説明
データ レコード
この オカレンス（観察データと標本) リソース内のデータは、1 つまたは複数のデータ テーブルとして生物多様性データを共有するための標準化された形式であるダーウィン コア アーカイブ (DwC-A) として公開されています。 コア データ テーブルには、135,440 レコードが含まれています。
拡張データ テーブルは2 件存在しています。拡張レコードは、コアのレコードについての追加情報を提供するものです。 各拡張データ テーブル内のレコード数を以下に示します。
この IPT はデータをアーカイブし、データ リポジトリとして機能します。データとリソースのメタデータは、 ダウンロード セクションからダウンロードできます。 バージョン テーブルから公開可能な他のバージョンを閲覧でき、リソースに加えられた変更を知ることができます。
バージョン
次の表は、公にアクセス可能な公開バージョンのリソースのみ表示しています。
引用方法
研究者はこの研究内容を以下のように引用する必要があります。:
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
権利
研究者は権利に関する下記ステートメントを尊重する必要があります。:
パブリッシャーとライセンス保持者権利者は NOAA Ocean Exploration。 To the extent possible under law, the publisher has waived all rights to these data and has dedicated them to the Public Domain (CC0 1.0). Users may copy, modify, distribute and use the work, including for commercial purposes, without restriction.
GBIF登録
このリソースをはGBIF と登録されており GBIF UUID: 9806a672-b859-4175-8432-f805b5ce8f30が割り当てられています。 GBIF-US によって承認されたデータ パブリッシャーとして GBIF に登録されているNOAA Ocean Exploration が、このリソースをパブリッシュしました。
キーワード
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
連絡先
- 最初のデータ採集者
- Research Scientist II
- 4301 Rickenbacker Cswy
https://orcid.org/0000-0002-6672-148X
- 最初のデータ採集者 ●
- 連絡先
- Research Professor
- 4301 Rickenbacker Cswy
- 最初のデータ採集者
- NOAA Omics Coordinator
- 最初のデータ採集者
- Project Scientist
- 1315 East-West Hwy
- 最初のデータ採集者
- Research Associate III
- 1021 Balch Blvd Ste 1003
- 最初のデータ採集者
- Operations Support Analyst
- 最初のデータ採集者
- Director and Research Zoologist
- MRC 163
- 最初のデータ採集者
- Genomics Specialist
- MRC 163
地理的範囲
Northeast Pacific (U.S. West Coast continental margin, northern California to Washington, ~40–48°N, ~125–126°W)
| 座標（緯度経度） | 南 西 [40.133, -126.126], 北 東 [48.171, -124.755] |
|---|
生物分類学的範囲
Marine organisms identified through eDNA metabarcoding
| Kingdom | Animalia, Bacteria, Chromista, Fungi, Plantae, Protozoa |
|---|
時間的範囲
| 開始日 / 終了日 | 2023-04-15 / 2023-04-26 |
|---|
プロジェクトデータ
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.
| タイトル | NOAA Ocean Exploration seawater eDNA metabarcoding |
|---|---|
| 識別子 | noaa-oer-okeanos |
| ファンデイング | "A Comprehensive Bioinformatics Platform for Marine eDNA and Microbiome Data" (Grant ID NA21OAR4320190-T3-01S040, NOAA Ocean Exploration) |
| Study Area Description | 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. |
| 研究の意図、目的、背景など（デザイン） | 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). |
| Project Award |
A Comprehensive Bioinformatics Platform for Marine eDNA and Microbiome Data NOAA Ocean Exploration NA21OAR4320190-T3-01S040 |
プロジェクトに携わる要員:
- キュレーター
収集方法
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.
| Study Extent | 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. |
|---|---|
| Quality Control | 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. |
Method step description:
- 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.
追加のメタデータ
| 目的 | |
|---|---|
| 代替識別子 | 9806a672-b859-4175-8432-f805b5ce8f30 |
| https://ipt-obis.gbif.us/resource?r=noaa-oer-okeanos-ex2301 |