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The region flanking the transposon insertion in each mutant was sequenced and compared with the sequenced genome of Xcc strain 8004.
The genome of the mutant was sequenced to ensure the successful insertion of the DNA fragments into the Mtb genome.
The open reading frame of each mutant was sequenced entirely.
Each NCKX4 mutant was sequenced to ensure only the intended change was present in the construct.
Additionally, the dnaE gene of each insertion and site-directed mutant was sequenced in its entirety to check for possible suppressor mutations.
Bcl-2 mutant was made with the QuikChange site-directed mutagenesis kit (Stratagene, La Jolla, CA, USA) using the following primers: Bcl-2 del122-129 Fw (5′-GGCAAAACGTCGAATCAGCTATTTACTGCAATATCATTTATTTTTTACATTATTAAGAA-3′) Bcl-2 del 122-129 Rv (5′-TTCTTAATAATGTAAAAAATAAATGATATTGCAGTAAATAGCTGATTCGACGTTTTGCC-3′) The mutant was sequenced to confirm the mutated product.
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The glpT gene of all mutants was sequenced, and compared with the wild type gene as described [37].
In addition, a library of 100 random mutants was sequenced to determine our ability to detect unique mutations.
In, addition, 61 and 54 mutants were sequenced in control and exposed groups, respectively.
Randomly selected transposon carrying protease negative mutants were sequenced and alignment of these sequences lead to the identification of the protease open reading frame (ORF).
The mutants were sequenced, and we verified by western blotting that the proteins expressed had the expected size.
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