Ran qPCR on a set of water filter, fecal and tissue DNA extractions of varying copy number (based on Nate’s previous pinto abalone results) in order to get a set of high, medium and low copy number samples of each type for use in running the reproducibility aspect of the qPCR assay validation. Master mix calcs are here
Plate layout, cycling params, etc can be found in the qPCR Report (see Results).
Standard curve was the p16RK7 NcoI-linearized curve made on 20120730.
Baseline threshold was set to 400 and cycles to analyze was set to 41.
qPCR Data File (CFX96)
qPCR Report (PDF)
Here’s the list of samples analyzed and a comparison with Nate’s original data. In all instances, my results show significantly lower copy numbers (orders of magnitude lower) than Nate’s. Whether this is due to sample degradation over time is unknown. All samples have been stored at -20C since ~2005. I will discuss with Lisa and select the samples that provide us with the best range of copy numbers for use in the assay validation.