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Following emulsion breaking and subsequent washing, enrichment for template beads was conducted using the SOLiD capture beads with P2 affinity.
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The rotation assay of the F1-bead was conducted using the following procedures.
Protein expression was induced via IPTG (Apex, San Diego CA) and protein purification was conducted using Glutathione beads (Sigma).
One set of experiment was conducted using Ca-alginate beads, which is free from M.oleifera.
Microarray analysis was conducted using the Illumina Bead Chip.
Image analysis was conducted using Illumina's Bead Studio software, and the raw data were exported into Microsoft Access [43].
Genotyping was conducted using Illumina Infinium Bead Arrays according to the manufacturer's protocols.
Library preparation was conducted using the "With-Bead" Method [ 47] with a slight modification: The Long PCR product was subsequently sheared to approximately 500 bp using a Covaris S2 Focused-ultrasonicator (Covaris, Inc., Woburn, Massachusetts, USA) before library preparation.
Measurement of expression levels of 79 proteins (HumanMAP, antigen panel) was conducted using fully automated, bead-based multiplex sandwich immunofluorescence assays (see list of proteins in additional file 1).
Next, the pull-down assay was conducted using S-S-2 and -LMM-N beads with cell lysates including myc-MYPT1(1 498) (N) and myc-MYPT1(495–1030) (C).
The GWAS was conducted using a subset of 14,503 SNPs from the PorcineSNP60 Genotyping Bead Chip (Illumina) previously selected for building a high-density linkage map [ 28].
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