title: RNA-Seq of mus musculus: embryo limbs
design: The E11.5 limb buds obtained from the Hoxd13 Q50R/Q50R and control mice were collected, and three specimens were prepared as the biological replicates of each genotype. Total RNA was isolated from the tissues by using TRIzol reagent (Ambion Life Technologies, Carlsbad, CA, USA). RNA-sequencing was performed on an Illumina Hiseq 2000/2500 platform (Chula Vista, CA, USA). Single-end clean reads were aligned to the reference genome by using Top Hat (v2.0.9, Johns Hopkins University, Baltimore, MD, USA). Differential gene expression between the two groups was verified with the DESeq R package (v1.10.1, Bioconductor). Between group differential gene expression was analyzed using the DEGseq (2010) R package. Significantly different expression was defined as P < 0.05.