Transcriptome sequencing of Water Buffalo embryos

The Mediterranea italiana River buffalo breed is known for its production of milk for the Mozzarella cheese. The aim of the work is to produce in vitro viable sexed and frozen embryos with superior genotype to spread the genetics of Mediterranea It. breed in response the increasing requests from other countries. The in vitro culture and cryo-conservation protocols have not been optimised for buffalo and are being investigated. RNA-seq from single and pool embryos (blastocyst at Day 7) has been performed to find markers of embryo quality and viability. RNA samples were amplified using the Ovation RNA-Seq System V2, enabled by Ribo-SPIA technology (NuGEN) using 1.43 and 3.20 ng of total RNA. cDNA libraries were constructed using Encore NGS Library Systems (NuGEN) with yields of 1.5 and 9.4 ug respectively. Samples were sequenced using Illumina Hi-Seq2000 to generate paired end reads of 100bp, producing on average 5,3M reads per embryo (high quality reads of 75bp) and ~33.3M reads for each pool (high quality reads of 73bp).  These data showed that RNA-Seq is well-suited to the analysis of low-input samples. The data produced in this study will be more precisely analysed for differential expression using the genome of Water Buffalo as reference.