This paper shows that mRNA-Seq result correlate more closely with protein levels than do Affy exon arrays.

The first complete sequence of a Fleckvieh breeding bull was carried out using predominantly 36-bp paired-end reads on the Genome Analyzer II. The authors covered 98% of the genome and identified 2.44 million single nucleotide polymorphisms (SNPs), 82% of which were novel, and 115,000 small indels, with a low false positive rate of 1.1%. Genotypes were determined using the BovineSNP50 BeacChip.

The authors used ultra highthroughput sequencing on the Genome Analyzer, with analysis using Pipeline software, to investigate small regulatory RNAs in adult bovine kidney cell lines, either control or infected with Bovine herpesvirus 1. Of the 356 known bovine miRNAs they detected 219 and found 115 miRNA* sequences of these expressed genes. They also found “five new bovine orthologs of known mammalian miRNAs,” 268 novel miRNAs, seven mirtron candidates and 10 small nucleolar RNA (snoRNA).