait gene for chr10 QTL.
The second goal of the study was to find biological processes and pathways associated with ageRD by Gene Ontology analysis of the microarray data. We concentrated on GO terms overrepresented in either strain at 8 months; the age when there is a difference in the phenotype (outer nuclear layer thickness). The GO analysis revealed that transcripts associated with inflammation, mitochondrial envelope, DNA repairing and oxidative stress were increased in the ageRD sensitive C strain with age (8 months). In the ageRD resistant B6a strain transcripts associated with antioxidant response, regulation of blood vessel size and growth factor activity were increased with age. Transcripts associated with cell remodeling and lipid metabolism were increased in either strain with age.
This study aims to identify gene expression differences in posterior eyecups between the strains C and B6a at 4 months and at 8 months. Twelve animals were used per strain and time point for a total of 48 mice. Total RNA for 3 animals (6 eyes) were pooled giving a total of 4 biological replicates per strain and time point.
The 4-month C samples labeled with Cy5 were hybridized with the 4-month B6a samples labeled with Cy3 (4 biological replicates); the 8-month C samples labeled with Cy5 were hybridized with the 8-month B6a samples labeled with Cy3, for 8 arrays (4 biological replicates). A second set of eight arrays were used to analyzed the same RNA samples but with the dye orientation reversed, yielding a total of 16 arrays in the experiment.

 
Overall design Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc.
 
Contributor(s) Alizadeh M
Citation(s) 20577653
Submission date Sep 17, 2009
Last update date Mar 21, 2012
Contact name Jun Li
E-mail(s) junzli@umich.edu
Phone 734-615-5754
Organization name University of Michigan
Street address 5789A Medical Science II, Box 5618
City Ann Arbor
State/province MI
ZIP/Postal code 48109
Country USA
 
Platforms (1)
GPL9214 SMD Print_1034 Mus musculus
Samples (16)
GSM453757 8M-Aging-BALBCvsC2J-MMAE199-Sample 8
GSM453758 4months C2J/BALBC-MMAE142-Sample 3
GSM453759 4M-Aging-BALBCvsC2J-MMAE184-Sample 3
Relations
BioProject PRJNA119485

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE18151_RAW.tar 2.6 Mb (http)(custom) TAR
Processed data included within Sample table

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