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This data set was collected to provide examples and aid in developing a standardized way of determining LOD and LOQ for eDNA assays and has 3 data files. GEDWG_LOD_DATA3.csv is raw qPCR data from multiple labs running multiple standards of known concentration for eDNA assays they regularly use. Comparison-Data.csv is the merged data output from running a generic LOD/LOQ calculator script multiple times with different LOD model settings. The generic LOD/LOQ calculator script is available at: https://github.com/cmerkes/qPCR_LOD_Calc, and details about the multiple settings used are commented in the analysis script available at: https://github.com/cmerkes/LOD_Analysis
This script is designed to analyze qPCR data for many replicates of known concentration DNA standards and determine the limit of detection (LoD) and limit of quantification (LoQ) for use in environmental DNA applications. It is written in the hopes that users with even limited knowledge of R will be able to successfully use the code to analyze their own data in the same way as other eDNA researchers to get similar results and automatically generate plots to visualize the data. The code has 5 lines for user input and requires a few simple restrictions on the input data, but after that the user should be able to run the code without any further coding or interventions. No R programming ability is required to run this...
Categories: Data
The use of carbon dioxide to control aquatic invasive species (AIS) prompted an evaluation of its effects on native freshwater mussels that may reside in areas of infusion. We exposed juvenile mussels (~6-mo old) of two species, the fat mucket (Lampsilis siliquoidea) and the federally endangered Higgins’ Eye (L. higginsii) to CO2 concentrations proposed for AIS control (24,000 – 96,000 µatm pCO2 ) for 28 d followed by a 14-d recovery period and compared their survival, growth, and behavior. Additionally, tissue and shell condition and transcriptomic response of four genes were measured in L. siliquoidea. Survival was similar between species; the 14-d postexposure LC50 for L.higginsii was 61,000 µatm pCO2 (95% CL...
Detection of environmental DNA (eDNA) has become a commonly used surveillance method for threatened or invasive vertebrates in both aquatic and terrestrial environments. However, use of eDNA methodologies for the detection of aquatic invertebrates (e.g., crayfish and insects) has been limited. Environmental DNA protocols can be especially useful for endangered invertebrates such as the Hine’s emerald dragonfly (Somatochlora hineana) where conservation efforts have been greatly hindered by the training, time, overall costs, and environmental impacts associated with conducting surveys in the calcareous fens occupied by this species. An essential step in developing such a protocol is to evaluate the dynamics of eDNA...
Categories: Data;
Tags: Aquatic Biology,
Door County, Wisconsin,
HED,
Hine's Emerald Dragonfly,
USGS Science Data Catalog (SDC),
This code supports the manuscript "Reporting the limits of detection (LOD) and quantification (LOQ) for environmental DNA assays". The code analyzes outputs generated by another more generic code to analyze raw qPCR data for LOD and LOQ. This code requires the generic LOD / LOQ calculator script to read in and prepare the data, with additional script runs as described in comments within this code. We wrote this code to specifically analyze our data and generate the figures for the above-mentioned manuscript, however it could be adaptped by a savvy programmer to run similar analyses.
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