Microbial ecology and molecular diagnostics
The cpn60 UT has been used extensively as a barcode gene for microbiome profiling. Methods were established initially using the Roche 454 platform but have more recently been established using sequencing by synthesis (Illumina). We have had good success following the Illumina "16S amplicon" protocol with minor adjustments.
Please note that we have optimized our protocols to exploit a "primer cocktail" approach we developed previously (Hill et al. 2006) to improve representation of microbial diversity in cpn60 amplicon libraries from complex microbial communities. Thus, the indexed primers are used in sets of four (2 forward, 2 reverse). If you'd like detailed protocols or information, please contact us.
mPUMA is a software package designed to allow researchers to profile microbial communities using a de novo assembly approach to form Operational Taxonomic Units (OTUs). While originally designed to support the analysis of cpn60 based amplicons, mPUMA can be used to analyze data from any suitable DNA barcode.