The 100bp paired-end reads obtained by RNA-Seq were compiled using manufacturer-provided pipeline software CASAVA 1.8.2. Reads were then aligned onto the equine chromosomes with TOPHAT 1.3.2 using default settings.
For RNA extraction the Guanidium-thiocyanate-phenol-chloroform technique, with ethanol extraction was used (Chomczynski, P. and N. Sacchi, Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem, 1987
Illumina HiSeq 2000
Full thickness cartilage was removed from the entire surface of MCPII.All samples were scored macroscopically to determine any pathological abnormalities of the distal condyles of the distal third metacarpus.