18S Monterey Bay Time Series: an eDNA data set from Monterey Bay, California, including years 2006, 2013 - 2016

Occurrence Observation
最新版本 published by NOAA Integrated Ocean Observing System on 7月 10, 2025 NOAA Integrated Ocean Observing System
發布日期:
2025年7月10日
授權條款:
CC-BY 4.0

下載最新版本的 Darwin Core Archive (DwC-A) 資源，或資源詮釋資料的 EML 或 RTF 文字檔。

DwC-A資料集 下載 64,903 紀錄 在 English 中 (2 MB) - 更新頻率: 有可能更新，但不確知何時
元數據EML檔 下載 在 English 中 (11 KB)
元數據RTF文字檔 下載 在 English 中 (8 KB)

說明

These data are from marine filtered seawater samples collected at a nearshore station in Monterey Bay, CA. They have undergone metabarcoding for the 18S V9 region. A selection of samples from this plate were included in the publication "Environmental DNA reveals seasonal shifts and potential interactions in a marine community" (Djurhuus et al., 2020). Samples were collected by CTD rosette and filtered by a peristaltic pump system.Illumina MiSeq metabarcoding data was processed in the following steps: (1) primer sequences were removed through atropos (Didion et al., 2017), (2) reads were denoised, ASV sequences inferred, paired reads merged and chimeras removed through Dada2 (Callahan et al., 2016), (3) taxonomic ranks were assigned through blastn searches to NCBI GenBank's non-redundant nucleotide database (nt) with hits filtered by lowest common ancestor algorithm within MEGAN6 (Huson et al., 2016). Furthermore, post-MEGAN6 filtering was performed to ensure only contigs with a hit of ≥97% sequence identity were annotated to the species level and only contigs with a hit of ≥95% sequence identity were annotated to the genus level. Annotations were elevated to the next highest taxonomic level for contigs that failed these conditions.Data are presented in two comma-separated values files: occurrence.csv, and DNADerivedData.csv. The former contains the taxonomic identification of each ASV observed and its number of reads, in addition to relevant metadata including the location the water sample was taken, references for the identification procedure, and links to archived sequences. The latter contains the DNA sequence of each ASV observed, in addition to relevant metadata including primer information and links to detailed field and laboratory methods. This data set was transformed from its native format into a table structure using Darwin Core and DNA Derived Data Extension term names as column names.References:Djurhuus, A, Closek, CJ, Kelly, RP et al. (2020). Environmental DNA reveals seasonal shifts and potential interactions in a marine community. Nat Commun 11, 254. https://doi.org/10.1038/s41467-019-14105-1Didion JP, Martin M, Collins FS. (2017) Atropos: specific, sensitive, and speedy trimming of sequencing reads. PeerJ 5:e3720 https://doi.org/10.7717/peerj.3720Callahan, B., McMurdie, P., Rosen, M. et al. (2016) DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods 13, 581–583 . https://doi.org/10.1038/nmeth.3869Huson DH, Beier S, Flade I, Górska A, El-Hadidi M, Mitra S, Ruscheweyh HJ, Tappu R. (2016) MEGAN community edition-interactive exploration and analysis of large-scale microbiome sequencing data. PLoS computational biology. Jun 21;12(6):e1004957.

資料紀錄

此資源出現紀錄的資料已發佈為達爾文核心集檔案（DwC-A），其以一或多組資料表構成分享生物多樣性資料的標準格式。 核心資料表包含 64,903 筆紀錄。

亦存在 1 筆延伸集的資料表。延伸集中的紀錄補充核心集中紀錄的額外資訊。 每個延伸集資料表中資料筆數顯示如下。

Occurrence (核心)
64903
dnaDerivedData 
64903

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版本

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權利

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此資料的發布者及權利單位為 NOAA Integrated Ocean Observing System。 This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

GBIF 註冊

此資源已向GBIF註冊，並指定以下之GBIF UUID: e0b59ee7-19ae-4eb0-9217-33317fb50d47。  NOAA Integrated Ocean Observing System 發佈此資源，並經由GBIF-US同意向GBIF註冊成為資料發佈者。

關鍵字

Occurrence; Observation

聯絡資訊

Francisco Chavez
  • 元數據提供者 ●
  • 出處 ●
  • 連絡人
  • Senior Scientist
Monterey Bay Aquarium Research Institute
Kathleen Pitz
  • 元數據提供者 ●
  • 出處 ●
  • 連絡人
  • Research Associate
Monterey Bay Aquarium Research Institute
Diana LaScala-Gruenewald
  • 元數據提供者 ●
  • 連絡人
  • Data Scientist
CeNCOOS/MBARI
Abigail Benson
  • 發布者
  • Biologist
U.S. Geological Survey
Mathew Biddle
  • 散布者
  • Physical Scientist
United States Marine Biodiversity Observation Network (US MBON)
  • 1315 East-West Highway
20910 Silver Spring
MD
US
  • 3017134928

額外的詮釋資料