Dataset Overview | National Centers for Environmental Information (NCEI)

Metabarcoding samples collected from surface and chlorophyll maximum depths from R/V Pt. Sur PS 18-09 Legs 01 and 03, Hurricane Harvey RAPID Response cruise (western Gulf of Mexico) September-October 2017 (NCEI Accession 0292220)

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This dataset contains biological data collected on R/V Point Sur during cruise PS1809 from 2017-09-23 to 2017-10-01. These data include taxon. The instruments used to collect these data include Automated DNA Sequencer, Niskin bottle, and Spectrophotometer. These data were collected by Darren W. Henrichs and Lisa Campbell of Texas A&M University as part of the "RAPID: Hurricane Impact on Phytoplankton Community Dynamics and Metabolic Response (HRR)" project. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) submitted these data to NCEI on 2021-02-10.

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

HRR metatranscriptome

Dataset Description:
Metabarcode samples collected from surface and chlorophyll maximum depths from R/V Pt. Sur PS 18-09 Legs 01 and 03, Hurricane Harvey RAPID Response cruise (western Gulf of Mexico) September-October 2017.

Dataset Citation

Cite as: Campbell, Lisa; Henrichs, Darren W. (2024). Metabarcoding samples collected from surface and chlorophyll maximum depths from R/V Pt. Sur PS 18-09 Legs 01 and 03, Hurricane Harvey RAPID Response cruise (western Gulf of Mexico) September-October 2017 (NCEI Accession 0292220). [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/0292220. Accessed [date].

Dataset Identifiers

ISO 19115-2 Metadata

gov.noaa.nodc:0292220

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	CSV 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	2017-09-23 to 2017-10-01
Spatial Bounding Box Coordinates	West: -97.268 East: -94.9 South: 27.2286 North: 29.0649
Spatial Coverage Map

General Documentation

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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.
Campbell, L., Henrichs, D. W. (2020) Metabarcoding samples collected from surface and chlorophyll maximum depths from R/V Pt. Sur PS 18-09 Legs 01 and 03, Hurricane Harvey RAPID Response cruise (western Gulf of Mexico) September-October 2017. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2020-09-14. https://doi.org/10.26008/1912/bco-dmo.824599.1
- https://doi.org/10.26008/1912/bco-dmo.824599.1 (download)
  originator dataset

gov.noaa.nodc:BCO-DMO

Publication Dates	publication: 2024-05-02
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: On each of 2 cruise legs 01 and 03, samples were collected at 7 stations (S01, S06, S11, S16, S21, SS and GI) from 2 depths [surface and chlorophyll maximum depth when possible; see HRR-bottle data] ) and triplicate 500-1000 ml samples were filtered and immediately fixed in RNALater. Triplicate samples from each station/depth were extracted with AllPrep DNA/RNA MiniKit (Qiagen, USA) following the manufacturer’s instructions. DNA concentration and quality were evaluated using a Nanodrop spectrophotometer (Thermo Fisher Scientific Inc, USA). All the samples extracted for DNA were normalized to 5ng/µl concentration for the amplicon library construction. The V4 regions of the 18S rRNA genes were amplified using customized V4 primers (Bradley et al. 2016; Kozich et al. 2013). Library construction and amplicon sequencing was performed at Texas A&M University Agrilife’s Genomics and Bioinformatics Services (https://www.txgen.tamu.edu) using custom designed primers (Bradley et al. 2016; Kozich et al. 2013). Output of MiSeq results as fasta files were deposited in GenBank under the project number PRJNA592369. Leg 01 Station 01 sample was not collected. Sampling locations: Sample ID Station Leg Location Lat o N/Long o W na 1 27.2286 -97.2686 L3_S01 S01 3 L1_S06 S06 1 27.8358 -96.9874 L3_S06 S06 3 L1_S11 S11 1 28.2614 -96.4129 L3_S11 S11 3 L1_S16 S16 1 28.5366 -95.8656 L3_S16 S16 3 L1_S21 S21 1 28.7644 -95.2978 L3_S21 S21 3 L1_SS SS 1 28.9600 -95.0946 L3_SS SS 3 L1_GI GI 1 29.0649 -94.9000 L3_GI GI 3
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: Campbell, Lisa; Henrichs, Darren W. (2024). Metabarcoding samples collected from surface and chlorophyll maximum depths from R/V Pt. Sur PS 18-09 Legs 01 and 03, Hurricane Harvey RAPID Response cruise (western Gulf of Mexico) September-October 2017 (NCEI Accession 0292220). [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/0292220. Accessed [date].
Cited Authors	Campbell, Lisa Texas A&M University Henrichs, Darren W. Texas A&M University
Principal Investigators	Lisa Campbell Texas A&M University (TAMU) Darren W. Henrichs Texas A&M University (TAMU)
Contributors	Texas A&M University (TAMU)
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-1760620

Theme keywords	NODC DATA TYPES THESAURUS TAXONOMIC CODE NODC OBSERVATION TYPES THESAURUS biological WMO_CategoryCode oceanography BCO-DMO Standard Parameters count no standard parameter sequence taxon Originator Parameter Names Gaps L1_GI L1_S06 L1_S11 L1_S16 L1_S21 L1_SS L3_GI L3_S01 L3_S06 L3_S11 L3_S16 L3_S21 L3_SS Length Mismatches OTU Q_end Q_start R_end R_start Score Sequence_ID Similarity Taxonomy e_value
Data Center keywords	NODC COLLECTING INSTITUTION NAMES THESAURUS Texas A&M University 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 POINT SUR BCO-DMO Platform Names R/V Point Sur Global Change Master Directory (GCMD) Platform Keywords Ships ICES/SeaDataNet Ship Codes POINT SUR (call sign: WSC2276, ICES code: 32P0, 1980)
Instrument keywords	NODC INSTRUMENT TYPES THESAURUS Niskin bottle spectrophotometer BCO-DMO Standard Instruments Automated DNA Sequencer Niskin bottle Spectrophotometer Global Change Master Directory (GCMD) Instrument Keywords NISKIN BOTTLES OPTSPEC > Optical Spectrometer Originator Instrument Names Illumina MiSeq Nanodrop spectrophotometer (Thermo Fisher Scientific Inc, USA) unknown (Niskin bottle)
Place keywords	Provider Place Names Western Gulf of Mexico, Continental Shelf, Louisiana and Texas coasts
Project keywords	BCO-DMO Standard Projects RAPID: Hurricane Impact on Phytoplankton Community Dynamics and Metabolic Response (HRR) Provider Cruise IDs PS1809 Provider Funding Award Information Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1760620
Keywords	NCEI ACCESSION NUMBER 0292220

Use Constraints	Cite as: Campbell, Lisa; Henrichs, Darren W. (2024). Metabarcoding samples collected from surface and chlorophyll maximum depths from R/V Pt. Sur PS 18-09 Legs 01 and 03, Hurricane Harvey RAPID Response cruise (western Gulf of Mexico) September-October 2017 (NCEI Accession 0292220). [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/0292220. 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	2024-05-02T20:40:19Z - NCEI Accession 0292220 v1.1 was published.
Output Datasets	NCEI Accession 0292220 v1.1 NCEI Accession 0292220 v1.1 (download) published 2024-05-02T20:40:19Z

Acquisition Information (collection)
Instrument	Niskin bottle spectrophotometer
Platform	POINT SUR

Last Modified: 2024-05-31T15:27:35Z
For questions about the information on this page, please email: ncei.info@noaa.gov

Metabarcoding samples collected from surface and chlorophyll maximum depths from R/V Pt. Sur PS 18-09 Legs 01 and 03, Hurricane Harvey RAPID Response cruise (western Gulf of Mexico) September-October 2017 (NCEI Accession 0292220)

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