Environmental Data: Field-based eDNA analysis to detect the threatened...

Keywords:
AFRICAN MANATEE
BIODIVERSITY MONITORING
CRISPR-CAS
CRISPR-DX
EDNA
ENVIRONMENTAL DNA
FIELD-BASED PROTOCOL
QPCR
THREATENED SPECIES
Keywords:
AFRICAN MANATEE
BIODIVERSITY MONITORING
CRISPR-CAS
CRISPR-DX
EDNA
ENVIRONMENTAL DNA
FIELD-BASED PROTOCOL
QPCR
THREATENED SPECIES

Description

# Data associated to the publication "Rapid field-based detection of a threatened and elusive species with environmental DNA and CRISPR-Dx" <br> ## Auth...

Citation

Leugger, F., Lüthi, M., Schmidlin, M., Kontarakis, Z., Pellissier, L. (2024). Field-based eDNA analysis to detect the threatened and elusive African manatee. EnviDat. https://www.doi.org/10.16904/envidat.560.

Resources

  • Readme.txt

    Description of project and folders and files

    Readme.txt

  • data.zip

    Folder containing the data files with Cp values (qPCR) and the CRISPR-Dx classifications. CRISPR_field_based_classifications.csv file contains the classifications per pool per extract (0: no detection, 1: detection) for the African manatee (Trichechus senegalensis). CRISPR_lab_based_classifications.csv file contains the classifications per pool per extract (0: no detection, 1: detection). qPCR_Cp_2nd_derivative.csv file contains the Cp value of the 8 replicates of each extract.

    data.zip

  • metadata.zip

    File containing overview of site names and extract number (field-based or lab-based extraction). The extract_number_field_based corresponds to the identically called column in CRISPR_field_based_classifications.csv file in the data folder, as the extract_number_lab_based to the column in the file CRISPR_lab_based_classifications.csv file and the qPCR_Cp_2nd_derivative.csv file (also in the data folder). The file includes the GPS coordinates of the sampling location (transect start point).

    metadata.zip

  • lateral_flow_tests_images.zip

    Images of the lateral flow tests used to analyze the eDNA extracts in the national park. File names correspond to the site names. At each site, we took two filter replicates. We ran 8 PCRs per filter/extract and pooled two PCRs together, resulting in 4 CRISPR-Dx assays per extract. The EVE number on top of the tests indicates the environmental extract number we use to track the extracts in our data base. It corresponds to the extract_number_field_based in the metadata and data folder. The negative extraction control with the strongest "band" was placed right to the eDNA extract on each image (labelled hand written with NC x.y).

    lateral_flow_tests_images.zip