Computational protocol: Pioglitazone administration alters ovarian gene expression in aging obese lethal yellow mice

Similar protocols

Protocol publication

[…] CodeLink Whole Mouse Genome Bioarrays (GE/Amersham, Piscataway, NJ, now Applied Micrarrays, Tempe, AZ) were used for the analysis of differential gene expression in this study. These microarrays contain 33,000 single-stranded 30-mer oligonucleotide probes for mouse genes and transcribed sequences. Biotinylated complementary RNA (cRNA) probes were synthesized from the extracted RNA samples per company directions as previously described [] using CodeLink Expression Assay Reagent Kit (GE-Amersham Biosciences). Individual samples were run on separate microarrays (n = 4/LY treatment group; n = 2 for BL controls); no samples were pooled. The biotinylated cRNA was fragmented and hybridized with the DNA microarray slides for 18 hours at 37°C. The hybridized slides were washed and incubated with streptavidin-Alexa Fluor 647 (Molecular Probes) to label the cRNA, and washed again. An Axon GenePix Scanner was used to scan the microarrays. GenePix Pro software (MDS, Inc., Toronto, ON) was used to acquire and align the microarray image. CodeLink software (Applied Microarrays, Tempe, AZ) applied the background correction. GeneSpring 7.0 software (Agilent, Santa Clara, CA) was used to normalize the expression of each gene to the median gene expression and to normalize each slide to the the 50th percentile of gene expression. Statistical analysis of the data was performed using GeneSpring 7.0 (Agilent). The p value was set at 0.05 for the t test. Multiple testing correction used the Benjamini and Hochberg False Discovery Rate. Approximately 5% of the genes would be expected to pass this restriction by chance with this test. […]

Pipeline specifications

Software tools GenePix Pro, GeneSpring GX
Application Gene expression microarray analysis
Organisms Mus musculus, Homo sapiens
Diseases Liver Diseases, Polycystic Ovary Syndrome
Chemicals Dimethyl Sulfoxide, Thiazolidinediones