The reads of all RNAseq samples were assembled using Trinity package [1] following the standard procedure.
Differential expression was assessed using the edgeR package [2] with default parameters.

[1]
Haas, B.J., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P.D., Bowden, J., Couger, M.B., Eccles, D., Li, B., Lieber, M., MacManes, M.D., Ott, M., Orvis, J., Pochet, N., Strozzi, F., Weeks, N., Westerman, R., William, T., Dewey, C.N., Henschel, R., LeDuc, R.D., Friedman, N., Regev, A.
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.
Nature Protocols 8:1494-1512 (2013)

[2]
Robinson, M.D., McCarthy, D.J. & Smyth, G.K.
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Bioinformatics 26, 139–140 (2010).