Papillae were clipped from the rumen wall and immediately frozen in liquid nitrogen. 50-100mg of tissue were homogenized in TriZol reagent. Manufacturers protocol was followed. oligo-dt beads were used to select poly-adenylated RNA to be sheared to appropriate size for the synthesis of cDNA.  The resulting double stranded cDNA was end-repaired and A-tailed in preparation for adaptor ligation.  Adaptors were indexed and ligated to the cDNA, which was then size selected on a 2% SizeSelect™ E-Gel (Invitrogen, Carlsbad, CA, USA).  The size selected cDNA was amplified via polymerase chain reaction.  Library quality was assessed by measuring nanomolar concentration and the fragment size in base pairs.  All 16 samples were sequenced at 1×50 basepairs per sequence read.
GEO Accession
GSM1828577