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Transformants were screened for their proper genotype by selecting for kanamycin resistance and colony PCR (GoTaq Green polymerase, Promega) using primers that flank the target gene.
Briefly, DNA isolated from conjunctival swabs was amplified using primers that flank the ompA gene.
Transformants were screened by colony PCR using primers that flank the multiple cloning site of pLL3.7 (Table S2).
The extracted RNA was then subjected to RT-PCR using primers that flank the intergenic region and are expected to generate a 773-nucleotide product.
This was confirmed by PCR amplification and sequencing using primers that flank the IR/LSC boundaries.
Gap regions (caused by unsuccessful PCR amplification or failed primer walking sequencing) were amplified using primers that flank the gaps, then cloned and sequenced as above.
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Further experiments using primers that flanked the deletion confirmed that the original Nnd-1 chromosome does not contain the deletion, as PCR product obtained from this chromosome was longer than the product obtained from the DSC Nnd1 chromosome (Fig. 1D).
Pooled colonies were assayed for the presence of the correctly sized episomal insert using primers that flanked the cloning site and genomic DNA prepared from the stably transfected cells.
Inserted donor fragments were screened by gel analysis of PCR amplicons made using primers that flanked the MCS; forward (5'-3'): AGT TCT GCA CTC GGC CTC TG, and reverse (5'-3'): CCA TGG TCT GCA GTC GCT AG.
The resulting Guca1aCOD3 mice were genotyped using primers that flanked a residual intronic loxP sequence to identify gene-targeted allele; the PCR products from homozygous and heterozygous mice (shown in Figure 1b) were sequenced to determine whether the loxP sequence segregated with the A-to-G transversion.
Only the blaCTX-M genes were sequenced using primers that flanked the full-length genes (See Methods section).
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