Gel doc xr software

PFGE was performed according to the PulseNet protocol developed for non-O157 E. coli (http://www.cdc.gov/pulsenet/PDF/ecoli-shigella-salmonella-pfge-protocol-508c.pdf). The genomic DNA was digested with 45 U of XbaI (Takara, China) at 37°C for 2 h. Macrorestriction fragments were resolved by counter-clamped homogeneous electric field electrophoresis in a CHEF-DRIII apparatus (Bio-Rad, USA). The run time was 19 h at 6.0 V/cm, with initial and final switch times of 6.76 s and 35.38 s, respectively. The image was captured with a Gel Doc XR+ software (Bio-Rad, USA). Data analysis was performed and an UPGMA dendrogram was constructed using Bionumerics (Version 4.0, Applied Maths BVBA, Belgium).

Amplified products were detached on 1% agarose gels in 1x TAE buffer at10 V mm-1
for 90 min and observed with a UV transilluminator and documented with GelDocXR
software (Biorad). The amplification product was purified using Gene jet Gel
Extraction PCR purification kit according to the manufacturer's instruction. The
purified PCR product was sequenced by Sanger dideoxy sequencing technology. DNA
Baser tool were used to assemble both the forward and reverse trace files
obtained from the sequencing. Clean traces were observed in both the traces. The
assembled sequences were further saved in FASTA format for further
bioinformatics analysis.