Normalized mRNA expression was calculated as RPKM (reads per kilobase gene model per million mapped reads) (Mortazavi et al., 2008) from aligned sequence reads; Z-scores were computed from frequency data using the following equation: (x - μ)/σ, x, sample frequency; μ, mean across all samples; σ, standard deviation across all samples. Gene expression data (Z-scores) were hierarchically clustered using Gene Cluster 3.0 (http://rana.lbl.gov/EisenSoftware.htm); heat maps were generated using Java Treeview (http://www.sourceforge.net/projects/jtreeview/files). Gene lists were submitted to the Panther website (http://www.pantherdb.org) for analysis of Pathway and Protein Class enrichment compared to the Mus musculus reference gene list. Western and qPCR analyses were performed as described (Eipper-Mains et al., 2011); primer sequences are in Table S1.
