http://lod.bco-dmo.org/id/dataset/528312
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
2014-09-16
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Links to a microarray and transcriptome for C. finmarchicus in the Gulf of Maine from 2008-2011 (CFINTRANSCRIPT project)
2017-12-06
publication
2017-12-06
revision
BCO-DMO Linked Data URI
2017-12-06
creation
http://lod.bco-dmo.org/id/dataset/528312
Petra H. Lenz
University of Hawaiʻi at Mānoa
principalInvestigator
Andrew E. Christie
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., Christie, A. E. (2017) Links to a microarray and transcriptome for C. finmarchicus in the Gulf of Maine from 2008-2011 (CFINTRANSCRIPT project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2017-12-06 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/528312 [access date]
Links to a microarray and transcriptome for C. finmarchicus Dataset Description: <p>This project focused on developing molecular tools based on relative gene expression to investigate physiological ecology of <em>Calanus finmarchicus</em> (Calanoida: Copepoda) in the Gulf of Maine. For this project, a <strong>custom microarray</strong> was developed for this species and tested on field and experimental data. Using <em>RNA-seq</em> technology, a <strong><em>de novo</em> transcriptome</strong> was obtained from RNA extracted from different developmental stages of <em>C. finmarchicus </em>from embryo to adult female.</p>
<p>Datasets generated through this project were deposited at NCBI (<a href="http://www.ncbi.nlm.nih.gov/">www.ncbi.nlm.nih.gov</a>) in 5 separate NCBI BioProjects:</p>
<ol>
<li>BioProject PRJNA151477 (<a href="http://www.ncbi.nlm.nih.gov/bioproject/PRJNA1495230" target="_blank">www.ncbi.nlm.nih.gov/bioproject/PRJNA151477</a>): Microarray platform information and relative expression data for lipid-rich vs. lipid-poor pre-adults (stage CV) and adult females maintained at high- and low-food levels.</li>
<li>BioProject PRJNA149523 (<a href="http://www.ncbi.nlm.nih.gov/bioproject/PRJNA1495230" target="_blank">www.ncbi.nlm.nih.gov/bioproject/PRJNA1495230</a>): Microarray platform information and relative expression data for pre-adults (stage CV) and adult females collected from depth (130-170 m) and from surface waters (0-30 m).</li>
<li>BioProject PRJNA236528 (<a href="http://www.ncbi.nlm.nih.gov/bioproject/PRJNA236528" target="_blank">www.ncbi.nlm.nih.gov/bioproject/PRJNA236528</a>): RNA-Seq data. Data includes biosample description, raw sequence data for each sample, and transcriptome shotgun assembly of sequences. <em>Calanus finmarchicus</em> transcriptome from 6 developmental stages (embryo, early nauplius, late nauplius, early copepodite, late copepodite and adult females).</li>
<li>BioProject PRJNA312028 <a href="http://www.ncbi.nlm.nih.gov/bioproject/PRJNA312028" target="_blank">(http://www.ncbi.nlm.nih.gov/bioproject/PRJNA312028</a>): RNA-Seq data. Data includes biosample description, raw sequence data for each sample, and transcriptome shotgun assembly of sequences. <em>Calanus finmarchicus</em> adult female transcriptome of Alexandrium fundyense response.</li>
<li>Bioproject: PRJNA356331(<a href="http://www.ncbi.nlm.nih.gov/bioproject/PRJNA356331" target="_blank">http://www.ncbi.nlm.nih.gov/bioproject/PRJNA356331</a>): RNA-Seq data. Data includes biosample description, raw sequence data for each sample, and transcriptome shotgun assembly of sequences <em>Calanus </em><em>finmarchicus</em> late nauplii (NV-NVI) transcriptome of <em>Alexandrium </em><em>fundyense</em> response.</li>
</ol>
<p><strong>Dataset Related References:</strong></p>
<p>Lenz, P.H., Roncalli, V., Hassett, R.P., Wu, L.-S., Cieslak, M.C., Hartline, D.K. and Christie, A.E. (2014) De novo assembly of a transcriptome for <em>Calanus </em><em>finmarchicus</em> (Crustacea, Copepoda) – the dominant zooplankter of the North Atlantic Ocean. Plos One 9: e885389 <a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0088589" target="_blank">DOI: 10.1371/journal.pone.0088589</a>)</p>
<p>Roncalli, V., Cieslak, M.C., Lenz, P.H. Transcriptomic responses of the calanoid copepod <em>Calanus </em><em>finmarchicus</em> to the saxitoxin producing dinoflagellate Alexandrium fundyense. Scientific Reports 6, Article number: 25708 (2016) <a href="http://www.nature.com/articles/srep25708">doi:10.1038/srep25708</a>.</p>
<p>Roncalli V., Cieslak M.C., Lenz P.H. (2016) Data from: Transcriptomic responses of the calanoid copepod <em>Calanus </em><em>finmarchicus</em> to the saxitoxin producing dinoflagellate Alexandrium fundyense. Dryad Digital Repository. <a href="http://dx.doi.org/10.5061/dryad.11978" target="_blank">http://dx.doi.org/10.5061/dryad.11978</a></p>
<p>Roncalli, V., Jungbluth, M.J., Lenz, P.H. (2016). Glutathione S-transferase regulation in <em>Calanus </em><em>finmarchicus</em> feeding on the toxic dinoflagellate Alexandrium fundyense. PloS One, 11(7): e0159563.</p>
<p>Roncalli, V., Turner, J.T., Kulis, D., Anderson, D.M., Lenz, P.H. (2016). The effect of the toxic dinoflagellate Alexandrium fundyense on the fitness of the calanoid copepod <em>Calanus </em><em>finmarchicus</em>. Harmful Algae, 51: 56-66</p>
<p>Roncalli, V., Lenz, P.H., Cieslak, M.C., Hartline, D.K. (2017). Complementary mechanisms for neurotoxin resistance in a copepod. Scientific Reports, 2017; 7: 14201, doi: 10.1038/s41598-017-14545-z</p>
<p><strong>Methodology References:</strong></p>
<p><u>Microarray</u></p>
<p>Lenz, P.H., Unal, E., Hassett, R.P., Smith, C.M., Bucklin, A., Christie, A.E. and Towle, D.W. (2012) Functional genomics resources for the North Atlantic copepod, <em>Calanus </em><em>finmarchicus</em>: EST database and physiological microarray. Comparative Biochemistry Physiology Part D, Genomics &amp; Proteomics, 7:110-123</p>
<p>Unal, E., Bucklin, A., Lenz, P.H. and Towle, D.W. (2013) Gene expression of the marine copepod <em>Calanus finmarchicus</em>: Responses to small-scale environmental variation in the Gulf of Maine (NW Atlantic Ocean). Journal of Experimental and Marine Biology and Ecology, 446:76-85</p>
<p><strong>Gene discovery studies using <em>C. finmarchicus</em> transcriptome:</strong></p>
<p>Christie, A.E., Fontanilla, T.M., Nesbit, K.T. and Lenz, P.H. (2013) Prediction of the protein components of a putative <em>Calanus </em><em>finmarchicus</em> (Crustacea, Copepoda) circadian signaling system using a de novo assembled transcriptome. Comparative Biochemistry and Physiology Part D, Genomics &amp; Proteomics, 8:165-193</p>
<p>Christie, A.E., Roncalli, V., Wu, L.-S., Garrote, C.L., Doak, T. and Lenz, P.H. (2013) Peptidergic signaling in <em>Calanus </em><em>finmarchicus</em> (Crustacea: Copepoda): in silico identification of putative peptide hormones and their receptors using a de novo assembled transcriptome. General and Comparative Endocrinology, 187:117-135</p>
<p>Christie, A.E., Roncalli, V., Batta Lona, P., McCoole, M.D., King, B.L., Bucklin, A., Hartline, D.K. and Lenz, P.H. (2013) In silico characterization of the insect diapause-associated protein couch potato (CPO) in <em>Calanus </em><em>finmarchicus</em> (Crustacea: Copepoda). Comparative Biochemistry and Physiology. Part D, Genomics &amp; Proteomics, 8:45-57.</p>
<p>Christie, A.E., Fontanilla, T.M., Roncalli, V., Cieslak, M.C. and Lenz, P.H. (2014) Diffusible gas transmitter signaling in the copepod crustacean <em>Calanus </em><em>finmarchicus</em>: Identification of the biosynthetic enzymes of nitric oxide (NO), carbon monoxide (CO) and hydrogen sulfide (H2S) using a de novo assembled transcriptome. General and Comparative Endocrinology 202: 76-86</p>
<p>Christie, A.E., Fontanilla, T.M., Roncalli, V., Cieslak, M.C. and Lenz, P.H. (2014) Identification and developmental expression of the enzymes responsible for dopamine, histamine, octopamine and serotonin biosynthesis in the copepod crustacean <em>Calanus </em><em>finmarchicus</em>. General and Comparative Endocrinology 195: 28-39.</p>
<p>Roncalli, V., Cieslak, M.C., Passamaneck, Y., Christie, A.E., &amp; Lenz, P.H. (2015). Glutathione S-Transferase (GST) Gene diversity in the crustacean <em>Calanus finmarchicus</em> - contributors to cellular detoxification. PloS One, 10(5): e012332.</p> Methods and Sampling: <p>See publications for detailed information on sample acquisition, experimental treatment and methodology.</p>
<p><u>Source of <em>C. finmarchicus</em>:</u></p>
<ol>
<li>Mid- and late copepodites and adults were collected during the summer (June and July, 2009, 2010, 2011, 2012) in the Gulf of Maine (Lat: 44°2′N; Long: 68°3′W) by towing a 75 cm diameter (560 μm mesh) net vertically from 75 m depth.&nbsp; These individuals were used in microarray (2009, 2010) and <em>RNA-Seq</em> (2011, 2012) studies.</li>
<li>Embryos, nauplii and early copepodites were obtained from offspring of field-collected adult females raised in laboratory cultures. These individuals were used in <em>RNA-Seq</em> studies.</li>
<li>Late stage copepodites (CV) for microarray analysis (Unal et al. 2013) were collected in April 17, 2008 from Wilkinson Basin in the Gulf of Maine as part of a multi-year time-series study by the Center for Coastal Ocean Observation and Analysis (COOA) at the University of New Hampshire, USA.&nbsp; Vertically-stratified plankton tows (0-30 m and 130-170 m) were taken using a 1/4-m MOCNESS equipped with 150 μm mesh nets.</li>
</ol>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1040597 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1040597
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
Andrew E. Christie
University of Hawaiʻi at Mānoa
Bekesy Laboratory of Neurobiology 1993 East-West Road
Honolulu
Hawaii
96822
crabman@pbrc.hawaii.edu
pointOfContact
asNeeded
Unknown
BioProject
description
species
date
lat
lon
comment
Automated Sequencer
theme
None, User defined
experiment id
experiment type
species scientific name (binomial)
date
latitude
longitude
comments
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Electrophoresis Chamber
instrument
BCO-DMO Standard Instruments
GoME_2008-2011
service
Deployment Activity
Gulf of Maine
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.
Application of transcriptomics to investigate organism-environment relationships in marine zooplankton
https://osprey.bco-dmo.org/project/527901
Application of transcriptomics to investigate organism-environment relationships in marine zooplankton
<p>This project focused on developing molecular tools based on relative gene expression to investigate physiological ecology of <em>Calanus finmarchicus</em> (Calanoida: Copepoda). For this project, a <strong>custom microarray</strong> was developed and tested for this species. In addition, using <em>RNA-seq</em> technology, a <strong><em>de novo</em> transcriptome</strong> was obtained from RNA extracted from different developmental stages of <em>C. finmarchicus </em>from embryo to adult female. </p>
<p><em>Description from NSF award abstract:</em><br />
This project will develop transcriptomics approaches to investigate gene regulation as a function of environmental cycles and in response to experimental manipulation. Currently, there are few tools to establish physiological state of marine zooplankton, in particular for oceanic species. Molecular approaches based on quantifying the transcriptome could serve as powerful tools to obtain a physiological profile for individuals and groups of individuals collected in the field. In combination with laboratory experiments, transcriptome analysis will provide a new approach to understanding organism-environment interactions in the pelagic zone.</p>
<p>The PI will focus on a model planktonic crustacean, <em>Calanus finmarchicus</em>, to develop the molecular tools. <em>C. finmarchicus</em>, a calanoid copepod, is highly abundant in the North Atlantic, with populations extending from the Gulf of Maine and Labrador Sea to the North Sea. Pyrosequencing and microarray technologies will be used to develop a diagnostic tool to determine physiological state in <em>C. finmarchicus</em>. The goal of having a measurement of physiological state is to determine if individuals in the population are growing, are synthesizing or catabolizing storage lipids, and are metabolically active and/or experiencing environmental stress. Specific objectives of this project include:</p>
<p>1. High throughput sequencing of <em>C. finmarchicus</em> transcriptome from pre-adult (copepodid stage V [CV]) individuals representing distinct phases of the annual cycle (late spring-early summer, early fall, diapausing individuals).</p>
<p>2. Analysis of the sequence data for discovery of seasonally regulated genes for the development of an ecologically relevant microarray. Probes for this microarray will include seasonally regulated genes, genes involved in the environmental stress response and control genes.</p>
<p>3. Preliminary testing of microarray on existing samples collected from the Gulf of Maine and stored in liquid nitrogen, as well as on experimentally manipulated animals.</p>
CFINTRANSCRIPT
largerWorkCitation
project
eng; USA
biota
oceans
Gulf of Maine
2017-12-06
Gulf of Maine, North Atlantic
0
BCO-DMO catalogue of parameters from Links to a microarray and transcriptome for C. finmarchicus in the Gulf of Maine from 2008-2011 (CFINTRANSCRIPT 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
http://lod.bco-dmo.org/id/dataset-parameter/528493.rdf
Name: BioProject
Units: unitless
Description: <p>NCBI BioProject number</p>
http://lod.bco-dmo.org/id/dataset-parameter/528494.rdf
Name: description
Units: unitless
Description: <p>type of analysis</p>
http://lod.bco-dmo.org/id/dataset-parameter/528495.rdf
Name: species
Units: unitless
Description: <p>specimen species</p>
http://lod.bco-dmo.org/id/dataset-parameter/528496.rdf
Name: date
Units: yyyy-month
Description: <p>For microarrays, this is the date specimens were collected; for transcriptomes, adult and CV were collected on Jul 14, 2011; embryo-CII were raised in the lab, and were produced by females collected both June 26 and July 14, 2011.</p>
http://lod.bco-dmo.org/id/dataset-parameter/528497.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/528498.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/528499.rdf
Name: comment
Units: unitless
Description: <p>comments</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
858
https://datadocs.bco-dmo.org/file/N77GrlnhZ2pWJl/CfinTrans_access_nums.csv
CfinTrans_access_nums.csv
Primary data file for dataset ID 528312
download
https://osprey.bco-dmo.org/dataset/528312/data/download
download
onLine
dataset
<p>See publications for detailed information on sample acquisition, experimental treatment and methodology.</p>
<p><u>Source of <em>C. finmarchicus</em>:</u></p>
<ol>
<li>Mid- and late copepodites and adults were collected during the summer (June and July, 2009, 2010, 2011, 2012) in the Gulf of Maine (Lat: 44°2′N; Long: 68°3′W) by towing a 75 cm diameter (560 μm mesh) net vertically from 75 m depth.&nbsp; These individuals were used in microarray (2009, 2010) and <em>RNA-Seq</em> (2011, 2012) studies.</li>
<li>Embryos, nauplii and early copepodites were obtained from offspring of field-collected adult females raised in laboratory cultures. These individuals were used in <em>RNA-Seq</em> studies.</li>
<li>Late stage copepodites (CV) for microarray analysis (Unal et al. 2013) were collected in April 17, 2008 from Wilkinson Basin in the Gulf of Maine as part of a multi-year time-series study by the Center for Coastal Ocean Observation and Analysis (COOA) at the University of New Hampshire, USA.&nbsp; Vertically-stratified plankton tows (0-30 m and 130-170 m) were taken using a 1/4-m MOCNESS equipped with 150 μm mesh nets.</li>
</ol>
Specified by the Principal Investigator(s)
<p><strong>Brief summary of methods</strong></p>
<p>RNA was extracted from fresh and preserved samples.&nbsp; Samples were preserved either in RNALater or in liquid nitrogen.&nbsp; RNA was extracted using the Qiagen RNeasy Mini or Mini Plus kits for both microarray and RNASeq. Quality and quantity of RNA was checked in an Agilent 2100 Bioanalyzer prior to further processing of samples as described in the references.&nbsp; Microarray hybridization incubations were performed in a Micro Array User Interface (MAUI) Hybridization Chamber (BioMicro Systems). For the RNASeq, high quality total RNA samples were sent to the Georgia Genomics Facility at U. of Georgia. Multiplex cDNA gene libraries were prepared from the samples, and these were sent to Alpha Hudson Institute for Biotechnology for paired 100-base-pair sequencing on an Illumina HISeq 2000 instrument.</p>
<p>The RNASeq data were used to assemble and annotate a de novo transcriptome. Raw reads were analyzed for quality: low quality and over-represented sequences were removed, and sequences were trimmed to remove the random primer sequences (first 9 bases) prior to assembly using Trinity (Trinity 2012-03-17-IU_ZIH_TUNED software, on the National Center for Genome Analysis Support’s [NCGAS; Indiana University, Bloomington, IN, USA] Mason Linux cluster; each node of this computer system is composed of four Intel Xeon L7555 8-core processors running at 1.87 GHz with 512 GB of memory. Assembled contigs were annotated using Blast2GO software and targeted gene discovery workflows.</p>
Specified by the Principal Investigator(s)
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
Automated Sequencer
Automated Sequencer
PI Supplied Instrument Name: Automated Sequencer PI Supplied Instrument Description:HiSeq2000 Illumina sequencer, in conjunction with Trinity software. Located at the Alpha Hudson Institute for Biotechnology, Huntsville, Alabama. 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.
PI Supplied Instrument Name: PI Supplied Instrument Description:2100 Bioanalyzer, Agilent Technologies, to check the quality and quantity of RNA. 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.
Deployment: GoME_2008-2011
GoME_2008-2011
Lenz_lab
laboratory
GoME_2008-2011
Petra H. Lenz
University of Hawaiʻi at Mānoa
Lenz_lab
laboratory