http://lod.bco-dmo.org/id/dataset/665427
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
2016-11-21
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) location information on samples obtained on Gould (LMG1411) in the Western Antarctica Peninsula during 2014 (Polar Transcriptomes project)
2016-11-21
publication
2016-11-21
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2019-04-17
publication
https://doi.org/10.1575/1912/bco-dmo.665427.1
Adrian Marchetti
University of North Carolina at Chapel Hill
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: Marchetti, A. (2016) Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) location information on samples obtained on Gould (LMG1411) in the Western Antarctica Peninsula during 2014 (Polar Transcriptomes project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2016-11-21 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.665427.1 [access date]
MMETSP location information on samples obtained on LMG1411. Dataset Description: <pre>
<span style="font-family:arial,helvetica,sans-serif">MMETSP location information on samples obtained on LMG1411.</span></pre>
<p>Diatom isolates were obtained from the Western Antarctic Peninsula surface waters.</p> Methods and Sampling: <p>Nine species of diatoms were isolated from the Western Antarctic Peninsula along the PalmerLTER sampling grid in 2013 and 2014. Isolations were performed using an Olympus CKX41 inverted microscope by single cell isolation with a micropipette (Anderson 2005). Diatom species were identified by morphological characterization and 18S rRNA gene (rDNA) sequencing. DNA was extracted with the DNeasy Plant Mini Kit according to the manufacturer’s protocols (Qiagen). Amplification of the nuclear 18S rDNA region was achieved with standard PCR protocols using eukaryotic-specific, universal 18S forward and reverse primers. Primer sequences were obtained from Medlin et al. (1982). The length of the region amplified is approximately 1800 base pairs (bp).&nbsp;Pseudo-nitzschia&nbsp;species are often difficult to identify by their 18S rDNA sequence, therefore, additional support of the taxonomic identification of&nbsp;P.&nbsp;subcurvata&nbsp;was provided through sequencing of the 18S-ITS1-5.8S regions. Amplification of this region was performed with the 18SF-euk and 5.8SR_euk primers of Hubbard et al. (2008). PCR products were purified using either QIAquick PCR Purification Kit (Qiagen) or ExoSAP-IT (Affymetrix) and sequenced by Sanger DNA sequencing (Genewiz). Sequences were edited using Geneious Pro software (<a href="http://www.geneious.com" target="_blank">http://www.geneious.com</a>, Kearse et al., 2012) and BLASTn sequence homology searches were performed against the NCBI nucleotide non-redundant (nr) database to determine species with a cutoff identity of 98%.</p>
<p>Diatom phylogenetic analysis was performed with Geneious Pro and included 71 additional diatom 18S rDNA sequences from publically available genomes and transcriptomes, including those in the MMETSP database. Diatom sequences were trimmed to the same length and aligned with MUSCLE (Edgar 2004). A phylogenetic tree was created in Mega with the Maximum-likelihood method of tree reconstruction, the Jukes-Cantor genetic distance model (Jukes and Cantor 1969), and 100 bootstrap replicates.</p>
<p>Illumina TruSeq adapters and poly-A tails were trimmed from raw reads using the Fastx_toolkit clipper function. Fastq_quality_filter was used to remove poor quality sequences, such that remaining sequences had a minimum quality score of 20 with a minimum of 80% of bases within a&nbsp;read&nbsp;meeting this quality score requirement. Any remaining raw sequences less than 50 base pairs in length were also removed. Merged files were assembled&nbsp;de novo&nbsp;using Trinity (Grabherr et al. 2011). The resulting assembly was filtered to remove contigs less than 200 bp in length. Trinity-assembled contigs which exhibited sequence overlap were grouped into isogroups which were then used for sequence homology searches (BLASTx E-value ≤ 10-4) against the Kyoto Encyclopedia of Genes and Genomes (KEGG) databases (Kanehisa 2006).</p>
<p>BUSCO (Benchmarking Universal Single-Copy Orthologs) was used to assess the completeness of genomes and transcriptomes based on sets of&nbsp;single copy&nbsp;orthologous groups derived from OrthoDB that are highly conserved within multiple lineages (Felipe et al. 2015). Completed, duplicated and fragmented orthologs were determined by meeting an ‘expected score’ and having aligned sequences within two standard deviations of the BUSCO gene’s length.&nbsp;A second&nbsp;metric of completeness was performed by evaluating conserved pathways, such as the ribosome and spliceosome, using the single-directional&nbsp;best-hit&nbsp;method in the KEGG Automatic Annotation Server (KAAS) (Moriya et al. 2007).&nbsp;Finally&nbsp;contiguity,&nbsp;was calculated at the 0.75 level as according to Martin and Wang (2011) with custom scripts.</p>
<p>For each transcriptome, unassembled sequence reads were aligned to the final Trinity assembly using Bowtie 2 (Langmead 2012). Mapped reads were normalized by the Reads per Kilobase per Million reads method (RPKM) (Mortazavi et al. 2008).</p>
<p>Gene biogeographical distributions -&nbsp;20 genes of interest were selected in the study to investigate the molecular basis of iron and light limitation in polar diatoms. Reference sequences for each of these genes were obtained from the&nbsp;F.&nbsp;cylindrus&nbsp;and&nbsp;P.&nbsp;tricornutum&nbsp;JGI genome portals and&nbsp;T.&nbsp;pseudonana&nbsp;and&nbsp;T.&nbsp;oceanica&nbsp;NCBI and GenBank repositories. Reference sequences were identified in the transcriptomes by translated nucleotide homology searches (tBLASTn) with an e-value cutoff of &lt;10-5. A reciprocal tBLASTn homology search was performed for each transcriptome against the KEGG GENES database, using the single-directional&nbsp;best-hit&nbsp;method in the KAAS online tool to ensure consistent gene annotations (Moriya et al. 2007).</p>
<p>Subsequently, reference sequences were identified in the MMETSP protein database by BLASTp (e-value &lt;10-5) homology searches among the diatom transcriptomes. The transcriptomes and their associated latitude and longitude were obtained from iMicrobe Data Commons (Project Code CAM_P_0001000) and the National Center for Marine Algae and Microbiota (NCMA). Custom Matlab scripts allowed global biogeographical distribution of key genes of interest to be mapped.</p>
Funding provided by NSF Office of Polar Programs (formerly NSF PLR) (NSF OPP) Award Number: PLR-1341479 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1341479
completed
Adrian Marchetti
University of North Carolina at Chapel Hill
919-843-3473
123 South Rd.
Chapel Hill
NC
27514
USA
amarchet@email.unc.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
phylum_max
genus_max
species_max
strain_max
TAXON_ID_mean
MMETSP_ID_paste
NCGR_PEP_ID_paste
evalue_paste
lat
lon
evalue_mean
lon_360
lat2
Agilent Bioanalyzer 2100
Olympus CKX41
theme
None, User defined
phylum
genus
species scientific name (binomial)
No BCO-DMO term
taxon
latitude
longitude
longitude from 0 to 360 degrees
featureType
BCO-DMO Standard Parameters
Bioanalyzer
Inverted Microscope
instrument
BCO-DMO Standard Instruments
LMG1401
service
Deployment Activity
Antarctica
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.
Iron and Light Limitation in Ecologically Important Polar Diatoms: Comparative Transcriptomics and Development of Molecular Indicators
http://www.nsf.gov/awardsearch/showAward?AWD_ID=1341479
Iron and Light Limitation in Ecologically Important Polar Diatoms: Comparative Transcriptomics and Development of Molecular Indicators
<p>The Southern Ocean surrounding Antarctica is changing rapidly in response to Earth's warming climate. These changes will undoubtedly influence communities of primary producers (the organisms at the base of the food chain, particularly plant-like organisms using sunlight for energy) by altering conditions that influence their growth and composition. Because primary producers such as phytoplankton play an important role in global biogeochemical cycling, it is essential to understand how they will respond to changes in their environment. The growth of phytoplankton in certain regions of the Southern Ocean is constrained by steep gradients in chemical and physical properties that vary in both space and time. Light and iron have been identified as key variables influencing phytoplankton abundance and distribution within Antarctic waters. Microscopic algae known as diatoms are dominant members of the phytoplankton and sea ice communities, accounting for significant proportions of primary production. The overall objective of this project is to identify the molecular bases for the physiological responses of polar diatoms to varying light and iron conditions. The project should provide a means of evaluating the extent these factors regulate diatom growth and influence net community productivity in Antarctic waters. The project will also further the NSF goals of making scientific discoveries available to the general public and of training new generations of scientists. It will facilitate the teaching and learning of polar-related topics by translating the research objectives into readily accessible educational materials for middle-school students. This project will also provide funding to enable a graduate student and several undergraduate students to be trained in the techniques and perspectives of modern biology.</p>
<p>Although numerous studies have investigated how polar diatoms are affected by varying light and iron, the cellular mechanisms leading to their distinct physiological responses remain unknown. Using comparative transcriptomics, the expression patterns of key genes and metabolic pathways in several ecologically important polar diatoms recently isolated from Antarctic waters and grown under varying iron and irradiance conditions will be examined. In addition, molecular indicators for iron and light limitation will be developed within these polar diatoms through the identification of iron- and light-responsive genes -- the expression patterns of which can be used to determine their physiological status. Upon verification in laboratory cultures, these indicators will be utilized by way of metatranscriptomic sequencing to examine iron and light limitation in natural diatom assemblages collected along environmental gradients in Western Antarctic Peninsula waters. In order to fully understand the role phytoplankton play in Southern Ocean biogeochemical cycles, dependable methods that provide a means of elucidating the physiological status of phytoplankton at any given time and location are essential.</p>
Polar_Transcriptomes
largerWorkCitation
project
eng; USA
oceans
Antarctica
58.853
132.4
-77.8333
77.8333
2014-01-01
2014-12-31
Antarctica
0
BCO-DMO catalogue of parameters from Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) location information on samples obtained on Gould (LMG1411) in the Western Antarctica Peninsula during 2014 (Polar Transcriptomes 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/665441.rdf
Name: phylum_max
Units: unitless
Description: <p>Phylum</p>
http://lod.bco-dmo.org/id/dataset-parameter/665442.rdf
Name: genus_max
Units: unitless
Description: <p>Genus</p>
http://lod.bco-dmo.org/id/dataset-parameter/665443.rdf
Name: species_max
Units: unitless
Description: <p>Species</p>
http://lod.bco-dmo.org/id/dataset-parameter/665444.rdf
Name: strain_max
Units: unitless
Description: <p>Strain ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/665445.rdf
Name: TAXON_ID_mean
Units: unitless
Description: <p>Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) taxon ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/665446.rdf
Name: MMETSP_ID_paste
Units: unitless
Description: <p>Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) taxon ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/665447.rdf
Name: NCGR_PEP_ID_paste
Units: unitless
Description: <p>National Center for Genome Resources (NCGR) protein ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/665448.rdf
Name: evalue_paste
Units: unitless
Description: <p>E-value</p>
http://lod.bco-dmo.org/id/dataset-parameter/665449.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude mean; N is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/665450.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude mean; E is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/665451.rdf
Name: evalue_mean
Units: unitless
Description: <p>Average E-value</p>
http://lod.bco-dmo.org/id/dataset-parameter/665452.rdf
Name: lon_360
Units: decimal degrees
Description: <p>360 Longitude; E is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/665453.rdf
Name: lat2
Units: decimal degrees
Description: <p>Latitude; N is positive</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
11168
https://darchive.mblwhoilibrary.org/bitstream/1912/24036/1/dataset-665427_mmetsp-locations-and-e-values__v1.tsv
download
https://doi.org/10.1575/1912/bco-dmo.665427.1
download
onLine
dataset
<p>Nine species of diatoms were isolated from the Western Antarctic Peninsula along the PalmerLTER sampling grid in 2013 and 2014. Isolations were performed using an Olympus CKX41 inverted microscope by single cell isolation with a micropipette (Anderson 2005). Diatom species were identified by morphological characterization and 18S rRNA gene (rDNA) sequencing. DNA was extracted with the DNeasy Plant Mini Kit according to the manufacturer’s protocols (Qiagen). Amplification of the nuclear 18S rDNA region was achieved with standard PCR protocols using eukaryotic-specific, universal 18S forward and reverse primers. Primer sequences were obtained from Medlin et al. (1982). The length of the region amplified is approximately 1800 base pairs (bp).&nbsp;Pseudo-nitzschia&nbsp;species are often difficult to identify by their 18S rDNA sequence, therefore, additional support of the taxonomic identification of&nbsp;P.&nbsp;subcurvata&nbsp;was provided through sequencing of the 18S-ITS1-5.8S regions. Amplification of this region was performed with the 18SF-euk and 5.8SR_euk primers of Hubbard et al. (2008). PCR products were purified using either QIAquick PCR Purification Kit (Qiagen) or ExoSAP-IT (Affymetrix) and sequenced by Sanger DNA sequencing (Genewiz). Sequences were edited using Geneious Pro software (<a href="http://www.geneious.com" target="_blank">http://www.geneious.com</a>, Kearse et al., 2012) and BLASTn sequence homology searches were performed against the NCBI nucleotide non-redundant (nr) database to determine species with a cutoff identity of 98%.</p>
<p>Diatom phylogenetic analysis was performed with Geneious Pro and included 71 additional diatom 18S rDNA sequences from publically available genomes and transcriptomes, including those in the MMETSP database. Diatom sequences were trimmed to the same length and aligned with MUSCLE (Edgar 2004). A phylogenetic tree was created in Mega with the Maximum-likelihood method of tree reconstruction, the Jukes-Cantor genetic distance model (Jukes and Cantor 1969), and 100 bootstrap replicates.</p>
<p>Illumina TruSeq adapters and poly-A tails were trimmed from raw reads using the Fastx_toolkit clipper function. Fastq_quality_filter was used to remove poor quality sequences, such that remaining sequences had a minimum quality score of 20 with a minimum of 80% of bases within a&nbsp;read&nbsp;meeting this quality score requirement. Any remaining raw sequences less than 50 base pairs in length were also removed. Merged files were assembled&nbsp;de novo&nbsp;using Trinity (Grabherr et al. 2011). The resulting assembly was filtered to remove contigs less than 200 bp in length. Trinity-assembled contigs which exhibited sequence overlap were grouped into isogroups which were then used for sequence homology searches (BLASTx E-value ≤ 10-4) against the Kyoto Encyclopedia of Genes and Genomes (KEGG) databases (Kanehisa 2006).</p>
<p>BUSCO (Benchmarking Universal Single-Copy Orthologs) was used to assess the completeness of genomes and transcriptomes based on sets of&nbsp;single copy&nbsp;orthologous groups derived from OrthoDB that are highly conserved within multiple lineages (Felipe et al. 2015). Completed, duplicated and fragmented orthologs were determined by meeting an ‘expected score’ and having aligned sequences within two standard deviations of the BUSCO gene’s length.&nbsp;A second&nbsp;metric of completeness was performed by evaluating conserved pathways, such as the ribosome and spliceosome, using the single-directional&nbsp;best-hit&nbsp;method in the KEGG Automatic Annotation Server (KAAS) (Moriya et al. 2007).&nbsp;Finally&nbsp;contiguity,&nbsp;was calculated at the 0.75 level as according to Martin and Wang (2011) with custom scripts.</p>
<p>For each transcriptome, unassembled sequence reads were aligned to the final Trinity assembly using Bowtie 2 (Langmead 2012). Mapped reads were normalized by the Reads per Kilobase per Million reads method (RPKM) (Mortazavi et al. 2008).</p>
<p>Gene biogeographical distributions -&nbsp;20 genes of interest were selected in the study to investigate the molecular basis of iron and light limitation in polar diatoms. Reference sequences for each of these genes were obtained from the&nbsp;F.&nbsp;cylindrus&nbsp;and&nbsp;P.&nbsp;tricornutum&nbsp;JGI genome portals and&nbsp;T.&nbsp;pseudonana&nbsp;and&nbsp;T.&nbsp;oceanica&nbsp;NCBI and GenBank repositories. Reference sequences were identified in the transcriptomes by translated nucleotide homology searches (tBLASTn) with an e-value cutoff of &lt;10-5. A reciprocal tBLASTn homology search was performed for each transcriptome against the KEGG GENES database, using the single-directional&nbsp;best-hit&nbsp;method in the KAAS online tool to ensure consistent gene annotations (Moriya et al. 2007).</p>
<p>Subsequently, reference sequences were identified in the MMETSP protein database by BLASTp (e-value &lt;10-5) homology searches among the diatom transcriptomes. The transcriptomes and their associated latitude and longitude were obtained from iMicrobe Data Commons (Project Code CAM_P_0001000) and the National Center for Marine Algae and Microbiota (NCMA). Custom Matlab scripts allowed global biogeographical distribution of key genes of interest to be mapped.</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Data Processing Notes:</strong></p>
<p>-reformatted column names to comply with BCO-DMO standards<br />
-replaced spaces with underscores<br />
-replaced "NA" with "nd"</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
Agilent Bioanalyzer 2100
Agilent Bioanalyzer 2100
PI Supplied Instrument Name: Agilent Bioanalyzer 2100 PI Supplied Instrument Description:Used to determine RNA integrity Instrument Name: Bioanalyzer Instrument Short Name:Bioanalyzer Instrument Description: A Bioanalyzer is a laboratory instrument that provides the sizing and quantification of DNA, RNA, and proteins. One example is the Agilent Bioanalyzer 2100.
Olympus CKX41
Olympus CKX41
PI Supplied Instrument Name: Olympus CKX41 PI Supplied Instrument Description:Used to perform isolations Instrument Name: Inverted Microscope Instrument Short Name: Instrument Description: An inverted microscope is a microscope with its light source and condenser on the top, above the stage pointing down, while the objectives and turret are below the stage pointing up. It was invented in 1850 by J. Lawrence Smith, a faculty member of Tulane University (then named the Medical College of Louisiana).
Inverted microscopes are useful for observing living cells or organisms at the bottom of a large container (e.g. a tissue culture flask) under more natural conditions than on a glass slide, as is the case with a conventional microscope. Inverted microscopes are also used in micromanipulation applications where space above the specimen is required for manipulator mechanisms and the microtools they hold, and in metallurgical applications where polished samples can be placed on top of the stage and viewed from underneath using reflecting objectives.
The stage on an inverted microscope is usually fixed, and focus is adjusted by moving the objective lens along a vertical axis to bring it closer to or further from the specimen. The focus mechanism typically has a dual concentric knob for coarse and fine adjustment. Depending on the size of the microscope, four to six objective lenses of different magnifications may be fitted to a rotating turret known as a nosepiece. These microscopes may also be fitted with accessories for fitting still and video cameras, fluorescence illumination, confocal scanning and many other applications. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/
Cruise: LMG1401
LMG1401
ARSV Laurence M. Gould
Community Standard Description
International Council for the Exploration of the Sea
ARSV Laurence M. Gould
vessel
ARSV Laurence M. Gould
Community Standard Description
International Council for the Exploration of the Sea
ARSV Laurence M. Gould
vessel