http://lod.bco-dmo.org/id/dataset/768550
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
2019-05-23
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
DYEatom Metatranscriptome metadata from RV/Point Sur cruise PS1312 in the Monterey Bay area, June-July 2013
2019-05-29
publication
2019-05-29
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2019-07-31
publication
https://doi.org/10.1575/1912/bco-dmo.768550.1
Kimberlee Thamatrakoln
Rutgers University
principalInvestigator
Andrew E. Allen
J. Craig Venter Institute
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: Thamatrakoln, K., Allen, A. (2019) DYEatom Metatranscriptome metadata from RV/Point Sur cruise PS1312 in the Monterey Bay area, June-July 2013. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2019-05-29 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.768550.1 [access date]
Dataset Description: <p>Metadata for assembled contigs and ORFS from metatranscriptome analysis from CTD casts in the Monterey Bay area on RV/Point Sur cruise PS1312, June-July 2013.</p> Methods and Sampling: <p>Water was collected using Niskin bottles mounted on a CTD rosette. Biomass for metatranscriptomic analysis was collected by filtration (after a 200 micron pre-filtration) onto 47 mm, 1.2-micron pore size polycarbonate filters at &lt;5 psi for no longer than 15 min to minimize degradation. Filters were flash frozen in liquid nitrogen and stored at -80 degrees C. Upon analysis, filters were thawed and RNA was extracted using TRIzol reagent according to the manufacturer’s protocol (Life Technologies). Metatranscriptome libraries were constructed using 500 ng of total RNA and a TruSeq RNA Sample Preparation Kit (Illumina; San Diego, CA) following the Low-Throughput protocol. The mean size of the final libraries was confirmed to be between 359-420 base pairs (bp) using an Agilent Bioanalyzer 2100 (Santa Clara, CA). Libraries were paired-end sequenced (2x150 bp) on the Illumina HiSeq platform. ORFs were annotated via BLASTP alignment (e-value &gt; 10-3) to a comprehensive protein database, phyloDB, as well as screened for function de-novo by assigning Pfams, TIGRfams and transmembrane tmHMMs with hmmer 3.0 (http://hmmer.org/). PhyloDB 1.076 consists of 24,509,327 peptides from 19,962 viral, 230 archaeal, 4,910 bacterial, and 894 eukaryotic taxa. It includes peptides at KEGG, GenBank, JGI, ENSEMBL, CAMERA, and various other repositories, as well as from the 410 taxa of the Marine Microbial Eukaryotic Transcriptome Sequencing Project. Taxonomic annotation of ORFs was also conducted via BLASTP to phyloDB.</p>
<p>All cruise related data are available publicly at the Biological and Chemical Oceanography Data Management Office under project number 550825 (https://www.bco-dmo.org/project/550825). The metatranscriptomic data have been deposited in the NCBI sequence read archive (BioProject accession no. PRJNA528986: BioSample accession nos. SAMN11263616 - SAMN11263639 and SAMN11258802-SAMN11258825). Assembled contigs used in this study can also be found at <a href="https://scripps.ucsd.edu/labs/aallen/data/">https://scripps.ucsd.edu/labs/aallen/data/</a>.</p>
<p>Unassembled reads and rRNA data from this study:&nbsp;https://www.ncbi.nlm.nih.gov/bioproject/PRJNA528986<br />
Assembled contigs: See Supplemental Files.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1333929 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1333929
completed
Kimberlee Thamatrakoln
Rutgers University
848-932-3464
Department of Marine and Coastal Sciences 71 Dudley Road
New Brunswick
NJ
08901
USA
thamat@marine.rutgers.edu
pointOfContact
Andrew E. Allen
J. Craig Venter Institute
858-200-1826
4120 Capricorn Lane
La Jolla
CA
92037
USA
aallen@jcvi.org
pointOfContact
asNeeded
Dataset Version: 1
Unknown
BioProject_type
BioProject_id
BioSample
Sample_name
SRA_id
Package_type
version
Accession
ID
cruise_id
CTD_cast
Lat
Long
Date_collection
station
depth_m
Illumina HiSeq platform
theme
None, User defined
experiment type
experiment id
accession number
sample identification
sample type
No BCO-DMO term
Cruise identfier
cast
latitude
longitude
date
station
depth
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
instrument
BCO-DMO Standard Instruments
PS1312
service
Deployment Activity
Central California Coast
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.
Linking physiological and molecular aspects of diatom silicification in field populations
https://osprey.bco-dmo.org/project/558198
Linking physiological and molecular aspects of diatom silicification in field populations
<p><em>Description from NSF award abstract:</em><br />
Diatoms, unicellular, eukaryotic photoautotrophs, are among the most ecologically successful and functionally diverse organisms in the ocean. In addition to contributing one-fifth of total global primary productivity, diatoms are also the largest group of silicifying organisms in the ocean. Thus, diatoms form a critical link between the carbon and silicon (Si) cycles. The goal of this project is to understand the molecular regulation of silicification processes in natural diatom populations to better understand the processes controlling diatom productivity in the sea. Through culture studies and two research cruises, this research will couple classical measurements of silicon uptake and silica production with molecular and biochemical analyses of Silicification-Related Gene (SiRG) and protein expression. The proposed cruise track off the West Coast of the US will target gradients in Si and iron (Fe) concentrations with the following goals: 1) Characterize the expression pattern of SiRGs, 2) Correlate SiRG expression patterns to Si concentrations, silicon uptake kinetics, and silica production rates, 3) Develop a method to normalize uptake kinetics and silica production to SiRG expression levels as a more accurate measure of diatom activity and growth, 4) Characterize the diel periodicity of silica production and SiRG expression.</p>
<p>It is estimated that diatoms process 240 Teramoles of biogenic silica each year and that each molecule of silicon is cycled through a diatom 39 times before being exported to the deep ocean. Decades of oceanographic and field research have provided detailed insight into the dynamics of silicon uptake and silica production in natural populations, but a molecular understanding of the factors that influence silicification processes is required for further understanding the regulation of silicon and carbon fluxes in the ocean. Characterizing the genetic potential for silicification will provide new information on the factors that regulate the distribution of diatoms and influence in situ rates of silicon uptake and silica production. This research is expected to provide significant information about the molecular regulation of silicification in natural populations and the physiological basis of Si limitation in the sea.</p>
Diatom Silicification
largerWorkCitation
project
eng; USA
biota
oceans
Central California Coast
-123.969
-121.981
36.455
38.265
2013-06-28
2013-07-05
Oregon/California Coastal Upwelling Zone, between 34-44N and 120-124W
0
BCO-DMO catalogue of parameters from DYEatom Metatranscriptome metadata from RV/Point Sur cruise PS1312 in the Monterey Bay area, June-July 2013
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/769688.rdf
Name: BioProject_type
Units: unitless
Description: <p>NCBI BioProject type</p>
http://lod.bco-dmo.org/id/dataset-parameter/769689.rdf
Name: BioProject_id
Units: unitless
Description: <p>NCBI BioProject identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/769690.rdf
Name: BioSample
Units: unitless
Description: <p>NCBI BioSample identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/769691.rdf
Name: Sample_name
Units: unitless
Description: <p>NCBI Sample identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/769692.rdf
Name: SRA_id
Units: unitless
Description: <p>NCBI SRA identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/769693.rdf
Name: Package_type
Units: unitless
Description: <p>NCBI Package type</p>
http://lod.bco-dmo.org/id/dataset-parameter/769694.rdf
Name: version
Units: unitless
Description: <p>NCBI version</p>
http://lod.bco-dmo.org/id/dataset-parameter/769695.rdf
Name: Accession
Units: unitless
Description: <p>NCBI Accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/769696.rdf
Name: ID
Units: unitless
Description: <p>NCBI ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/769697.rdf
Name: cruise_id
Units: unitless
Description: <p>cruise identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/769698.rdf
Name: CTD_cast
Units: unitless
Description: <p>CTD cast number</p>
http://lod.bco-dmo.org/id/dataset-parameter/769699.rdf
Name: Lat
Units: decimal degrees
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/769700.rdf
Name: Long
Units: decimal degrees
Description: <p>longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/769701.rdf
Name: Date_collection
Units: unitless
Description: <p>date of collection; formatted as yyyy-mm-dd</p>
http://lod.bco-dmo.org/id/dataset-parameter/769702.rdf
Name: station
Units: unitless
Description: <p>station number</p>
http://lod.bco-dmo.org/id/dataset-parameter/769703.rdf
Name: depth_m
Units: meters
Description: <p>depth of sample</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
11400
https://darchive.mblwhoilibrary.org/bitstream/1912/24379/1/dataset-768550_dyeatom-metatranscriptome-accessions-and-assembled-contigs__v1.tsv
download
https://doi.org/10.1575/1912/bco-dmo.768550.1
download
onLine
dataset
<p>Water was collected using Niskin bottles mounted on a CTD rosette. Biomass for metatranscriptomic analysis was collected by filtration (after a 200 micron pre-filtration) onto 47 mm, 1.2-micron pore size polycarbonate filters at &lt;5 psi for no longer than 15 min to minimize degradation. Filters were flash frozen in liquid nitrogen and stored at -80 degrees C. Upon analysis, filters were thawed and RNA was extracted using TRIzol reagent according to the manufacturer’s protocol (Life Technologies). Metatranscriptome libraries were constructed using 500 ng of total RNA and a TruSeq RNA Sample Preparation Kit (Illumina; San Diego, CA) following the Low-Throughput protocol. The mean size of the final libraries was confirmed to be between 359-420 base pairs (bp) using an Agilent Bioanalyzer 2100 (Santa Clara, CA). Libraries were paired-end sequenced (2x150 bp) on the Illumina HiSeq platform. ORFs were annotated via BLASTP alignment (e-value &gt; 10-3) to a comprehensive protein database, phyloDB, as well as screened for function de-novo by assigning Pfams, TIGRfams and transmembrane tmHMMs with hmmer 3.0 (http://hmmer.org/). PhyloDB 1.076 consists of 24,509,327 peptides from 19,962 viral, 230 archaeal, 4,910 bacterial, and 894 eukaryotic taxa. It includes peptides at KEGG, GenBank, JGI, ENSEMBL, CAMERA, and various other repositories, as well as from the 410 taxa of the Marine Microbial Eukaryotic Transcriptome Sequencing Project. Taxonomic annotation of ORFs was also conducted via BLASTP to phyloDB.</p>
<p>All cruise related data are available publicly at the Biological and Chemical Oceanography Data Management Office under project number 550825 (https://www.bco-dmo.org/project/550825). The metatranscriptomic data have been deposited in the NCBI sequence read archive (BioProject accession no. PRJNA528986: BioSample accession nos. SAMN11263616 - SAMN11263639 and SAMN11258802-SAMN11258825). Assembled contigs used in this study can also be found at <a href="https://scripps.ucsd.edu/labs/aallen/data/">https://scripps.ucsd.edu/labs/aallen/data/</a>.</p>
<p>Unassembled reads and rRNA data from this study:&nbsp;https://www.ncbi.nlm.nih.gov/bioproject/PRJNA528986<br />
Assembled contigs: See Supplemental Files.</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing Notes:</strong><br />
- created flat table from info at GenBank and metadata submitted by PI<br />
- added conventional header with dataset name, PI name, version date<br />
- modified parameter names to conform with BCO-DMO naming conventions<br />
- added cruise_id</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
Illumina HiSeq platform
Illumina HiSeq platform
PI Supplied Instrument Name: Illumina HiSeq platform 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.
Cruise: PS1312
PS1312
R/V Point Sur
Community Standard Description
International Council for the Exploration of the Sea
R/V Point Sur
vessel
PS1312
Jeffrey W. Krause
Dauphin Island Sea Lab
R/V Point Sur
Community Standard Description
International Council for the Exploration of the Sea
R/V Point Sur
vessel