The BWA workflow employed refflat.txt annotation for mouse build mm9 from UCSC genome browser. The TopHat workflow employed GTF annotation for mouse build mm9 from the Ensembl database. After FPKM filtering (see Materials and Methods), transcribed features were classified as protein coding mRNAs and non-coding (nc) RNAs. The features classified as protein-coding mRNAs were further filtered based on fold change (≥1.5) and p-value (<0.05) to be considered significantly differentially expressed transcripts (DETs).