http://lod.bco-dmo.org/id/dataset/924260
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
2024-04-03
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
NCBI accession numbers from a study of two tintinnid ciliate species, Schmidingerella arcuata and Schmidingerella meunieri
2024-06-13
publication
2024-06-13
revision
BCO-DMO Linked Data URI
2024-06-13
creation
http://lod.bco-dmo.org/id/dataset/924260
George McManus
University of Connecticut
principalInvestigator
Laura A. Katz
Smith College
principalInvestigator
Luciana Santoferrara
Hofstra University
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: McManus, G., Katz, L. A., Santoferrara, L. (2024) NCBI accession numbers from a study of two tintinnid ciliate species, Schmidingerella arcuata and Schmidingerella meunieri. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-06-13 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/924260 [access date]
NCBI accession numbers for S. arcuata and S. meunieri Dataset Description: Methods and Sampling: <p>This project required sequencing whole genomes and transcriptomes from single cells picked from two cultures. One was <em>Schmidingerella arcuata</em> (urn:lsid:marinespecies.org:taxname:732664), isolated from the East Coast of the United States in Long Island Sound; the other was <em>Schmidingerella meunieri</em> (urn:lsid:marinespecies.org:taxname:732864), isolated by S. Strom from Puget Sound on the West Coast of the United States. <em>S. arcuata</em> was collected from the surface waters of northeastern Long Island Sound, CT (41.31°N, 72.06°W), using a 20-micrometer (µm) mesh plankton net. Single cells were isolated with drawn capillaries and moved to six-well culture plates with 0.2-µm-filtered sample water. The goal was to quantify the degree of difference in genome architecture for these two close congeners.</p>
<p>The cultures were grown in filtered seawater at 18 degrees Celsius (°C) on a 12:12 light cycle and fed the dinoflagellate <em>Heterocapsa triquetra</em> and the prymnesiophyte <em>Isochrysis galbana</em>. Individual cells were picked with a drawn capillary pipette and processed for sequencing as detailed below (from Smith et al 2020).</p>
<p>The SMART-Seq2 v4 Ultra Low input RNA kit (Cat: 634889; Takara, Mountain View, CA) was used for whole transcriptome amplification (WTA) following the manufacturer's protocols, with the exception that we quartered the reaction volumes. For whole-genome amplification (WGA), the Repli-g single-cell kit (Cat: 150343; Qiagen, Hilden, Germany) was used following the manufacturer’s protocols. The products (cDNA for WTA, gDNA for WGA) were quantified with the dsDNA Qubit assay (Invitrogen, Waltham, MA) and polymerase chain reaction-checked with eukaryotic 18S rDNA and genus-specific ITS primers. Minimum bacterial contamination was confirmed by polymerase chain reaction with 16S rDNA primers Sequencing libraries were prepared with the Illumina Nextera XT kit (Cat: FC1311096; Illumina, San Diego, CA), then processed with Illumina HiSeq 2500 at Macrogen Sequencing (Geumcheon-gu, Seoul, South Korea).</p>
<p>The isolation/cultivation was done in 2014-2015. The sequencing work was all completed and analyzed by the suummer of 2020.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1924570 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1924570
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1924527 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1924527
onGoing
George McManus
University of Connecticut
860-405-8602
Department of Marine Sciences, University of Connecticut 1080 Shennecossett Rd.
Groton
CT
06340
USA
george.mcmanus@uconn.edu
pointOfContact
Laura A. Katz
Smith College
413-585-3825
Department of Biological Sciences Smith College Burton Hall 201
Northampton
MA
01063
USA
lkatz@smith.edu
pointOfContact
Luciana Santoferrara
Hofstra University
516-463-7718
Biology Dept Room 301 Gittleson Hall
Hempstead
NY
11549-1000
USA
luciana.santoferrara@hofstra.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
species
latitude
longitude
depth
date
NCBI_BioprojectProject_ID
Sample_Accession
Sequence_Accession
sample
other_links
Illumina HiSeq 2500
20-µm-mesh plankton net
theme
None, User defined
species scientific name (binomial)
latitude
longitude
depth
year
NCBI BioProject accession
NCBI BioSample accession
accession number
sample description
external_link
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Phytoplankton Net
instrument
BCO-DMO Standard Instruments
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 Research: Combining single-cell and community 'omics' to test hypotheses about diversity and function of planktonic ciliates
http://microzooplankton.uconn.edu
Collaborative Research: Combining single-cell and community 'omics' to test hypotheses about diversity and function of planktonic ciliates
<p><em>NSF Award Abstract:</em><br />
Planktonic ciliates are key members of marine food webs where they serve diverse roles, including as food chain links between smaller microbes and larger plankton. Due to their small size and difficulties in identifying and cultivating them, we know less about ciliate diversity and distributions in the ocean than we do about larger organisms such as fish and invertebrates. Previous work from this team measured ciliate diversity in coastal waters and found that distinct genetic variants were separated in time and space in a way that could be related to factors such as ocean temperature, salinity, and depth gradients. Many questions remained unanswered, and it is important to understand the environmental factors that control the diversity and distribution of plankton such as ciliates to predict how these organisms may respond to a changing enviroment in the coming decades. This project focuses on: 1) how ciliate species are delineated using single-cell genomics and transcriptomics; 2) DNA-based studies of all ciliates and other planktonic members of the SAR clade (Stramenopila, Alveolata, Rhizaria), which will provide ecological context; 3) in situ gene expression by single-cell and meta- transcriptomics; and 4) laboratory studies of gene expression in cultivated ciliate species. This project involves training of postdoctoral scholars, graduate students, and undergraduates. The researchers are committed to creating diverse and inclusive research labs; recruitment of participants will be done through partnership with appropriate groups on our campuses. The project integrates with summer Research Experiences for Undergraduates (REU) activities at both Smith College and UCONN (including the UCONN/Mystic Aquarium joint REU), which are especially focused on underrepresented students. This project also enhances efforts to broaden understanding of biodiversity in partnership with the UCONN Noyce Scholars Program, which facilitates career-changing STEM professionals to become teachers in underserved secondary schools.</p>
<p>This project will assess distributions of reproductively-isolated species, determined using a new method to characterize regions of the ciliate germline genome. Furthermore, it will use phylogenomic methods to identify clade-specific transcripts (e.g. those of spirotrich ciliates) within metatranscriptomes from the shelf environment and to expand knowledge of ciliate function with single-cell transcriptomics of field-collected cells. These approaches will be a substantial improvement over the culture-based methods that are potentially biased towards "weedy" species in the ocean. The combination of definitive species identification with assessment of function via single-cell and meta- transcriptomics promises to provide significant advances in marine plankton ecology. The research focuses on two broad questions: 1) does the observed high diversity in phylogenetically-informative genes reflect reproductive isolation and functional differentiation in planktonic ciliates? and 2) do different co-occurring species of planktonic ciliates show substantial functional differences that correspond to different niches in the ocean? The project assesses species boundaries (i.e. reproductive isolation) through analyses of patterns in the germline micronuclei of planktonic ciliate morphospecies; characterizes transitions of closely-related ciliates across ecological gradients in the ocean; and examines functional differences within and between species, and in communities, through analyses of transcriptomics.</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>
Ciliate Omics
largerWorkCitation
project
eng; USA
oceans
-122.7
-72.06
41.31
48.5
2019-01-01
2019-12-31
New England continental shelf
0
BCO-DMO catalogue of parameters from NCBI accession numbers from a study of two tintinnid ciliate species, Schmidingerella arcuata and Schmidingerella meunieri
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/924377.rdf
Name: species
Units: unitless
Description: <p>Scientific name (Genus species) or "primer"</p>
http://lod.bco-dmo.org/id/dataset-parameter/924378.rdf
Name: latitude
Units: decimal degrees
Description: <p>latitude of location from which species was isolated; positive values = North</p>
http://lod.bco-dmo.org/id/dataset-parameter/924379.rdf
Name: longitude
Units: decimal degrees
Description: <p>longitude of location from which species was isolated; negative values = West</p>
http://lod.bco-dmo.org/id/dataset-parameter/924380.rdf
Name: depth
Units: meters
Description: <p>depth from which ciliate was isolated</p>
http://lod.bco-dmo.org/id/dataset-parameter/924381.rdf
Name: date
Units: unitless
Description: <p>year of ciliate isolation</p>
http://lod.bco-dmo.org/id/dataset-parameter/924382.rdf
Name: NCBI_BioprojectProject_ID
Units: unitless
Description: <p>NCBI BioProject identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/924383.rdf
Name: Sample_Accession
Units: unitless
Description: <p>NCBI BioSample identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/924384.rdf
Name: Sequence_Accession
Units: unitless
Description: <p>Accession numbers at NCBI (sample or sequence) (Genbank or SRA database)</p>
http://lod.bco-dmo.org/id/dataset-parameter/924385.rdf
Name: sample
Units: unitless
Description: <p>sequence locus or library type</p>
http://lod.bco-dmo.org/id/dataset-parameter/924386.rdf
Name: other_links
Units: unitless
Description: <p>web links to data illustrations on figshare website</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
https://osprey.bco-dmo.org/dataset/924260/data/download
download
onLine
dataset
<p>This project required sequencing whole genomes and transcriptomes from single cells picked from two cultures. One was <em>Schmidingerella arcuata</em> (urn:lsid:marinespecies.org:taxname:732664), isolated from the East Coast of the United States in Long Island Sound; the other was <em>Schmidingerella meunieri</em> (urn:lsid:marinespecies.org:taxname:732864), isolated by S. Strom from Puget Sound on the West Coast of the United States. <em>S. arcuata</em> was collected from the surface waters of northeastern Long Island Sound, CT (41.31°N, 72.06°W), using a 20-micrometer (µm) mesh plankton net. Single cells were isolated with drawn capillaries and moved to six-well culture plates with 0.2-µm-filtered sample water. The goal was to quantify the degree of difference in genome architecture for these two close congeners.</p>
<p>The cultures were grown in filtered seawater at 18 degrees Celsius (°C) on a 12:12 light cycle and fed the dinoflagellate <em>Heterocapsa triquetra</em> and the prymnesiophyte <em>Isochrysis galbana</em>. Individual cells were picked with a drawn capillary pipette and processed for sequencing as detailed below (from Smith et al 2020).</p>
<p>The SMART-Seq2 v4 Ultra Low input RNA kit (Cat: 634889; Takara, Mountain View, CA) was used for whole transcriptome amplification (WTA) following the manufacturer's protocols, with the exception that we quartered the reaction volumes. For whole-genome amplification (WGA), the Repli-g single-cell kit (Cat: 150343; Qiagen, Hilden, Germany) was used following the manufacturer’s protocols. The products (cDNA for WTA, gDNA for WGA) were quantified with the dsDNA Qubit assay (Invitrogen, Waltham, MA) and polymerase chain reaction-checked with eukaryotic 18S rDNA and genus-specific ITS primers. Minimum bacterial contamination was confirmed by polymerase chain reaction with 16S rDNA primers Sequencing libraries were prepared with the Illumina Nextera XT kit (Cat: FC1311096; Illumina, San Diego, CA), then processed with Illumina HiSeq 2500 at Macrogen Sequencing (Geumcheon-gu, Seoul, South Korea).</p>
<p>The isolation/cultivation was done in 2014-2015. The sequencing work was all completed and analyzed by the suummer of 2020.</p>
Specified by the Principal Investigator(s)
<p>Raw reads from WTA and WGA sequencing were trimmed for quality and size (Q28 and minimum length of 200 and 1,500 bp, respectively) using BBMap (V38.39). After trimming, two single-cell WTAs were assembled together using rnaSPAdes (V3.13.1), and seven singe-cell WGAs were assembled together using both SPAdes (V3.13.1) and MEGAHIT (V1.2.9). The MEGAHIT genome assembly was used for the final analysis.</p>
<p>Assemblies were processed through custom python scripts (<a href="https://github.com/maurerax/KatzLab/tree/HTS-Processing-PhyloGenPipeline" target="_blank">https://github.com/maurerax/KatzLab/tree/HTS-Processing-PhyloGenPipeline</a>) for the removal of rDNA and prokaryotic transcripts, and for the identification of orthologous gene families using USEARCH (V9.2) with OrthoMCLdatabases (V2.0.9).</p>
Specified by the Principal Investigator(s)
- Imported original file "NCBI_data_Schmidingerella.csv" into the BCO-DMO system.
- Removed "N" and "W" from the latitude and longitude columns.
- Made longitude negative to indicate the west direction.
- Renamed fields to comply with BCO-DMO naming conventions.
- Saved the final file as "924260_v1_ncbi_accessions.csv"
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 HiSeq 2500
Illumina HiSeq 2500
PI Supplied Instrument Name: Illumina HiSeq 2500 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.
20-µm-mesh plankton net
20-µm-mesh plankton net
PI Supplied Instrument Name: 20-µm-mesh plankton net Instrument Name: Phytoplankton Net Instrument Short Name:Phytoplankton Net Instrument Description: A Phytoplankton Net is a generic term for a sampling net having mesh size of 150 microns or less that is used to collect phytoplankton. It is used only when detailed instrument documentation is not available. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/22/