Sex-dependent and strain-dependent gene liver gene expression

A series of dual-channel gene expression profiles obtained using Agilent Mouse TOE 75k microarrays was used to examine the sex-dependent differences in gene expression across three outbred mouse strains, 129J x Black Swiss, 129J x BALB/c, and ICR. This series is comprised of samples obtained from 3 pools of randomly chosen independent cDNA samples of male and female 129Jx BALB/c mice and 3 randomly chosen independent cDNA samples of male and female 129J x Black Swiss mice and 5 randomly chosen independent cDNA samples of male and female ICR mice. The ICR mice were randomly distributed into three and two member pools for each sex and two of the 5 samples for each sex were independently hybridized separately as well. Comparison of the sex-specific genes for the three outbred strains generated lists of strain-dependent and strain-independent sex-specific genes. Keywords: sex response and strain response A Cy3-labeled cDNA sample is co-hybridized with a Cy5-labeled cDNA sample depending on the comparison being made. The samples are then dye-swapped and compared again on a second microarray chip. The two pairs are averaged together, the averages are normalized across the fluorescent reverse pairings, and the normalized ratio is reported along with the two separate intensities. This is replicated 3 times with independent samples of cDNA for the 129J x BALB/c and 129J x Black Swiss Mice and 2 times each for the ICR pools and single samples. There are a total of 3 outbred strains being compared for a grand total of 10 samples.