Описание
Записи данных
Данные этого находка ресурса были опубликованы в виде Darwin Core Archive (DwC-A), который является стандартным форматом для обмена данными о биоразнообразии в виде набора из одной или нескольких таблиц. Основная таблица данных содержит 135 440 записей.
Также в наличии 2 таблиц с данными расширений. Записи расширений содержат дополнительную информацию об основной записи. Число записей в каждой таблице данных расширения показано ниже.
Данный экземпляр IPT архивирует данные и таким образом служит хранилищем данных. Данные и метаданные ресурсов доступны для скачивания в разделе Загрузки. В таблице версий перечислены другие версии ресурса, которые были доступны публично, что позволяет отслеживать изменения, внесенные в ресурс с течением времени.
Версии
В таблице ниже указаны только опубликованные версии ресурса, которые доступны для свободного скачивания.
Как оформить ссылку
Исследователи должны дать ссылку на эту работу следующим образом:
Coclet C, Thompson L, Miller N, Marranzino A, Green J, Kline L, Collins A, Auscavitch S (2026). NOAA Ocean Exploration seawater eDNA metabarcoding (EX2301). Version 1.4. NOAA Ocean Exploration. Occurrence dataset. https://ipt-obis.gbif.us/resource?r=noaa-oer-okeanos-ex2301&v=1.4
Права
Исследователи должны соблюдать следующие права:
Публикующей организацией и владельцем прав на данную работу является NOAA Ocean Exploration. Насколько это возможно по закону, издатель отказался от всех прав на эти данные и посвятил их Public Domain (CC0 1.0). Пользователи могут без ограничений копировать, изменять, распространять и использовать работу, в том числе в коммерческих целях.
Регистрация в GBIF
Этот ресурс был зарегистрирован в GBIF, ему был присвоен следующий UUID: 9806a672-b859-4175-8432-f805b5ce8f30. NOAA Ocean Exploration отвечает за публикацию этого ресурса, и зарегистрирован в GBIF как издатель данных при оподдержке GBIF-US.
Ключевые слова
marine biome; marine epipelagic zone; marine mesopelagic zone; marine bathypelagic zone; seawater; Pacific Ocean; 18S rRNA (SSU eukaryote); 12S rRNA (SSU mitochondria); COI (cytochrome oxidase I); eDNA; metabarcoding; marine biodiversity; environmental DNA; Occurrence
Контакты
- Originator
- Research Scientist II
- 4301 Rickenbacker Cswy
https://orcid.org/0000-0002-6672-148X
- Originator ●
- Point Of Contact
- Research Professor
- 4301 Rickenbacker Cswy
- Originator
- NOAA Omics Coordinator
- Originator
- Project Scientist
- 1315 East-West Hwy
- Originator
- Research Associate III
- 1021 Balch Blvd Ste 1003
- Originator
- Operations Support Analyst
- Originator
- Director and Research Zoologist
- MRC 163
- Originator
- Genomics Specialist
- MRC 163
Географический охват
Northeast Pacific (U.S. West Coast continental margin, northern California to Washington, ~40–48°N, ~125–126°W)
| Ограничивающие координаты | Юг Запад [40,133, -126,126], Север Восток [48,171, -124,755] |
|---|
Таксономический охват
Marine organisms identified through eDNA metabarcoding
| Kingdom | Animalia, Bacteria, Chromista, Fungi, Plantae, Protozoa |
|---|
Временной охват
| Дата начала / Дата окончания | 2023-04-15 / 2023-04-26 |
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Данные проекта
The mission of NOAA Ocean Exploration is to explore the ocean for national benefit, including discovery and characterization of deep-sea environments and biodiversity. This project provides preliminary environmental DNA metabarcoding data from plankton, metazoa, cnidaria, and fish collected aboard NOAA Ship Okeanos Explorer, operated by NOAA Ocean Exploration. Sample archiving and management, wet lab processing, and sequencing was conducted by the Smithsonian National Museum of Natural History and the NOAA National Systematics Laboratory. DNA sequence analysis was performed by the NOAA Atlantic Oceanographic and Meteorological Laboratory.
| Название | NOAA Ocean Exploration seawater eDNA metabarcoding |
|---|---|
| Идентификатор | noaa-oer-okeanos |
| Финансирование | "A Comprehensive Bioinformatics Platform for Marine eDNA and Microbiome Data" (Grant ID NA21OAR4320190-T3-01S040, NOAA Ocean Exploration) |
| Описание района исследования | Atlantic (SE U.S., Gulf of America, Puerto Rico/Puerto Rico Trench, Azores) and Pacific (U.S. West Coast) from 2021-10-27 to 2023-04-26. |
| Описание плана выполнения исследований | To characterize biodiversity in sampled ocean environments using eDNA metabarcoding data from NOAA Ship Okeanos Explorer expeditions, with emphasis on deep-sea communities in the abyssal zone (depths below 4,000 m). |
| Грант проекта |
A Comprehensive Bioinformatics Platform for Marine eDNA and Microbiome Data NOAA Ocean Exploration NA21OAR4320190-T3-01S040 |
Исполнители проекта:
- Curator
Методы сбора
Seawater samples were collected aboard NOAA Ship Okeanos Explorer during ROV dives and CTD casts. Water was drawn from Niskin bottles mounted on either the Deep Discoverer ROV or a CTD rosette. Standard collection volumes were 1.7 L for water samples and 2.0 L for distilled water blanks. Samples were filtered through 0.45 um or 0.22 um membrane filters. Sample and environmental metadata - including dive or CTD cast ID, date, time, location, in-situ measurements (salinity, temperature, dissolved oxygen), and estimated bottom depth - were recorded electronically and transferred to the Sample Operator User Portal (SOUP). Laboratory procedures followed documented protocols (https://github.com/aomlomics/protocols). DNA was extracted from filters and amplified by PCR targeting three metabarcoding markers: 18S rRNA (protists/eukaryotes), COI (metazoa), and 12S rRNA (fish). Sequencing was performed on the Illumina NextSeq platform at the NOAA National Systematics Laboratory. Bioinformatic processing was performed on the Northern Gulf Institute's Orion computing cluster using the Tourmaline 2 pipeline. Steps included adapter trimming and quality filtering (Cutadapt), denoising and representative sequence determination (DADA2), and taxonomic assignment using a naive Bayes classifier and consensus VSEARCH (QIIME 2). Raw sequence data in FASTQ format were submitted to the NCBI Sequence Read Archive (SRA). FAIRe-formatted sample metadata were submitted to NCBI BioSample. Taxonomic occurrence data were formatted for submission to OBIS.
| Охват исследования | Northeast Pacific (U.S. West Coast continental margin, northern California to Washington, ~40–48°N, ~125–126°W) from 2023-04-15 to 2023-04-26. |
|---|---|
| Контроль качества | Quality control measures were implemented across all stages of the workflow. During sample collection, laboratory errors and deviations from standard operating procedures (NOAA Ocean Exploration eDNA Sample Workflow, Revision 2.3) were recorded per sample in a physical notebook and transferred to the Sample Operator User Portal (SOUP). Negative controls (distilled water blanks, extraction blanks, PCR blanks, and sequencing blanks) were included throughout sampling and processing to monitor for contamination. Control samples were excluded from the final published dataset but are archived in NCBI SRA and BioSample records for transparency. Raw sequence data were processed using the Tourmaline 2 pipeline. Low-quality bases and adapters were trimmed using Cutadapt, and sequences were denoised using DADA2 to generate representative sequences. Taxonomic assignments were made using a naive Bayes classifier and consensus VSEARCH, with confidence thresholds applied to ensure reliable identifications. Post-assignment filters were applied to remove sequences associated with domestic or human taxa (Bovidae, Suidae, Felidae, Canidae, Primates, Homo sapiens), unresolved assignments (Unassigned), and terrestrial organisms as flagged by WoRMS habitat classifications. |
Описание этапа методики:
- DNA was extracted from seawater filters, amplified by PCR for 18S, COI, and 12S metabarcoding markers, sequenced on Illumina, and analyzed with the Tourmaline 2 pipeline. Field sampling design and detailed procedures are described under sampling; bioinformatic QC and filtering are described under quality control.
Дополнительные метаданные
| Цель | |
|---|---|
| Альтернативные идентификаторы | 9806a672-b859-4175-8432-f805b5ce8f30 |
| https://ipt-obis.gbif.us/resource?r=noaa-oer-okeanos-ex2301 |