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Data and Code Release: Comparison of Recovery Rates from Rapid DNA Extraction Kits for Point of Use eDNA Detection
We evaluated extraction efficiency of four DNA rapid extraction protocols using filters spiked with primary cultured grass carp (Ctenopharyngodon idella) gill cells. The extraction methods included two syringe-based column extractions, an extraction solution, and a Chelex extraction protocol alongside a laboratory-based spin column kit. We estimated DNA yield using a newly designed quantitative PCR assay targeting the grass carp nuclear genome. We evaluated two additional factors, filter type (mixed cellulose ester and polyethersulfone) and background eDNA source (aquaculture or river). The enzyme extraction solution and Chelex extraction both had the highest overall yield, the magnitude of which was moderated by both filter type and eDNA background source. Our results suggest that rapid extraction protocols, such as solutions with short heating steps, are effective for DNA isolation and help to increase the overall accessibility of eDNA.
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Complete Metadata
| @type | dcat:Dataset |
|---|---|
| accessLevel | public |
| bureauCode |
[ "010:12" ] |
| contactPoint |
{ "fn": "Stephen F Spear", "@type": "vcard:Contact", "hasEmail": "mailto:sfspear@usgs.gov" } |
| description | We evaluated extraction efficiency of four DNA rapid extraction protocols using filters spiked with primary cultured grass carp (Ctenopharyngodon idella) gill cells. The extraction methods included two syringe-based column extractions, an extraction solution, and a Chelex extraction protocol alongside a laboratory-based spin column kit. We estimated DNA yield using a newly designed quantitative PCR assay targeting the grass carp nuclear genome. We evaluated two additional factors, filter type (mixed cellulose ester and polyethersulfone) and background eDNA source (aquaculture or river). The enzyme extraction solution and Chelex extraction both had the highest overall yield, the magnitude of which was moderated by both filter type and eDNA background source. Our results suggest that rapid extraction protocols, such as solutions with short heating steps, are effective for DNA isolation and help to increase the overall accessibility of eDNA. |
| distribution |
[ { "@type": "dcat:Distribution", "title": "Digital Data", "format": "XML", "accessURL": "https://doi.org/10.5066/P13GMSWV", "mediaType": "application/http", "description": "Landing page for access to the data" }, { "@type": "dcat:Distribution", "title": "Original Metadata", "format": "XML", "mediaType": "text/xml", "description": "The metadata original format", "downloadURL": "https://data.usgs.gov/datacatalog/metadata/USGS.67cef523d34ecfe34cc86669.xml" } ] |
| identifier | http://datainventory.doi.gov/id/dataset/USGS_67cef523d34ecfe34cc86669 |
| keyword |
[ "DNA extraction", "Invasive Species", "Point-of-Use", "USGS:67cef523d34ecfe34cc86669", "eDNA", "environment", "environmental DNA", "inlandWaters", "invasive species" ] |
| modified | 2025-04-22T00:00:00Z |
| publisher |
{ "name": "U.S. Geological Survey", "@type": "org:Organization" } |
| spatial | -91.3376, 44.0022, -91.3184, 43.9780 |
| theme |
[ "geospatial" ] |
| title | Data and Code Release: Comparison of Recovery Rates from Rapid DNA Extraction Kits for Point of Use eDNA Detection |
