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

Occurrence Observation
Versão mais recente published by NOAA Integrated Ocean Observing System on jul 10, 2025 NOAA Integrated Ocean Observing System
Publication date:
10 de julho de 2025
Licença:
CC-BY 4.0

Baixe a última versão do recurso de dados, como um Darwin Core Archive (DwC-A) ou recurso de metadados, como EML ou RTF:

Dados como um arquivo DwC-A download 64.903 registros em English (2 MB) - Frequência de atualização: desconhecido
Metadados como um arquivo EML download em English (11 KB)
Metadados como um arquivo RTF download em English (8 KB)

Descrição

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.

Registros de Dados

Os dados deste recurso de ocorrência foram publicados como um Darwin Core Archive (DwC-A), que é o formato padronizado para compartilhamento de dados de biodiversidade como um conjunto de uma ou mais tabelas de dados. A tabela de dados do núcleo contém 64.903 registros.

Também existem 1 tabelas de dados de extensão. Um registro de extensão fornece informações adicionais sobre um registro do núcleo. O número de registros em cada tabela de dados de extensão é ilustrado abaixo.

Occurrence (core)
64903
dnaDerivedData 
64903

This IPT archives the data and thus serves as the data repository. The data and resource metadata are available for download in the downloads section. The versions table lists other versions of the resource that have been made publicly available and allows tracking changes made to the resource over time.

Versões

A tabela abaixo mostra apenas versões de recursos que são publicamente acessíveis.

Direitos

Pesquisadores devem respeitar a seguinte declaração de direitos:

O editor e o detentor dos direitos deste trabalho é NOAA Integrated Ocean Observing System. This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

GBIF Registration

Este recurso foi registrado no GBIF e atribuído ao seguinte GBIF UUID: e0b59ee7-19ae-4eb0-9217-33317fb50d47.  NOAA Integrated Ocean Observing System publica este recurso, e está registrado no GBIF como um publicador de dados aprovado por GBIF-US.

Palavras-chave

Occurrence; Observation

Contatos

Francisco Chavez
  • Provedor Dos Metadados ●
  • Originador ●
  • Ponto De Contato
  • Senior Scientist
Monterey Bay Aquarium Research Institute
Kathleen Pitz
  • Provedor Dos Metadados ●
  • Originador ●
  • Ponto De Contato
  • Research Associate
Monterey Bay Aquarium Research Institute
Diana LaScala-Gruenewald
  • Provedor Dos Metadados ●
  • Ponto De Contato
  • Data Scientist
CeNCOOS/MBARI
Abigail Benson
  • Publicador
  • Biologist
U.S. Geological Survey
Mathew Biddle
  • Distribuidor
  • Physical Scientist
United States Marine Biodiversity Observation Network (US MBON)
  • 1315 East-West Highway
20910 Silver Spring
MD
US
  • 3017134928

Metadados Adicionais

marine, harvested by OBIS

Identificadores alternativos e0b59ee7-19ae-4eb0-9217-33317fb50d47
https://obis.org/dataset/62b97724-da17-4ca7-9b26-b2a22aeaab51
https://ipt-obis.gbif.us/resource?r=18s_monterey_bay_time_series_edna