Accessing BCO-DMO data
log in    
Brought to you by BCO-DMO    

ERDDAP > info > bcodmo_dataset_665454

Title Sum-
Institution Dataset ID
     data   graph     files  public BLASTp homology data from genes obtained in samples collected on the Gould (LMG1411) cruise
in the Western Antarctica Peninsula during 2014 (Polar Transcriptomes project).
   ?     I   M   background (external link) RSS Subscribe BCO-DMO bcodmo_dataset_665454

The Dataset's Variables and Attributes

Row Type Variable Name Attribute Name Data Type Value
attribute NC_GLOBAL access_formats String .htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson
attribute NC_GLOBAL acquisition_description String 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\u2019s 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
).\u00a0Pseudo-nitzschia\u00a0species are often difficult to identify by their
18S rDNA sequence, therefore, additional support of the taxonomic
identification of\u00a0P.\u00a0subcurvata\u00a0was 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
([http://www.geneious.com](\\"http://www.geneious.com\\"), 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%.

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\u00a0read\u00a0meeting
this quality score requirement. Any remaining raw sequences less than 50 base
pairs in length were also removed. Merged files were assembled\u00a0de
novo\u00a0using 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 \u2264 10-4)
against the Kyoto Encyclopedia of Genes and Genomes (KEGG) databases (Kanehisa

Gene biogeographical distributions -\u00a020 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\u00a0F.\u00a0cylindrus\u00a0and\u00a0P.\u00a0tricornutum\u00a0JGI
genome portals
and\u00a0T.\u00a0pseudonana\u00a0and\u00a0T.\u00a0oceanica\u00a0NCBI and
GenBank repositories. Reference sequences were identified in the
transcriptomes by translated nucleotide homology searches (tBLASTn) with an
e-value cutoff of <10-5. A reciprocal tBLASTn homology search was performed
for each transcriptome against the KEGG GENES database, using the single-
directional\u00a0best-hit\u00a0method in the KAAS online tool to ensure
consistent gene annotations (Moriya et al. 2007).

Subsequently, reference sequences were identified in the MMETSP protein
database by BLASTp (e-value <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
attribute NC_GLOBAL awards_0_award_nid String 653228
attribute NC_GLOBAL awards_0_award_number String PLR-1341479
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1341479 (external link)
attribute NC_GLOBAL awards_0_funder_name String NSF Division of Ocean Sciences
attribute NC_GLOBAL awards_0_funding_acronym String NSF OCE
attribute NC_GLOBAL awards_0_funding_source_nid String 355
attribute NC_GLOBAL awards_0_program_manager String Dr Chris H. Fritsen
attribute NC_GLOBAL awards_0_program_manager_nid String 50502
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String BLASTp Homology Data
Adrian Marchetti, PI
Version 11 October 2016
attribute NC_GLOBAL Conventions String COARDS, CF-1.6, ACDD-1.3
attribute NC_GLOBAL creator_email String info at bco-dmo.org
attribute NC_GLOBAL creator_name String BCO-DMO
attribute NC_GLOBAL creator_type String institution
attribute NC_GLOBAL creator_url String https://www.bco-dmo.org/ (external link)
attribute NC_GLOBAL data_source String extract_data_as_tsv version 2.3 19 Dec 2019
attribute NC_GLOBAL date_created String 2016-11-21T21:11:01Z
attribute NC_GLOBAL date_modified String 2019-06-11T16:47:19Z
attribute NC_GLOBAL defaultDataQuery String &amp;time&lt;now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.665454.1
attribute NC_GLOBAL Easternmost_Easting double 163.0
attribute NC_GLOBAL geospatial_lat_max double 77.8333
attribute NC_GLOBAL geospatial_lat_min double -77.8333
attribute NC_GLOBAL geospatial_lat_units String degrees_north
attribute NC_GLOBAL geospatial_lon_max double 163.0
attribute NC_GLOBAL geospatial_lon_min double -159.4166667
attribute NC_GLOBAL geospatial_lon_units String degrees_east
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/665454 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String Inverted Microscope
attribute NC_GLOBAL instruments_0_dataset_instrument_description String Used to perform isolations
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 665461
attribute NC_GLOBAL instruments_0_description String 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.
attribute NC_GLOBAL instruments_0_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/LAB05/ (external link)
attribute NC_GLOBAL instruments_0_instrument_name String Inverted Microscope
attribute NC_GLOBAL instruments_0_instrument_nid String 675
attribute NC_GLOBAL instruments_0_supplied_name String Olympus CKX41
attribute NC_GLOBAL instruments_1_acronym String Bioanalyzer
attribute NC_GLOBAL instruments_1_dataset_instrument_description String Used to determine RNA integrity
attribute NC_GLOBAL instruments_1_dataset_instrument_nid String 665464
attribute NC_GLOBAL instruments_1_description String A Bioanalyzer is a laboratory instrument that provides the sizing and quantification of DNA, RNA, and proteins. One example is the Agilent Bioanalyzer 2100.
attribute NC_GLOBAL instruments_1_instrument_name String Bioanalyzer
attribute NC_GLOBAL instruments_1_instrument_nid String 626182
attribute NC_GLOBAL instruments_1_supplied_name String Agilent Bioanalyzer 2100
attribute NC_GLOBAL keywords String bco, bco-dmo, biological, chemical, clade, data, dataset, dmo, e_value, erddap, gene, genus, latitude, longitude, management, mmetsp, MMETSP_ID, oceanography, office, preliminary, species, strain, subject, subject_ID, value
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/665454/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/665454 (external link)
attribute NC_GLOBAL Northernmost_Northing double 77.8333
attribute NC_GLOBAL param_mapping String {'665454': {'lat': 'master - latitude', 'lon': 'master - longitude'}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/665454/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String University of North Carolina at Chapel Hill
attribute NC_GLOBAL people_0_affiliation_acronym String UNC-Chapel Hill
attribute NC_GLOBAL people_0_person_name String Adrian Marchetti
attribute NC_GLOBAL people_0_person_nid String 527120
attribute NC_GLOBAL people_0_role String Principal Investigator
attribute NC_GLOBAL people_0_role_type String originator
attribute NC_GLOBAL people_1_affiliation String University of North Carolina at Chapel Hill
attribute NC_GLOBAL people_1_affiliation_acronym String UNC-Chapel Hill
attribute NC_GLOBAL people_1_person_name String Adrian Marchetti
attribute NC_GLOBAL people_1_person_nid String 527120
attribute NC_GLOBAL people_1_role String Contact
attribute NC_GLOBAL people_1_role_type String related
attribute NC_GLOBAL people_2_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_2_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_2_person_name String Hannah Ake
attribute NC_GLOBAL people_2_person_nid String 650173
attribute NC_GLOBAL people_2_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_2_role_type String related
attribute NC_GLOBAL project String Polar_Transcriptomes
attribute NC_GLOBAL projects_0_acronym String Polar_Transcriptomes
attribute NC_GLOBAL projects_0_description String 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.
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.
attribute NC_GLOBAL projects_0_end_date String 2017-07
attribute NC_GLOBAL projects_0_geolocation String Antarctica
attribute NC_GLOBAL projects_0_name String Iron and Light Limitation in Ecologically Important Polar Diatoms: Comparative Transcriptomics and Development of Molecular Indicators
attribute NC_GLOBAL projects_0_project_nid String 653229
attribute NC_GLOBAL projects_0_project_website String http://www.nsf.gov/awardsearch/showAward?AWD_ID=1341479 (external link)
attribute NC_GLOBAL projects_0_start_date String 2014-08
attribute NC_GLOBAL publisher_name String Biological and Chemical Oceanographic Data Management Office (BCO-DMO)
attribute NC_GLOBAL publisher_type String institution
attribute NC_GLOBAL sourceUrl String (local files)
attribute NC_GLOBAL Southernmost_Northing double -77.8333
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL summary String BLASTp homology data from genes obtained in samples collected on the Gould (LMG1411) cruise in the Western Antarctica Peninsula during 2014 (Polar Transcriptomes project).
attribute NC_GLOBAL title String BLASTp homology data from genes obtained in samples collected on the Gould (LMG1411) cruise in the Western Antarctica Peninsula during 2014 (Polar Transcriptomes project).
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL Westernmost_Easting double -159.4166667
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable gene   String  
attribute gene bcodmo_name String unknown
attribute gene description String Gene analyzed
attribute gene long_name String Gene
attribute gene units String unitless
variable genus   String  
attribute genus bcodmo_name String genus
attribute genus description String Genus analyzed
attribute genus long_name String Genus
attribute genus units String unitless
variable species   String  
attribute species bcodmo_name String species
attribute species description String Species analyzed
attribute species long_name String Species
attribute species units String unitless
variable strain   String  
attribute strain bcodmo_name String unknown
attribute strain description String Strain ID
attribute strain long_name String Strain
attribute strain units String unitless
variable MMETSP_ID   String  
attribute MMETSP_ID bcodmo_name String unknown
attribute MMETSP_ID description String MMETSP ID
attribute MMETSP_ID long_name String MMETSP ID
attribute MMETSP_ID units String unitless
variable subject_ID   String  
attribute subject_ID bcodmo_name String sample
attribute subject_ID description String Strain ID
attribute subject_ID long_name String Subject ID
attribute subject_ID nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute subject_ID units String unitless
variable e_value   double  
attribute e_value _FillValue double NaN
attribute e_value actual_range double 0.0, 5.0E-6
attribute e_value bcodmo_name String unknown
attribute e_value description String E-value
attribute e_value long_name String E Value
attribute e_value units String unitless
variable latitude   double  
attribute latitude _CoordinateAxisType String Lat
attribute latitude _FillValue double NaN
attribute latitude actual_range double -77.8333, 77.8333
attribute latitude axis String Y
attribute latitude bcodmo_name String latitude
attribute latitude colorBarMaximum double 90.0
attribute latitude colorBarMinimum double -90.0
attribute latitude description String Latitude; N is positive
attribute latitude ioos_category String Location
attribute latitude long_name String Latitude
attribute latitude nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/LATX/ (external link)
attribute latitude standard_name String latitude
attribute latitude units String degrees_north
variable longitude   double  
attribute longitude _CoordinateAxisType String Lon
attribute longitude _FillValue double NaN
attribute longitude actual_range double -159.4166667, 163.0
attribute longitude axis String X
attribute longitude bcodmo_name String longitude
attribute longitude colorBarMaximum double 180.0
attribute longitude colorBarMinimum double -180.0
attribute longitude description String Longitude; E is positive
attribute longitude ioos_category String Location
attribute longitude long_name String Longitude
attribute longitude nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/LONX/ (external link)
attribute longitude standard_name String longitude
attribute longitude units String degrees_east
variable clade   String  
attribute clade bcodmo_name String unknown
attribute clade description String Clade category
attribute clade long_name String Clade
attribute clade units String unitless

The information in the table above is also available in other file formats (.csv, .htmlTable, .itx, .json, .jsonlCSV1, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.

ERDDAP, Version 2.02
Disclaimers | Privacy Policy | Contact