Dataset Overview | National Centers for Environmental Information (NCEI)

Operational taxonomic unit (OTU) table for 18S rRNA gene tag sequences from DNA and RNA from samples collected in coastal California in 2013 and 2014 (NCEI Accession 0277250)

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This dataset contains biological data collected on R/V Yellowfin during cruise SPOT_Yellowfin_Cruises from 2013-04-24 to 2014-01-15. These data include taxon and taxon_code. The instruments used to collect these data include Automated DNA Sequencer, CTD Sea-Bird SBE 911plus, and Niskin bottle. These data were collected by David Caron and Sarah K Hu of University of Southern California as part of the "Protistan, prokaryotic, and viral processes at the San Pedro Ocean Time-series (SPOT)" project. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) submitted these data to NCEI on 2023-01-23.

The following is the text of the dataset description provided by BCO-DMO:

Dataset Description: This dataset is a raw output operational taxonomic unit (OTU) table generated by processing and clustering raw 18S rRNA gene tag sequences from extracted DNA and RNA. Columns represent samples, including month sampled, material (either extracted RNA or DNA), and depth (in meters); thus values in each column represent the number of sequences in that sample that belong to a given OTU (OTUs by row). Each row represents a single OTU. The last column lists the taxonomic identifier assigned to each OTU. The raw sequence data can be found in the NCBI SRA database under accession number SRP070577 with the associated BioProject PRJNA311248.

Metadata for these sequences can be found in the dataset: ”18S rRNA gene tag sequences from DNA and RNA": https://www.bco-dmo.org/dataset/745527

Dataset Citation

Cite as: Caron, David; Hu, Sarah K. (2023). Operational taxonomic unit (OTU) table for 18S rRNA gene tag sequences from DNA and RNA from samples collected in coastal California in 2013 and 2014 (NCEI Accession 0277250). [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/0277250. Accessed [date].

Dataset Identifiers

ISO 19115-2 Metadata

gov.noaa.nodc:0277250

Full Text · XML

Download Data	HTTPS (download) Navigate directly to the URL for data access and direct download. FTP (download) These data are available through the File Transfer Protocol (FTP). FTP is no longer supported by most internet browsers. You may copy and paste the FTP link to the data into an FTP client (e.g., FileZilla or WinSCP).
Distribution Formats	TSV
Ordering Instructions	Contact NCEI for other distribution options and instructions.
Distributor	NOAA National Centers for Environmental Information +1-301-713-3277 NCEI.Info@noaa.gov
Dataset Point of Contact	NOAA National Centers for Environmental Information ncei.info@noaa.gov

Time Period	2013-04-24 to 2014-01-15
Spatial Bounding Box Coordinates	West: -118.475167 East: -118.259167 South: 33.452833 North: 33.7125
Spatial Coverage Map

General Documentation

NCEI Dataset Landing Page
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Descriptive Information
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Associated Resources

Biological, chemical, physical, biogeochemical, ecological, environmental and other data collected from around the world during historical and contemporary periods of biological and chemical oceanographic exploration and research managed and submitted by the Biological and Chemical Oceanography Data Management Office (BCO-DMO)
- NCEI Collection
  Navigate directly to the URL for data access and direct download.
Caron, D., Hu, S. K. (2018) Operational taxonomic unit (OTU) table for 18S rRNA gene tag sequences from DNA and RNA from samples collected in coastal California in 2013 and 2014. Dataset version 2018-10-15. https://doi.org/10.26008/1912/bco-dmo.748064.1
- https://doi.org/10.26008/1912/bco-dmo.748064.1 (download)
  originator dataset

gov.noaa.nodc:BCO-DMO

Publication Dates	publication: 2023-03-30
Data Presentation Form	Digital table - digital representation of facts or figures systematically displayed, especially in columns
Dataset Progress Status	Complete - production of the data has been completed Historical archive - data has been stored in an offline storage facility
Data Update Frequency	As needed
Supplemental Information	Acquisition Description: These data were published in Hu et al., 2016. This dataset is a raw output operational taxonomic unit (OTU) table generated by processing and clustering raw 18S rRNA gene tag sequences from DNA and RNA. The numbers in each column represent the number of sequences from that sample belonging to a given OTU (row), with the last column listing the taxonomic ID assigned to each OTU. The raw sequence data can be found in the NCBI SRA database under accession number with the associated BioProject . Metadata for these sequences can be found in the dataset: ”18S rRNA gene tag sequences from DNA and RNA": https://www.bco-dmo.org/dataset/745527 Nucleotide bases with a Q score lower than 20 for the last 30 bp of each sequence were trimmed. Paired-end sequences were merged using FLASh (Magoc and Salzberg 2011) with a minimum of 10 bp and maximum of 150 bp overlap between each sequence pair. Sequences shorter than 350 bp, longer than 460 bp, or which had an average quality score lower than 25 were discarded using QIIME v1.8 (Caporaso et al . 2010). Chimeric sequences were identified and removed, by either de novo or reference-based chimera checking (identify chimeric seqs.py in QIIME, intersection method). The code release v2 associated with this version of the dataset can be downloaded as a .zip file from the Supplemental Documents section of this page. Future code updates will be accessible from the GitHub repository .
Purpose	This dataset is available to the public for a wide variety of uses including scientific research and analysis.
Use Limitations	accessLevel: Public Distribution liability: NOAA and NCEI make no warranty, expressed or implied, regarding these data, nor does the fact of distribution constitute such a warranty. NOAA and NCEI cannot assume liability for any damages caused by any errors or omissions in these data. If appropriate, NCEI can only certify that the data it distributes are an authentic copy of the records that were accepted for inclusion in the NCEI archives.

Dataset Citation	Cite as: Caron, David; Hu, Sarah K. (2023). Operational taxonomic unit (OTU) table for 18S rRNA gene tag sequences from DNA and RNA from samples collected in coastal California in 2013 and 2014 (NCEI Accession 0277250). [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/0277250. Accessed [date].
Cited Authors	Caron, David University of Southern California Hu, Sarah K. University of Southern California
Principal Investigators	David Caron University of Southern California (USC) Sarah K. Hu University of Southern California (USC)
Contributors	University of Southern California (USC)
Resource Providers	Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Points of Contact	Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Publishers	NOAA National Centers for Environmental Information
Acknowledgments	Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1737409 Award URL: http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1737409

Theme keywords	NODC DATA TYPES THESAURUS TAXONOMIC CODE NODC OBSERVATION TYPES THESAURUS biological WMO_CategoryCode oceanography BCO-DMO Standard Parameters sequence taxon taxon_code Originator Parameter Names April_150m_DNA April_150m_cDNA April_5m_DNA April_5m_cDNA April_890m_DNA April_890m_cDNA April_CAT_DNA April_CAT_cDNA April_DCM_DNA April_DCM_cDNA April_POLA_DNA April_POLA_cDNA Jan_150m_DNA Jan_150m_cDNA Jan_5m_DNA Jan_5m_cDNA Jan_890m_DNA Jan_890m_cDNA Jan_CAT_DNA Jan_CAT_cDNA Jan_DCM_DNA Jan_DCM_cDNA Jan_POLA_DNA Jan_POLA_cDNA July_150m_DNA July_150m_cDNA July_5m_DNA July_5m_cDNA July_890m_DNA July_890m_cDNA July_CAT_DNA July_CAT_cDNA July_DCM_DNA July_DCM_cDNA July_POLA_DNA July_POLA_cDNA OTU_ID Oct_150m_DNA Oct_150m_cDNA Oct_5m_DNA Oct_5m_cDNA Oct_890m_DNA Oct_890m_cDNA Oct_CAT_DNA Oct_CAT_cDNA Oct_DCM_DNA Oct_DCM_cDNA Oct_POLA_DNA Oct_POLA_cDNA taxonomy
Data Center keywords	NODC COLLECTING INSTITUTION NAMES THESAURUS University of Southern California NODC SUBMITTING INSTITUTION NAMES THESAURUS Biological and Chemical Oceanography Data Management Office Global Change Master Directory (GCMD) Data Center Keywords BCO-DMO > Biological and Chemical Oceanography Data Management Office
Platform keywords	NODC PLATFORM NAMES THESAURUS YELLOWFIN BCO-DMO Platform Names R/V Yellowfin Global Change Master Directory (GCMD) Platform Keywords Ships ICES/SeaDataNet Ship Codes YELLOWFIN (call sign: WSA3704, ICES code: 31YE)
Instrument keywords	NODC INSTRUMENT TYPES THESAURUS bottle CTD BCO-DMO Standard Instruments Automated DNA Sequencer CTD Sea-Bird SBE 911plus Niskin bottle Global Change Master Directory (GCMD) Instrument Keywords CTD > Conductivity, Temperature, Depth Originator Instrument Names Illumina MiSeq unknown (CTD Sea-Bird SBE 911plus) unknown (Niskin bottle)
Place keywords	Provider Place Names San Pedro Ocean Time Series
Project keywords	NODC PROJECT NAMES THESAURUS San Pedro Ocean Time-series (SPOT) BCO-DMO Standard Projects Protistan, prokaryotic, and viral processes at the San Pedro Ocean Time-series (SPOT) Provider Cruise IDs SPOT_Yellowfin_Cruises Provider Funding Award Information Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1737409
Keywords	NCEI ACCESSION NUMBER 0277250

Use Constraints	Cite as: Caron, David; Hu, Sarah K. (2023). Operational taxonomic unit (OTU) table for 18S rRNA gene tag sequences from DNA and RNA from samples collected in coastal California in 2013 and 2014 (NCEI Accession 0277250). [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/0277250. Accessed [date].
Data License	This dataset is licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) License. SPDX License: Creative Commons Attribution 4.0 International (CC-BY-4.0)
Access Constraints	Use liability: NOAA and NCEI cannot provide any warranty as to the accuracy, reliability, or completeness of furnished data. Users assume responsibility to determine the usability of these data. The user is responsible for the results of any application of this data for other than its intended purpose.
Fees	In most cases, electronic downloads of the data are free. However, fees may apply for custom orders, data certifications, copies of analog materials, and data distribution on physical media.

Lineage information for: dataset
Processing Steps	2023-03-30T14:50:31Z - NCEI Accession 0277250 v1.1 was published.
Output Datasets	NCEI Accession 0277250 v1.1 NCEI Accession 0277250 v1.1 (download) published 2023-03-30T14:50:31Z

Acquisition Information (collection)
Instrument	bottle CTD
Platform	YELLOWFIN

Last Modified: 2024-05-31T15:15:28Z
For questions about the information on this page, please email: ncei.info@noaa.gov

Operational taxonomic unit (OTU) table for 18S rRNA gene tag sequences from DNA and RNA from samples collected in coastal California in 2013 and 2014 (NCEI Accession 0277250)

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