http://lod.bco-dmo.org/id/dataset/922330
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2024-03-15
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Multiyear RNA-Seq of Neocalanus flemingeri stages CV and Adult Female from the R/V Tiglax and R/V Sikuliaq in the Northern Gulf of Alaska from 2015-2022
2024-07-26
publication
2024-07-26
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2024-08-14
publication
https://doi.org/10.26008/1912/bco-dmo.922330.1
Petra H. Lenz
University of Hawaiʻi at Mānoa
principalInvestigator
Vittoria Roncalli
University of Hawaiʻi at Mānoa
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Lenz, P. H., Roncalli, V., Cieslak, M. C. (2024) Multiyear RNA-Seq of Neocalanus flemingeri stages CV and Adult Female from the R/V Tiglax and R/V Sikuliaq in the Northern Gulf of Alaska from 2015-2022. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-07-26 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.922330.1 [access date]
Multiyear RNA-Seq of Neocalanus flemingeri stages CV and Adult Female Dataset Description: Methods and Sampling: <p>In collaboration with the Seward Long-Term Observation Program (LTOP) (<a href="https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.sfos.uaf.edu%2Fsewardline%2F&amp;data=05%7C02%7Clynne.merchant%40whoi.edu%7Cf8155b0002c74a05c21508dcb70b16dc%7Cd44c5cc6d18c46cc8abd4fdf5b6e5944%7C0%7C0%7C638586505480119332%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&amp;sdata=2bhmDZMhb5aoswXOGXSshl0PMuf1laDLJO9XhomwMAw%3D&amp;reserved=0">http://www.sfos.uaf.edu/sewardline/</a>) and the NGA LTER Program (<a href="https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fnga.lternet.edu%2F&amp;data=05%7C02%7Clynne.merchant%40whoi.edu%7Cf8155b0002c74a05c21508dcb70b16dc%7Cd44c5cc6d18c46cc8abd4fdf5b6e5944%7C0%7C0%7C638586505480133405%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&amp;sdata=3HtOIqdFDdfNZVDohmwM00fLqMqe2goa3UTQQX5YIoI%3D&amp;reserved=0">https://nga.lternet.edu/</a>), we obtained Neocalanus flemingeri individuals during the annual April-May and September oceanographic cruises. During the spring cruises stage CV individuals were collected from four to six locations: spanning the inner shelf to outer shelf gradient along the Seward Line in the northern Gulf of Alaska and at least one station in adjoining Prince William Sound. Samples were collected using a CalVET net (53-µm mesh) towed vertically from 100 m depth to surface. Mixed plankton samples were immediately diluted with surface seawater, and maintained at ~5ºC prior to and during sorting. From each station actively swimming (healthy) N. flemingeri CVs were rapidly sorted under the microscope and preserved within 15 minutes to 1hr of the tow in RNALater Stabilization Reagent (QIAGEN). The rapid sorting of live plankton can lead to misidentifications given the presence of closely related congeners, thus species verification is recommended using the RNA-seq data to check the cytochrome c oxidase subunit 1 (mtCOI) sequence. In September, diapausing N. flemingeri adult females were sorted from collections obtained with a Midi Multinet towed vertically. Collections were diluted with seawater upon net retrieval. Individuals were sorted under the microscope from the 300-700 depth collections and either preserved immediately in RNALater or separated into holding containers for incubation experiments. In three years (2015, 2016, 2017) additional adult females were incubated for different lengths of time and preserved after a specified interval as indicated in the sample information. In July, 2019 we participated in a ship of opportunity cruise to the Gulf of Alaska Seamounts (SKQ201916S) and preserved diapausing adult females collected between 1000-2000 meters from two offshore stations (GAK19 and DeepQuinn).</p>
<p><em>RNA extraction, gene library preparation and RNA-seq</em></p>
<p>Total RNA was extracted from individual CV from each station 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 -80ºC. Total RNA concentration and quality were checked using an Agilent Model 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, USA). For each station, total RNA from three of the ten individuals with high quality RNA yields were selected for RNA-seq and shipped on dry ice to the University of Georgia Genomics 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 DNA. Each sample was tagged with an indexed adapter and they were simultaneously paired-end sequenced (PE150 or PE75 bp) using an Illumina NextSeq 500 instrument using High-Output Flow Cell.&nbsp;Data in NCBI are the raw sequence reads.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1459235 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1459235
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1459826 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1459826
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1756767 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1756767
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1756859 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1756859
Funding provided by North Pacific Research Board (NPBR) Award Number: NPRB-1709 Award URL: https://nprb.org/project-search/#metadata/26adee7d-cb61-4aa4-8c63-cfe1c7d87f1d/project
completed
Petra H. Lenz
University of Hawaiʻi at Mānoa
808-956-8003
Pacific Biosciences Research Center (PBRC), Bekesy Laboratory of Neurobiology 1993 East-West Road
Honolulu
HI
96822
United States
petra@hawaii.edu
pointOfContact
Vittoria Roncalli
University of Hawaiʻi at Mānoa
Bekesy Laboratory of Neurobiology and Zoology Dept. 1993 East-West Road
Honolulu
Hawaii
96822
roncalli@hawaii.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Experiment_Accession
Experiment_Title
Organism_Name
Station
Latitude
Longitude
Depth_Range
Date
Year
Month
Day
Life_Stage
Sex
BioProject
BioSample
Sample_Accession
SRA_Run_Accession
Study_Accession
Study_Title
Illumina NextSeq 500
Agilent Model 2100 Bioanalyzer
Midi MultiNet
CalVET QuadNet
theme
None, User defined
NCBI SRA experiment accession (SRX)
seq_descrip
species
station
latitude
longitude
depth range
date
year
month of year
day of month
stage
sex
NCBI BioProject accession
NCBI BioSample accession
NCBI SRA Sample accession (SRS)
NCBI SRA run accession (SRR)
NCBI SRA study accession (SRP)
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Electrophoresis Chamber
MultiNet
Plankton Net
instrument
BCO-DMO Standard Instruments
TXS15
TXF15
TXF16
TXF17
TXF18
TXS19
TXF19
TXS17
SKQ201810S
SKQ201916S
SKQ202006S
SKQ202106S
TXF21
SKQ202207S
service
Deployment Activity
Northern Gulf of Alaska
Gulf of Alaska
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Collaborative Proposal: Optimizing Recruitment of Neocalanus copepods through Strategic Timing of Reproduction and Growth in the Gulf of Alaska
https://osprey.bco-dmo.org/project/542182
Collaborative Proposal: Optimizing Recruitment of Neocalanus copepods through Strategic Timing of Reproduction and Growth in the Gulf of Alaska
<p>NSF abstract:</p>
<p>The Gulf of Alaska supports a diverse and productive marine community that includes many commercially important fishes. Toward the base of this food web are small planktonic crustaceans that serve as the primary food source for many of these fish, as well as seabirds and marine mammals. The copepod Neocalanus flemingeri is one of these crustaceans, and it experiences rapid population growth during each spring's algal, or phytoplankton, bloom. An apparent mismatch between the presence of the youngest stages of the copepod, or nauplii, in early winter and the unpredictable timing of the spring phytoplankton bloom several months later raises important questions about when females reproduce and how this relates to survival and growth of nauplii. Two types of dormancy, diapause in adult females and physiological quiescence in nauplii, may be the key to the success of this copepod species. Timing and duration of the egg-laying period by adult females is linked to emergence from diapause. In addition, nauplii may enter a state of physiological quiescence while food resources are low, resuming growth after phytoplankton levels increase. This research will address a long-standing goal of biological oceanographers to understand dormancy and its role in controlling population cycles in marine copepods. It will use new technologies in molecular biology called transcriptomics to catalog the messages used by the cells to control copepod life processes, in this case those related to dormancy in adults and nauplii. Undergraduate students and a postdoctoral investigator will be trained in interdisciplinary research, and students from Native Hawaiian and Native Alaskan groups will be targeted for participation. Fishing is a major industry in the Gulf of Alaska, and outreach will focus on communicating the role copepods play in marine ecosystems. New content, including images, will be generated for existing websites: the Seward Line long-term observation program, the Alaska Ocean Observing System and the Gulf Watch Alaska Program.</p>
<p>Recruitment to the Neocalanus flemingeri spring population is dependent on successful emergence from diapause followed by reproduction, survival, and growth of the next generation. Individual-based models have made significant progress in predicting population growth in calanoid copepods using food, temperature, and advection as key environmental factors. Few of these models include predictors for naupliar recruitment, however, because little is known about this part of the life cycle given sampling difficulties and the lack of biomarkers to evaluate physiological state. This study will leverage existing monitoring efforts to track the N. flemingeri population during the winter and early spring. The research team will combine laboratory and field approaches to determine duration and synchronization of reproduction in emerging females and strategies for naupliar survival during low food conditions. Zooplankton samples will be processed to enumerate nauplii to species and to determine physiological condition of both nauplii and adult females. Gene expression studies will develop molecular markers for female dormancy and reproductive readiness and for naupliar growth and possible dormancy, which in turn will be used to evaluate field collected individuals. This will be the first comprehensive study to combine molecular and traditional tools to connect diapausing adults, naupliar production, and the resulting spring population of copepodites.</p>
Neocalanus Gulf of Alaska
largerWorkCitation
project
Collaborative Research: Molecular profiling of the ecophysiology of dormancy induction in calanid copepods of the Northern Gulf of Alaska LTER site
https://osprey.bco-dmo.org/project/720280
Collaborative Research: Molecular profiling of the ecophysiology of dormancy induction in calanid copepods of the Northern Gulf of Alaska LTER site
<p>NSF Award Abstract:<br />
The sub-arctic Pacific sustains major fisheries with nearly all commercially important species depending either directly or indirectly on lipid-rich copepods (Neocalanus flemingeri, Neocalanus plumchrus, Neocalanus cristatus and Calanus marshallae). In turn, these species depend on a short-lived spring algal bloom for growth and the accumulation of lipid stores in order to complete an annual life cycle that includes a period of dormancy. The intellectual thrust of this project measures how the timing and magnitude of algal blooms affect preparation for dormancy using a combination of field and experimental observations. The Northern Gulf of Alaska - with four calanid species that experience dormancy, steep environmental gradients, well-described phytoplankton bloom dynamics, and a concurrent NSF-LTER program - provides an unusual opportunity to identify the factors that affect dormancy preparation. Education and outreach plans are integrated with the research. Educational efforts focus on interdisciplinary opportunities for undergraduate, graduate and post-doctoral trainees. The project will generate content for existing graduate and undergraduate courses. U. of Alaska Fairbanks and U. Hawaii at Manoa are Alaska Native and Native Hawaiian Serving Institutions, and students from these groups will be recruited to participate in the project. Because fishing is a major industry in the Gulf of Alaska, outreach will communicate the role copepods play in marine ecosystems using the concept of a dynamic food web tied to production cycles.</p>
<p>Diapause (dormancy) and the accompanying accumulation of lipids in copepods have been identified as key drivers in high latitude ecosystems that support economically important fisheries, including those of the Gulf of Alaska. While the disappearance of lipid-rich copepods has been linked to severe declines in fish stocks, little is known about the environmental conditions that are required for the successful completion of the copepod's life cycle. A physiological profiling approach that measures relative gene expression will be used to test two alternative hypotheses: the lipid accumulation window hypothesis, which holds that individuals enter diapause only after they have accumulated sufficient lipid stores, and the developmental program hypothesis, which holds that once the diapause program is activated, progression occurs independent of lipid accumulation. The specific objectives are: 1) determine the effect of food levels during N. flemingeri copepodite stages on progression towards diapause using multiple physiological and developmental markers; 2) characterize the seasonal changes in the physiological profile of N. flemingeri across environmental gradients and across years; 3) compare physiological profiles across co-occurring calanid species (N. flemingeri, Neocalanus plumchrus, Neocalanus cristatus and Calanus marshallae); and 4) estimate the reproductive potential of the overwintering populations of N. flemingeri. The broader scientific significance includes the acquisition of new genomic data and molecular resources that will be made publicly available through established data repositories, and the development of new tools for routinely obtaining physiological profiles of copepods.</p>
<p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
<p> </p>
<p><strong>NOTE:</strong> Petra Lenz is a former Principal Investigator (PI) and Andrew Christie is a former Co-Principal Investigator (Co-PI) on this project (award #1756767). Daniel Hartline is the PI listed for the award #1756767 and is now a former Co-PI on this project.</p>
Diapause preparation
largerWorkCitation
project
eng; USA
oceans
Northern Gulf of Alaska; Gulf of Alaska
-149.7195
-145.4238
56.2321
60.8243
2015-05-06
2022-05-06
From projects that focused on the following 2 locations: 1. Gulf of Alaska; Seward Line 2. Northern Gulf of Alaska LTER
0
BCO-DMO catalogue of parameters from Multiyear RNA-Seq of Neocalanus flemingeri stages CV and Adult Female from the R/V Tiglax and R/V Sikuliaq in the Northern Gulf of Alaska from 2015-2022
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/932954.rdf
Name: Experiment_Accession
Units: unitless
Description: <p>Experiment metadata table (SRX) accession number in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA).</p>
http://lod.bco-dmo.org/id/dataset-parameter/932955.rdf
Name: Experiment_Title
Units: unitless
Description: <p>Title of the the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) experiment metadata table (SRX). Descriptive name of individual samples. All samples of stage CV individuals were preserved immediately. All samples of adult females labeled either Week 0 or Time 0 were preserved right after collection, samples with other time stamps (weeks or hours) were incubated in the laboratory for the specified amount of time prior to preservation</p>
http://lod.bco-dmo.org/id/dataset-parameter/932956.rdf
Name: Organism_Name
Units: unitless
Description: <p>species name (Crustacea: Copepoda: Calanoida)</p>
http://lod.bco-dmo.org/id/dataset-parameter/932957.rdf
Name: Station
Units: unitless
Description: <p>Station identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/932958.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Sampling location latitude, south is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/932959.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Sampling location longitude, west is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/932960.rdf
Name: Depth_Range
Units: meters (m)
Description: <p>Depth range of collection using depth stratified vertical net collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/932961.rdf
Name: Date
Units: unitless
Description: <p>Collection date of organism</p>
http://lod.bco-dmo.org/id/dataset-parameter/932962.rdf
Name: Year
Units: unitless
Description: <p>Collection year of organism</p>
http://lod.bco-dmo.org/id/dataset-parameter/932963.rdf
Name: Month
Units: unitless
Description: <p>Collection month of organism</p>
http://lod.bco-dmo.org/id/dataset-parameter/932964.rdf
Name: Day
Units: unitless
Description: <p>Collection day of organism</p>
http://lod.bco-dmo.org/id/dataset-parameter/932965.rdf
Name: Life_Stage
Units: unitless
Description: <p>Life stage (CV or Adult)</p>
http://lod.bco-dmo.org/id/dataset-parameter/932966.rdf
Name: Sex
Units: unitless
Description: <p>Sex</p>
http://lod.bco-dmo.org/id/dataset-parameter/932967.rdf
Name: BioProject
Units: unitless
Description: <p>NCBI BioProject accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/932968.rdf
Name: BioSample
Units: unitless
Description: <p>NCBI BioSample accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/932969.rdf
Name: Sample_Accession
Units: unitless
Description: <p>NCBI SRA Sample accession (SRS)</p>
http://lod.bco-dmo.org/id/dataset-parameter/932970.rdf
Name: SRA_Run_Accession
Units: unitless
Description: <p>Run accession in the Sequence Read Archive (SRA) at NCBI</p>
http://lod.bco-dmo.org/id/dataset-parameter/932971.rdf
Name: Study_Accession
Units: unitless
Description: <p>NCBI SRA study accession (SRP)</p>
http://lod.bco-dmo.org/id/dataset-parameter/932972.rdf
Name: Study_Title
Units: unitless
Description: <p>Title of the NCBI SRA study</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
91993
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/fb444544-405e-4aa5-a6c4-9a321ab98b33/content
download
https://doi.org/10.26008/1912/bco-dmo.922330.1
download
onLine
dataset
<p>In collaboration with the Seward Long-Term Observation Program (LTOP) (<a href="https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.sfos.uaf.edu%2Fsewardline%2F&amp;data=05%7C02%7Clynne.merchant%40whoi.edu%7Cf8155b0002c74a05c21508dcb70b16dc%7Cd44c5cc6d18c46cc8abd4fdf5b6e5944%7C0%7C0%7C638586505480119332%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&amp;sdata=2bhmDZMhb5aoswXOGXSshl0PMuf1laDLJO9XhomwMAw%3D&amp;reserved=0">http://www.sfos.uaf.edu/sewardline/</a>) and the NGA LTER Program (<a href="https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fnga.lternet.edu%2F&amp;data=05%7C02%7Clynne.merchant%40whoi.edu%7Cf8155b0002c74a05c21508dcb70b16dc%7Cd44c5cc6d18c46cc8abd4fdf5b6e5944%7C0%7C0%7C638586505480133405%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&amp;sdata=3HtOIqdFDdfNZVDohmwM00fLqMqe2goa3UTQQX5YIoI%3D&amp;reserved=0">https://nga.lternet.edu/</a>), we obtained Neocalanus flemingeri individuals during the annual April-May and September oceanographic cruises. During the spring cruises stage CV individuals were collected from four to six locations: spanning the inner shelf to outer shelf gradient along the Seward Line in the northern Gulf of Alaska and at least one station in adjoining Prince William Sound. Samples were collected using a CalVET net (53-µm mesh) towed vertically from 100 m depth to surface. Mixed plankton samples were immediately diluted with surface seawater, and maintained at ~5ºC prior to and during sorting. From each station actively swimming (healthy) N. flemingeri CVs were rapidly sorted under the microscope and preserved within 15 minutes to 1hr of the tow in RNALater Stabilization Reagent (QIAGEN). The rapid sorting of live plankton can lead to misidentifications given the presence of closely related congeners, thus species verification is recommended using the RNA-seq data to check the cytochrome c oxidase subunit 1 (mtCOI) sequence. In September, diapausing N. flemingeri adult females were sorted from collections obtained with a Midi Multinet towed vertically. Collections were diluted with seawater upon net retrieval. Individuals were sorted under the microscope from the 300-700 depth collections and either preserved immediately in RNALater or separated into holding containers for incubation experiments. In three years (2015, 2016, 2017) additional adult females were incubated for different lengths of time and preserved after a specified interval as indicated in the sample information. In July, 2019 we participated in a ship of opportunity cruise to the Gulf of Alaska Seamounts (SKQ201916S) and preserved diapausing adult females collected between 1000-2000 meters from two offshore stations (GAK19 and DeepQuinn).</p>
<p><em>RNA extraction, gene library preparation and RNA-seq</em></p>
<p>Total RNA was extracted from individual CV from each station 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 -80ºC. Total RNA concentration and quality were checked using an Agilent Model 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, USA). For each station, total RNA from three of the ten individuals with high quality RNA yields were selected for RNA-seq and shipped on dry ice to the University of Georgia Genomics 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 DNA. Each sample was tagged with an indexed adapter and they were simultaneously paired-end sequenced (PE150 or PE75 bp) using an Illumina NextSeq 500 instrument using High-Output Flow Cell.&nbsp;Data in NCBI are the raw sequence reads.</p>
Specified by the Principal Investigator(s)
<p>Raw sequence reads have been deposited with links to BioProject accession numbers PRJNA324453, and PRJNA324453 in the NCBI (National Center for Biotechnology Information) BioProject database (<a href="https://www.ncbi.nlm.nih.gov/bioproject/">https://www.ncbi.nlm.nih.gov/bioproject/</a>).</p>
Specified by the Principal Investigator(s)
To include BioProject, BioSample, and the SRA run accession to the submitted dataset, two tables from search results at NCBI were downloaded.
From a search at NCBI on the BioProject PRJNA324453 for the Adult Female dataset (https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA324453), the results table of 175 rows was downloaded and named SraRunInfo_adult_females.csv for Adult Females. And results table of 204 rows for a search at NCBI on the BioProject PRJNA496596 for the CV dataset (https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA496596) was downloaded and named SraRunInfo_cv.csv.
The NCBI metadata table and submitted table were then processed with the BCO-DMO laminar tool.
Imported data from the submitted file CV-2015-2022-BCO-DMO.xlsx sheet name "Sheet 1 - sra_result" into laminar.
Imported data from the submitted file AdultFem-2015-2021-BCO-DMO.xlsx sheet name "Sheet 1 - sra_result (1)" into laminar.
Renamed parameter names according to BCO-DMO naming standards by replacing spaces with underscores.
A date column was added using the values of the existing year, month and day columns with the parameter name “Date” and format %Y-%m-%d.
Renamed the parameter Depth to Depth_Range to convey the parameter represents a range of depths.
Join the NCBI metadata file SraRunInfo_adult_females.csv onto the submitted adult female data file AdultFem-2015-2021-BCO-DMO.xlsx on the Experimental Accession SRX column.
Join the NCBI metadata file SraRunInfo_cv.csv onto the submitted CV data file CV-2015-2022-BCO-DMO.xlsx on the Experimental Accession SRX column.
These two joined tables were then combined together vertically to form the final dataset file named 922330_v1_rna_seq_flemingeri_cv_and_adult_female_2015-2022.csv.
Taxonomic names in the dataset were checked using the World Register of Marine Species (WoRMS) taxa match tool. All names matched accepted names exactly as of 2024-07-26. A supplemental file using taxonomy values from WoRMS was created and named species_list.csv and contains the following columns: ScientificName, AphiaID, LSID, Authority, Kingdom, Phylum, Class, Order, Family, Genus, Species.
Specified by BCO-DMO Data Managers
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Illumina NextSeq 500
Illumina NextSeq 500
PI Supplied Instrument Name: Illumina NextSeq 500 PI Supplied Instrument Description:Desktop sequencer. Illumina NextSeq 500 instrument using High-Output Flow Cell. Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
Agilent Model 2100 Bioanalyzer
Agilent Model 2100 Bioanalyzer
PI Supplied Instrument Name: Agilent Model 2100 Bioanalyzer PI Supplied Instrument Description:Agilent Technologies, Inc., Santa Clara, CA, USA
The 2100 Bioanalyzer system is an established automated electrophoresis tool for the sample quality control of biomolecules. Instrument Name: Electrophoresis Chamber Instrument Short Name: Instrument Description: General term for an apparatus used in clinical and research laboratories to separate charged colloidal particles (or molecules) of varying size through a medium by applying an electric field.
Midi MultiNet
Midi MultiNet
PI Supplied Instrument Name: Midi MultiNet PI Supplied Instrument Description:0.25 m2 mouth area; 150 μm mesh nets Instrument Name: MultiNet Instrument Short Name:MultiNet Instrument Description: The MultiNet© Multiple Plankton Sampler is designed as a sampling system for horizontal and vertical collections in successive water layers. Equipped with 5 or 9 net bags, the MultiNet© can be delivered in 3 sizes (apertures) : Mini (0.125 m2), Midi (0.25 m2) and Maxi (0.5 m2). The system consists of a shipboard Deck Command Unit and a stainless steel frame to which 5 (or 9) net bags are attached by means of zippers to canvas. The net bags are opened and closed by means of an arrangement of levers that are triggered by a battery powered Motor Unit. The commands for actuation of the net bags are given via single or multi-conductor cable between the Underwater Unit and the Deck Command Unit. Although horizontal collections typically use a mesh size of 300 microns, mesh sizes from 100 to 500 may also be used. Vertical collections are also common. The shipboard Deck Command Unit displays all relevant system data, including the actual operating depth of the net system. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/NETT0099/
CalVET QuadNet
CalVET QuadNet
PI Supplied Instrument Name: CalVET QuadNet PI Supplied Instrument Description:53 µm mesh nets Instrument Name: Plankton Net Instrument Short Name:Plankton Net Instrument Description: A Plankton Net is a generic term for a sampling net that is used to collect plankton. It is used only when detailed instrument documentation is not available. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/22/
Cruise: TXS15
TXS15
R/V Tiglax
Community Standard Description
International Council for the Exploration of the Sea
R/V Tiglax
vessel
TXS15
Russell R. Hopcroft
https://www.ncei.noaa.gov/access/ocean-carbon-acidification-data-system/oceans/Coastal/seward.html
Report describing TXS15
Cruise: TXF15
TXF15
R/V Tiglax
Community Standard Description
International Council for the Exploration of the Sea
R/V Tiglax
vessel
TXF15
Russell R. Hopcroft
University of Alaska Fairbanks
https://www.ncei.noaa.gov/access/ocean-carbon-acidification-data-system/oceans/Coastal/seward.html
Report describing TXF15
Cruise: TXF16
TXF16
R/V Tiglax
Community Standard Description
International Council for the Exploration of the Sea
R/V Tiglax
vessel
TXF16
Russell R. Hopcroft
University of Alaska Fairbanks
https://www.ncei.noaa.gov/access/ocean-carbon-acidification-data-system/oceans/Coastal/seward.html
Report describing TXF16
Cruise: TXF17
TXF17
R/V Tiglax
Community Standard Description
International Council for the Exploration of the Sea
R/V Tiglax
vessel
TXF17
Russell R. Hopcroft
University of Alaska Fairbanks
https://www.ncei.noaa.gov/access/ocean-carbon-acidification-data-system/oceans/Coastal/seward.html
Report describing TXF17
Cruise: TXF18
TXF18
R/V Tiglax
Community Standard Description
International Council for the Exploration of the Sea
R/V Tiglax
vessel
TXF18
Russell R. Hopcroft
University of Alaska Fairbanks
https://nga.lternet.edu/wp-content/uploads/2019/04/Cruise-Report-TXF18.pdf
Report describing TXF18
Cruise: TXS19
TXS19
R/V Tiglax
Community Standard Description
International Council for the Exploration of the Sea
R/V Tiglax
vessel
TXS19
Russell R. Hopcroft
University of Alaska Fairbanks
https://nga.lternet.edu/wp-content/uploads/2019/10/Cruise-Report-TXS19.pdf
Report describing TXS19
Cruise: TXF19
TXF19
R/V Tiglax
Community Standard Description
International Council for the Exploration of the Sea
R/V Tiglax
vessel
TXF19
Russell R. Hopcroft
University of Alaska Fairbanks
https://nga.lternet.edu/wp-content/uploads/2020/02/Cruise-Report-TXF19.pdf
Report describing TXF19
Cruise: TXS17
TXS17
R/V Tiglax
Community Standard Description
International Council for the Exploration of the Sea
R/V Tiglax
vessel
TXS17
Russell R. Hopcroft
https://www.ncei.noaa.gov/access/ocean-carbon-acidification-data-system/oceans/Coastal/seward.html
Report describing TXS17
Cruise: SKQ201810S
SKQ201810S
R/V Sikuliaq
Community Standard Description
International Council for the Exploration of the Sea
R/V Sikuliaq
vessel
SKQ201810S
Russell R. Hopcroft
https://nga.lternet.edu/wp-content/uploads/2019/04/Cruise-Report-SKQ201810S.pdf
Report describing SKQ201810S
Cruise: SKQ201916S
SKQ201916S
R/V Sikuliaq
Community Standard Description
International Council for the Exploration of the Sea
R/V Sikuliaq
vessel
SKQ201916S
Russell R. Hopcroft
Cruise: SKQ202006S
SKQ202006S
R/V Sikuliaq
Community Standard Description
International Council for the Exploration of the Sea
R/V Sikuliaq
vessel
SKQ202006S
Russell R. Hopcroft
https://nga.lternet.edu/wp-content/uploads/2020/07/Cruise-Report-SKQ202006S_v2.pdf
Report describing SKQ202006S
Cruise: SKQ202106S
SKQ202106S
R/V Sikuliaq
Community Standard Description
International Council for the Exploration of the Sea
R/V Sikuliaq
vessel
SKQ202106S
Russell R. Hopcroft
Cruise: TXF21
TXF21
R/V Tiglax
Community Standard Description
International Council for the Exploration of the Sea
R/V Tiglax
vessel
TXF21
Russell R. Hopcroft
https://nga.lternet.edu/wp-content/uploads/2022/03/Cruise-Report-TGX202109.pdf
Report describing TXF21
Cruise: SKQ202207S
SKQ202207S
R/V Sikuliaq
Community Standard Description
International Council for the Exploration of the Sea
R/V Sikuliaq
vessel
SKQ202207S
Russell R. Hopcroft
R/V Tiglax
Community Standard Description
International Council for the Exploration of the Sea
R/V Tiglax
vessel
R/V Sikuliaq
Community Standard Description
International Council for the Exploration of the Sea
R/V Sikuliaq
vessel