title: Deep Sequencing of HLA-DR401 Random 9mer Library
design: Libraries were deep sequenced to determine the peptide repertoire at each round of selection. Plasmid DNA was extracted from 5x107 yeast from each round of selection with the Zymoprep Yeast Miniprep Kit (Zymo Research, Irvine CA), according to manufacturers instructions. Amplicons were generated by PCR with primers designed to capture the peptide encoding region through the polymorphic region that differentiates HLA-DR401 from HLA-DR402. An additional PCR round was then performed to add P5 and P7 paired-end handles with inline sequencing barcodes unique to each library and round of selection. Amplicons were sequenced on an Illumina MiSeq (Illumina Incorporated, San Diego CA) with the paired-end MiSeq v2 500bp kit at the MIT BioMicroCenter.