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| "author": "[{\"given_name\": \"Flurin\", \"name\": \"Leugger\", | | "author": "[{\"given_name\": \"Flurin\", \"name\": \"Leugger\", |
| \"email\": \"flurin.leugger@usys.ethz.ch\", \"data_credit\": | | \"email\": \"flurin.leugger@usys.ethz.ch\", \"data_credit\": |
| [\"software\", \"curation\", \"collection\", \"validation\", | | [\"software\", \"curation\", \"collection\", \"validation\", |
| \"publication\"], \"identifier\": \"\", \"affiliation\": \"WSL / | | \"publication\"], \"identifier\": \"\", \"affiliation\": \"WSL / |
| ETH\"}, {\"given_name\": \"Martina\", \"name\": \"L\\u00fcthi\", | | ETH\"}, {\"given_name\": \"Martina\", \"name\": \"L\\u00fcthi\", |
| \"email\": \"martina.luethi@usys.ethz.ch\", \"data_credit\": | | \"email\": \"martina.luethi@usys.ethz.ch\", \"data_credit\": |
| [\"publication\", \"curation\", \"validation\", \"collection\", | | [\"publication\", \"curation\", \"validation\", \"collection\", |
| \"supervision\"], \"identifier\": \"\", \"affiliation\": \"ETH / | | \"supervision\"], \"identifier\": \"\", \"affiliation\": \"ETH / |
| WSL\"}, {\"given_name\": \"Michel\", \"name\": \"Schmidlin\", | | WSL\"}, {\"given_name\": \"Michel\", \"name\": \"Schmidlin\", |
| \"email\": \"michelschmidlin@gmail.com\", \"data_credit\": | | \"email\": \"michelschmidlin@gmail.com\", \"data_credit\": |
| [\"publication\", \"collection\", \"validation\"], \"identifier\": | | [\"publication\", \"collection\", \"validation\"], \"identifier\": |
| \"\", \"affiliation\": \"ETH/WSL\"}, {\"given_name\": \"Zacharias\", | | \"\", \"affiliation\": \"ETH/WSL\"}, {\"given_name\": \"Zacharias\", |
| \"name\": \"Kontarakis\", \"email\": | | \"name\": \"Kontarakis\", \"email\": |
| \"zacharias.kontarakis@fgcz.ethz.ch\", \"data_credit\": | | \"zacharias.kontarakis@fgcz.ethz.ch\", \"data_credit\": |
| [\"publication\", \"supervision\", \"validation\", \"curation\"], | | [\"publication\", \"supervision\", \"validation\", \"curation\"], |
| \"identifier\": \"\", \"affiliation\": \"ETH\"}, {\"given_name\": | | \"identifier\": \"\", \"affiliation\": \"ETH\"}, {\"given_name\": |
| \"Lo\\u00efc\", \"name\": \"Pellissier\", \"email\": | | \"Lo\\u00efc\", \"name\": \"Pellissier\", \"email\": |
| \"loic.pellissier@usys.ethz.ch\", \"data_credit\": [\"publication\", | | \"loic.pellissier@usys.ethz.ch\", \"data_credit\": [\"publication\", |
| \"supervision\", \"validation\", \"curation\"], \"identifier\": | | \"supervision\", \"validation\", \"curation\"], \"identifier\": |
| \"0000-0002-2289-8259 \", \"affiliation\": \"Ecosystems and Landscape | | \"0000-0002-2289-8259 \", \"affiliation\": \"Ecosystems and Landscape |
| Evolution, Dep. of Environmental Systems Science, ETH Zurich\"}]", | | Evolution, Dep. of Environmental Systems Science, ETH Zurich\"}]", |
| "author_email": null, | | "author_email": null, |
| "creator_user_id": "29b58075-315f-4aa2-bfff-425ea9553e90", | | "creator_user_id": "29b58075-315f-4aa2-bfff-425ea9553e90", |
| "date": | | "date": |
| :\"collected\",\"date\":\"2023-10-30\",\"end_date\":\"2023-11-10\"}]", | | :\"collected\",\"date\":\"2023-10-30\",\"end_date\":\"2023-11-10\"}]", |
| "doi": "10.16904/envidat.560", | | "doi": "10.16904/envidat.560", |
| "funding": | | "funding": |
| \",\"institution_url\":\"https://data.snf.ch/grants/grant/203550\"}]", | | \",\"institution_url\":\"https://data.snf.ch/grants/grant/203550\"}]", |
| "groups": [], | | "groups": [], |
| "id": "4a99830f-a254-4179-a490-d7ca76c5ed56", | | "id": "4a99830f-a254-4179-a490-d7ca76c5ed56", |
| "isopen": true, | | "isopen": true, |
| "license_id": "cc-by-sa", | | "license_id": "cc-by-sa", |
| "license_title": "Creative Commons Attribution Share-Alike | | "license_title": "Creative Commons Attribution Share-Alike |
| (CC-BY-SA)", | | (CC-BY-SA)", |
| "license_url": "https://creativecommons.org/licenses/by-sa/4.0/", | | "license_url": "https://creativecommons.org/licenses/by-sa/4.0/", |
| "maintainer": | | "maintainer": |
| ugger@usys.ethz.ch\",\"given_name\":\"Flurin\",\"name\":\"Leugger\"}", | | ugger@usys.ethz.ch\",\"given_name\":\"Flurin\",\"name\":\"Leugger\"}", |
| "maintainer_email": null, | | "maintainer_email": null, |
| "metadata_created": "2024-11-27T16:58:50.243757", | | "metadata_created": "2024-11-27T16:58:50.243757", |
n | "metadata_modified": "2024-11-29T06:46:18.872487", | n | "metadata_modified": "2024-11-29T06:46:41.040275", |
| "name": | | "name": |
| d-edna-analysis-to-detect-the-threatened-and-elusive-african-manatee", | | d-edna-analysis-to-detect-the-threatened-and-elusive-african-manatee", |
| "notes": "# Data associated to the publication \"Rapid field-based | | "notes": "# Data associated to the publication \"Rapid field-based |
| detection of a threatened and elusive species with environmental DNA | | detection of a threatened and elusive species with environmental DNA |
| and CRISPR-Dx\"\n\n<br> \n\n## Authors:\n\n<br>\n\nFlurin Leugger, | | and CRISPR-Dx\"\n\n<br> \n\n## Authors:\n\n<br>\n\nFlurin Leugger, |
| Martina L\u00fcthi, Michel Schmidlin, Zacharias Kontarakis and | | Martina L\u00fcthi, Michel Schmidlin, Zacharias Kontarakis and |
| Lo\u00efc Pellissier\n\n<br>\n\n## | | Lo\u00efc Pellissier\n\n<br>\n\n## |
| n\nflurinleugger@gmail.com\nloic.pellissier@usys.ethz.ch\n\n<br>\n\n## | | n\nflurinleugger@gmail.com\nloic.pellissier@usys.ethz.ch\n\n<br>\n\n## |
| Project description:\n\n<br>\n\nWe collected eDNA samples in the | | Project description:\n\n<br>\n\nWe collected eDNA samples in the |
| Conkouati-Douli National Park in the Republic of Congo in 2023 in | | Conkouati-Douli National Park in the Republic of Congo in 2023 in |
| collaboration with Beauval Nature and HELP Congo. We analyzed the | | collaboration with Beauval Nature and HELP Congo. We analyzed the |
| samples on site in the national park using CRISPR-Dx assays to detect | | samples on site in the national park using CRISPR-Dx assays to detect |
| the African manatee (*Trichechus senegalensis*). Additionally, we | | the African manatee (*Trichechus senegalensis*). Additionally, we |
| transported the remaining samples (buffer) to Switzerland and used a | | transported the remaining samples (buffer) to Switzerland and used a |
| high-sensitivity protocol with CRISPR-Dx assays and a qPCR assay to | | high-sensitivity protocol with CRISPR-Dx assays and a qPCR assay to |
| verify the field-based detections. The qPCR of Hunter et al. (2018) | | verify the field-based detections. The qPCR of Hunter et al. (2018) |
| detects the genus manatee (Trichechus). See publication for more | | detects the genus manatee (Trichechus). See publication for more |
| details (doi will be added after publication).\n\n<br>\n\n## | | details (doi will be added after publication).\n\n<br>\n\n## |
n | Folders:\n\n<br>\n\n### lateral_flow_tests_images\\:\n\n<br>\n\nimages | n | Folders:\n\n<br>\n\n### lateral_flow_tests_images\\:\n\n<br>\n\nImages |
| of the lateral flow tests used to analyze the eDNA extracts in the | | 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, | | 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 | | 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. | | pooled two PCRs together, resulting in 4 CRISPR-Dx assays per extract. |
| The EVE number on top of the tests indicates the environmental 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 | | number we use to track the extracts in our data base. It corresponds |
t | to the extract_number_field_based in the metadata and data | t | 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 |
| folder.\n\n<br>\n\n### metadata\\:\n\n<br>\n\nFile containing overview | | x.y).\n\n<br>\n\n### metadata\\:\n\n<br>\n\nFile containing overview |
| of site names and extract number (field-based or lab-based | | of site names and extract number (field-based or lab-based |
| extraction). The extract_number_field_based corresponds to the | | extraction). The extract_number_field_based corresponds to the |
| identically called column in CRISPR_field_based_classifications.csv | | identically called column in CRISPR_field_based_classifications.csv |
| file, as the extract_number_lab_based to the column in the file | | file, as the extract_number_lab_based to the column in the file |
| CRISPR_lab_based_classifications.csv file and the | | CRISPR_lab_based_classifications.csv file and the |
| qPCR_Cp_2nd_derivative.csv file. The file includes the GPS coordinates | | qPCR_Cp_2nd_derivative.csv file. The file includes the GPS coordinates |
| of the sampling location (transect start point).\n\n<br>\n\n### | | of the sampling location (transect start point).\n\n<br>\n\n### |
| data\\:\n\n<br>\n\nFolder containing the files with Cp values (qPCR) | | data\\:\n\n<br>\n\nFolder containing the files with Cp values (qPCR) |
| and the CRISPR-Dx classifications. | | and the CRISPR-Dx classifications. |
| CRISPR_field_based_classifications.csv file contains the | | CRISPR_field_based_classifications.csv file contains the |
| classifications per pool per extract (0: no detection, 1: detection) | | classifications per pool per extract (0: no detection, 1: detection) |
| for the African manatee (Trichechus | | for the African manatee (Trichechus |
| senegalensis).\nCRISPR_lab_based_classifications.csv file contains the | | senegalensis).\nCRISPR_lab_based_classifications.csv file contains the |
| classifications per pool per extract (0: no detection, 1: | | classifications per pool per extract (0: no detection, 1: |
| detection).\nqPCR_Cp_2nd_derivative.csv file contains the Cp value of | | detection).\nqPCR_Cp_2nd_derivative.csv file contains the Cp value of |
| the 8 replicates of each extract. \n", | | the 8 replicates of each extract. \n", |
| "num_resources": 4, | | "num_resources": 4, |
| "num_tags": 9, | | "num_tags": 9, |
| "organization": { | | "organization": { |
| "approval_status": "approved", | | "approval_status": "approved", |
| "created": "2018-12-01T11:59:01.791513", | | "created": "2018-12-01T11:59:01.791513", |
| "description": "We are an international research team with diverse | | "description": "We are an international research team with diverse |
| scientific expertise and backgrounds, connected by the goal to | | scientific expertise and backgrounds, connected by the goal to |
| understand biodiversity. We study the mechanisms that shape | | understand biodiversity. We study the mechanisms that shape |
| biodiversity patterns across spatial and temporal scales - in both | | biodiversity patterns across spatial and temporal scales - in both |
| terrestrial and aquatic ecosystems -\u200bsuch as mountain ranges and | | terrestrial and aquatic ecosystems -\u200bsuch as mountain ranges and |
| tropical reefs. We use an interdisciplinary approach, whereby we | | tropical reefs. We use an interdisciplinary approach, whereby we |
| bridge ecology, evolution, Earth history and global change.\r\nTo make | | bridge ecology, evolution, Earth history and global change.\r\nTo make |
| these connections, we collect data through biological monitoring, | | these connections, we collect data through biological monitoring, |
| environmental DNA methods, remote sensing, and field sampling, and use | | environmental DNA methods, remote sensing, and field sampling, and use |
| these data to answer questions with statistical and | | these data to answer questions with statistical and |
| process-\u200bbased models of biological diversity.\r\nOur group is | | process-\u200bbased models of biological diversity.\r\nOur group is |
| affiliated with ETH and WSL, but is also associated with Agroscope, | | affiliated with ETH and WSL, but is also associated with Agroscope, |
| EAWAG, the European Joint Research Centre and Vogelwarte.", | | EAWAG, the European Joint Research Centre and Vogelwarte.", |
| "id": "153392ee-d556-4b16-a330-dedb177e87f9", | | "id": "153392ee-d556-4b16-a330-dedb177e87f9", |
| "image_url": | | "image_url": |
| le.ethz.ch/_jcr_content/orgbox/image.imageformat.logo.1254626489.png", | | le.ethz.ch/_jcr_content/orgbox/image.imageformat.logo.1254626489.png", |
| "is_organization": true, | | "is_organization": true, |
| "name": "ele-group", | | "name": "ele-group", |
| "state": "active", | | "state": "active", |
| "title": "Ecosystems and Landscape Evolution", | | "title": "Ecosystems and Landscape Evolution", |
| "type": "organization" | | "type": "organization" |
| }, | | }, |
| "owner_org": "153392ee-d556-4b16-a330-dedb177e87f9", | | "owner_org": "153392ee-d556-4b16-a330-dedb177e87f9", |
| "private": false, | | "private": false, |
| "publication": | | "publication": |
| "{\"publisher\":\"EnviDat\",\"publication_year\":\"2024\"}", | | "{\"publisher\":\"EnviDat\",\"publication_year\":\"2024\"}", |
| "publication_state": "published", | | "publication_state": "published", |
| "relationships_as_object": [], | | "relationships_as_object": [], |
| "relationships_as_subject": [], | | "relationships_as_subject": [], |
| "resource_type": "dataset", | | "resource_type": "dataset", |
| "resource_type_general": "dataset", | | "resource_type_general": "dataset", |
| "resources": [ | | "resources": [ |
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| "description": "Folder containing the data files with Cp values | | "description": "Folder containing the data files with Cp values |
| (qPCR) and the CRISPR-Dx classifications. | | (qPCR) and the CRISPR-Dx classifications. |
| CRISPR_field_based_classifications.csv file contains the | | CRISPR_field_based_classifications.csv file contains the |
| classifications per pool per extract (0: no detection, 1: detection) | | classifications per pool per extract (0: no detection, 1: detection) |
| for the African manatee (Trichechus | | for the African manatee (Trichechus |
| senegalensis).\nCRISPR_lab_based_classifications.csv file contains the | | senegalensis).\nCRISPR_lab_based_classifications.csv file contains the |
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| "description": "File containing overview of site names and | | "description": "File containing overview of site names and |
| extract number (field-based or lab-based extraction). The | | extract number (field-based or lab-based extraction). The |
| extract_number_field_based corresponds to the identically called | | extract_number_field_based corresponds to the identically called |
| column in CRISPR_field_based_classifications.csv file in the data | | column in CRISPR_field_based_classifications.csv file in the data |
| folder, as the extract_number_lab_based to the column in the file | | folder, as the extract_number_lab_based to the column in the file |
| CRISPR_lab_based_classifications.csv file and the | | CRISPR_lab_based_classifications.csv file and the |
| qPCR_Cp_2nd_derivative.csv file (also in the data folder). The file | | qPCR_Cp_2nd_derivative.csv file (also in the data folder). The file |
| includes the GPS coordinates of the sampling location (transect start | | includes the GPS coordinates of the sampling location (transect start |
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| "description": "Images of the lateral flow tests used to analyze | | "description": "Images of the lateral flow tests used to analyze |
| the eDNA extracts in the national park. File names correspond to the | | 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 | | 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 | | per filter/extract and pooled two PCRs together, resulting in 4 |
| CRISPR-Dx assays per extract. The EVE number on top of the tests | | CRISPR-Dx assays per extract. The EVE number on top of the tests |
| indicates the environmental extract number we use to track the | | indicates the environmental extract number we use to track the |
| extracts in our data base. It corresponds to the | | extracts in our data base. It corresponds to the |
| extract_number_field_based in the metadata and data folder. The | | extract_number_field_based in the metadata and data folder. The |
| negative extraction control with the strongest \"band\" was placed | | negative extraction control with the strongest \"band\" was placed |
| right to the eDNA extract on each image (labelled hand written with NC | | right to the eDNA extract on each image (labelled hand written with NC |
| x.y).", | | x.y).", |
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