RNA-Seq sample information and accessions numbers for the copepods Neocalanus flemingeri (Prince William Sound, Gulf of Alaska)(2015-2017) and Labidocera madurae (Kane‘ohe Bay, Oahu, Hawaii)(2017) (NCEI Accession 0294371)
This dataset contains biological data collected in the Gulf of Alaska and North Pacific Ocean from 2015-05-11 to 2017-09-27. These data include taxon. These data were collected by Russell R. Hopcroft of University of Alaska Fairbanks and Dr Daniel K Hartline, Dr Petra Lenz, and Vittoria Roncalli of University of Hawaii at Manoa as part of the "Collaborative Proposal: Optimizing Recruitment of Neocalanus copepods through Strategic Timing of Reproduction and Growth in the Gulf of Alaska (Neocalanus Gulf of Alaska)" project. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) submitted these data to NCEI on 2020-09-17.
The following is the text of the dataset description provided by BCO-DMO:
Dataset Description:
This dataset includes accession information for RNA-seq data for the copepods Neocalanus flemingeri and Labidocera madurae used to generate de novo reference transcriptomes and for gene expression analysis. N. flemingeri adult females (CVI) were collected in Prince Williams Sound (Gulf of Alaska) during the fall (September 2015 and 2017) oceanographic cruises of the Seward line long-term observation program (ltop)(http://www.sfos.uaf.edu/sewardline/) and Northern Gulf of Alaska Long-Term Ecological Research Program (NGA LTER). For each sample collection date and preservation dates are listed. Labidocera madurae adult females (CVI) and mixed copepodid stages (CIII-CV) were collected in Kane‘ohe Bay, Oahu (Hawaii) in August 2015.
The following is the text of the dataset description provided by BCO-DMO:
Dataset Description:
This dataset includes accession information for RNA-seq data for the copepods Neocalanus flemingeri and Labidocera madurae used to generate de novo reference transcriptomes and for gene expression analysis. N. flemingeri adult females (CVI) were collected in Prince Williams Sound (Gulf of Alaska) during the fall (September 2015 and 2017) oceanographic cruises of the Seward line long-term observation program (ltop)(http://www.sfos.uaf.edu/sewardline/) and Northern Gulf of Alaska Long-Term Ecological Research Program (NGA LTER). For each sample collection date and preservation dates are listed. Labidocera madurae adult females (CVI) and mixed copepodid stages (CIII-CV) were collected in Kane‘ohe Bay, Oahu (Hawaii) in August 2015.
Dataset Citation
- Cite as: Hartline, Daniel K.; Lenz, Petra H.; Hopcroft, Russell R.; Roncalli, Vittoria (2024). RNA-Seq sample information and accessions numbers for the copepods Neocalanus flemingeri (Prince William Sound, Gulf of Alaska)(2015-2017) and Labidocera madurae (Kane‘ohe Bay, Oahu, Hawaii)(2017) (NCEI Accession 0294371). [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/0294371. Accessed [date].
Dataset Identifiers
ISO 19115-2 Metadata
gov.noaa.nodc:0294371
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Ordering Instructions | Contact NCEI for other distribution options and instructions. |
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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 | 2015-05-11 to 2017-09-27 |
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West: -157.117
East: -147.803
South: 21.283
North: 60.535
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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: Materials and Methods Copepod collections, transfer to laboratory and preservation Neocalanus flemingeri adult females were collected in Prince Williams Sound during the fall oceanographic cruises of the Seward Line Long-term Observation Program (LTOP) (http://www.sfos.uaf.edu/sewardline/) and northern Gulf of Alaska Long-term Ecological Research Program (NGA LTER). Samples were collected between 700 and 400 m, using an opening and closing multiple plankton sampler (0.5 m2 cross-sectional area; 153 µm mesh nets; Multinet, Hydro-Bios) towed vertically from 700 m depth. Plankton collections were immediately diluted with deep seawater, and a set of N. flemingeri adult females were sorted within 15 min (T0) or within 45 min (Wk1) of net retrieval and preserved individually in microcentrifuge tubes in RNAlater Stabilization Reagent (QIAGEN). Additional females were stored in the cold and dark (5°C) prior to sorting and placed in incubation flasks (Falcon flasks, 750 ml) and maintained up to 9.5 weeks at 5-6°C before microscopic examination and preservation in RNAlater. Labidocera madurae were live sorted from mixed zooplankton samples collected in Kane‘ohe Bay, Oahu, Hawaii with a zooplankton net (30 cm diameter, 123 µm mesh) towed horizontally subsurface from a slowly moving boat. Collections were immediately diluted in seawater and transported to the laboratory. Adult females and mixed copepodid stages (CIII-CV) were live sorted within six hours of collection and either preserved in RNALater, or immediately processed for total RNA extraction. Each sample consisted of a group of individuals. RNA extraction, gene library preparation and RNASeq Total RNA was extracted from individuals using QIAGEN RNeasy Plus Mini Kit (catalog # 74134) in combination with a Qiashredder column (catalog # 79654) following the instructions of the manufacturer and stored at -80°C. Total RNA concentration and quality were checked using an Agilent Model 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, USA). Samples of extracted total RNA from individuals or group of copepods were shipped on dry ice to the University of Georgia Genomics and Bioinformatics Core (GGBC) Facility (dna.uga.edu). There, double-stranded cDNA libraries were prepared from total RNA extracted using the Kapa Stranded mRNA Seq kit (KK8420) following manufacturer’s instructions. Briefly, RNA samples were first purified with two oligo-dT selection (polyA enrichment using oligodT beds), and then fragmented and reverse transcribed into double-stranded complementary cDNA. Each sample was tagged with an indexed adapter and paired-end sequenced (PE150 bp or PE75 bp) using an Illumina NextSeq 500 instrument using a High or Medium Output Flow Cells. Short-sequence reads (RNA-Seq) were submitted to the short read archive (SRA) database at the National Center for Biotechnology Information (NCBI) for public access (see BioProjects PRJNA324453 and PRJNA324849) . Additional cruise data can be found at https://portal.aoos.org/ and https://nga.lternet.edu/. Station information: Gulf Of Alaska Stations: PWS2 (Lat: 60° 32.1′N; Long: 147° 48.2′W) KIP2 (Lat: 60°17'N; Long: 147° 59'W) Hawai’i: Kane‘ohe Bay, Oahu (Hawaii) (Lat: 21 ̊4’N; Long: 157 ̊7’W) |
Purpose | This dataset is available to the public for a wide variety of uses including scientific research and analysis. |
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Data Center keywords | NODC COLLECTING INSTITUTION NAMES THESAURUS NODC SUBMITTING INSTITUTION NAMES THESAURUS Global Change Master Directory (GCMD) Data Center Keywords |
Place keywords | NODC SEA AREA NAMES THESAURUS Global Change Master Directory (GCMD) Location Keywords |
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Last Modified: 2024-06-28T17:36:12Z
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For questions about the information on this page, please email: ncei.info@noaa.gov