Target resequencing of the MHC locus in Phacochoerus africanus isolate NM125
For each sample, 1.5 ug of gDNA was measured using a Qubit (Invitrogen), resuspended in 130 uL of H2O and fragmented with a Covaris S-2 (Covaris). The samples were purified with 1.8X AMPure Beads (Beckman Coulter Genomics) and resuspended in 60 uL of Resuspension buffer (Illumina). The TruSeq DNA Sample Preparation Kit (Illumina) was used for end-repair, A-tailing, and adaptor ligation, and size selection was omitted. After ligation, indexed samples were PCR amplified following the NimbleGen Array Users Guide Version 3.2. A 385K custom array (NimbleGen) was used to hybridise 12 uniquely indexed libraries in parallel. The libraries were pooled in equimolar ratios to a final amount of 5 ug of DNA. Then, 100 ug of pig Cot-1 DNA (Applied Genetics Laboratories) and 10 uL of six different 100 uM blocking oligonucleotides (Eurofins MWG Operon) were added, the mix was dried in a SpeedVac (Thermo Scientific), and the NimbleGen Array Users Guide Version 3.2 was used for downstream hybridisation, washing, and elution. Eluted pooled libraries were amplified by PCR using the protocol recommended by Illumina.