Liao Y, Smyth GK and Shi W. featureCounts: an efficient general-purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7):923-30, 2014

ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus

Using custom R scripts, all fold changes were calculated using a one read pseudocount as lfc=log2((1+condictionRPKM)/(1+referenceRPKM)).
Significance of the fold changes was assessed using two-sided Student-s t-tests and adjusted p-values were calculated using the Benjamini and Yekutieli method [3] to compensate for multiple testing.

Benjamini Y, and Yekutieli D. The control of the false discovery rate in multiple testing under dependency. Annals of Statistics 2001, 29, 1165–1188. doi: 10.1214/aos/1013699998