Effect of Plasmid Design and Type of Integration Event on Recombinant Protein Expression in Pichia pastoris

Supplemental material

• Supplemental file 1 -

  BAM and TPM copy number calculations (Data Set S7).

  XLSX, 24K

• Supplemental file 2 -

  SNP identification (Data Set S8).

  XLSX, 61K

• Supplemental file 3 -

  Complete screening data for 755 transformants from three plasmid/linearization combinations and transformation performed in triplicate (Fig. S1); integration rates of specific and nonspecific GUT1-SwaI transformants from different replicates (Table S2); rescreening results of 44 selected transformants (Table S3 and Fig. S3); summary of statistics from Illumina MiSeq sequencing of 25 transformants and two controls and mapping to CBS7435, the mitochondrial genome and respective plasmid (Table S4); example of sequence mapping to identify the insertions sites listed in Table 1 (Fig. S5); genes deleted in the approximate 69-kbp fragment lost on chromosome 4 in QTV84 (Table S6); copy number estimates for each transformant (Table S7); raw data on SNP identification after filtering (Fig. S8); no correlation between number of sequence variants and reporter protein fluorescence (Fig. S9); extended discussion on effects of GUT1/STD vectors and linearization by SwaI/SacI (Supplement S10).

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