Fig. 1.

Preparation and sequencing of samples. a) Whole blood from each animal is separated using Ficoll-Paque centrifugation and PBMCs are collected. b) Total RNA is isolated from PBMCs using standard RNA isolation methods and cDNA is synthesized. c) The MHC class I cDNAs are amplified as a full-length PCR product or a fragment containing parts of exons 2-4. d) The exon 2-4 amplicon containing MID tags and adaptors added during the primary PCR is sequenced by Roche/454 pyrosequencing using a GS Junior. e) The full-length PCR amplicon is fragmented using Nextera XT transposons. f) Fragmented full-length amplicon libraries containing indices added during fragmentation undergoes paired-end llumina MiSeq sequencing