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Surface water samples (n = 33) were collected in fall of 2023 at stream sites in Scott County Iowa, USA and were analyzed for microbial source tracking markers by quantitative polymerase chain reaction at the Laboratory for Infectious Disease and the Environment (LIDE). Microbial source tracking markers identify fecal sources of contamination by detecting microbes that are specific to certain animals. Cooperators include Partners of Scott County Watersheds, Prairie Rivers of Iowa, and U.S. Department of Agriculture-Agricultural Research Service.
Categories: Data;
Tags: Iowa,
Microbial source tracking,
USGS Science Data Catalog (SDC),
Water Quality,
environment,
The dataset includes aggregated precipitation data from a USGS rain gauge for specified 7- or 8-day time periods between May and November 2017. Daily precipitation measurements were summed to produce 7- or 8-day totals over the specified time period.
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
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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