http://lod.bco-dmo.org/id/dataset/988266
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
2025-11-04
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Metabarcoding data from samples collected at shore-based tide pools and ocean samples in New England waters in 2019
2025-11-04
publication
2025-11-04
revision
BCO-DMO Linked Data URI
2025-11-04
creation
http://lod.bco-dmo.org/id/dataset/988266
Laura A. Katz
Smith College
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: Katz, L. A. (2025) Metabarcoding data from samples collected at shore-based tide pools and ocean samples in New England waters in 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-11-04 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/988266 [access date]
Dataset Description: <p>See the "Related Datasets" section for methods and data from additional datasets from this study (CTD profile data and&nbsp;single-cell transcriptomic data).</p> Methods and Sampling: <p>Sample type: Amplicon = communities collected on filters at varying sizes and amplified using primers as described in Grow et al. (2023, doi:10.3354/ame02003).</p>
<p>Metabarcoding relied on taxon-specifc primers to characters ciliates and close relatives.&nbsp;&nbsp;<br />
<br />
Raw sequences are available in the Sequence Read Archive (SRA) at the National Center for Biotechnology Information (NCBI) under BioProject https://www.ncbi.nlm.nih.gov/bioproject/<strong>PRJNA952215</strong><br />
<strong>* BioProject Title: "</strong>Exploring the diversity of microeukaryotic communities in New England tide pools"<br />
<strong>* BioProject Description:&nbsp;</strong> "Extraction of community DNA &amp; RNA from Acadia National Park, ME tide pool and ocean samples, amplification of SSU rRNA using SAR (Stramenopila, Alveolata, Rhizaria) primers, metabarcoding sequencing of amplified DNA."</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 Environmental Biology (NSF DEB) Award Number: DEB-1651908 Award URL: https://www.nsf.gov/awardsearch/show-award/?AWD_ID=1651908
Funding provided by NSF Division of Environmental Biology (NSF DEB) Award Number: DEB-1541511 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1541511
onGoing
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
asNeeded
Dataset Version: 1
Unknown
SRA_Run
SRA_Study
bioproject_accession
biosample_accession
LKH_Number
Sample_ID
Year
Month
Sampling_Day
Time_local
ISO_DateTime_UTC
Tide
Sample
Filter_Size
Sample_Type
Sampling_Location
Sample_Site_Type
Location_Details
GPS_Lat
GPS_Lon
Water_Temperature
Salinity
pH
Depth
Instrument
Illumina NovaSeq 6000
theme
None, User defined
NCBI SRA run accession (SRR)
NCBI SRA study accession (SRP)
NCBI BioProject accession
NCBI BioSample accession
sample identification
year
month_local
day_local
time_local
ISO_DateTime_UTC
tide
sample description
filter_size
sample type
site description
site
latitude
longitude
water temperature at measurement depth
salinity
pH
depth
instrument
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
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
-68.3125
-68.3125
44.2283
44.2283
2019-05-20
2019-10-14
New England continental shelf
0
BCO-DMO catalogue of parameters from Metabarcoding data from samples collected at shore-based tide pools and ocean samples in New England waters in 2019
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/988292.rdf
Name: SRA_Run
Units: unitless
Description: <p>NCBI Sequence Read Archive (SRA) Run accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/988293.rdf
Name: SRA_Study
Units: unitless
Description: <p>NCBI Sequence Read Archive (SRA) Study accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/988294.rdf
Name: bioproject_accession
Units: unitless
Description: <p>NCBI BioProject accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/988295.rdf
Name: biosample_accession
Units: unitless
Description: <p>NCBI BioSample accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/988296.rdf
Name: LKH_Number
Units: unitless
Description: <p>LKH Number. In house tracking system sample identifier.</p>
http://lod.bco-dmo.org/id/dataset-parameter/988297.rdf
Name: Sample_ID
Units: unitless
Description: <p>Sample identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/988298.rdf
Name: Year
Units: unitless
Description: <p>Sampling year</p>
http://lod.bco-dmo.org/id/dataset-parameter/988299.rdf
Name: Month
Units: unitless
Description: <p>Sampling month (Full month name)</p>
http://lod.bco-dmo.org/id/dataset-parameter/988300.rdf
Name: Sampling_Day
Units: unitless
Description: <p>Sampling day</p>
http://lod.bco-dmo.org/id/dataset-parameter/988301.rdf
Name: Time_local
Units: unitless
Description: <p>Sampling time. Local time zone (EDT/EST)</p>
http://lod.bco-dmo.org/id/dataset-parameter/988302.rdf
Name: ISO_DateTime_UTC
Units: unitless
Description: <p>Sampling datetime with timezone (ISO 8601 format). UTC</p>
http://lod.bco-dmo.org/id/dataset-parameter/988303.rdf
Name: Tide
Units: unitless
Description: <p>Tide (e.g. Ebbing or Flooding)</p>
http://lod.bco-dmo.org/id/dataset-parameter/988304.rdf
Name: Sample
Units: unitless
Description: <p>Sample number</p>
http://lod.bco-dmo.org/id/dataset-parameter/988305.rdf
Name: Filter_Size
Units: unitless
Description: <p>Filter Size</p>
http://lod.bco-dmo.org/id/dataset-parameter/988306.rdf
Name: Sample_Type
Units: unitless
Description: <p>Sample type (RNA or DNA)</p>
http://lod.bco-dmo.org/id/dataset-parameter/988307.rdf
Name: Sampling_Location
Units: unitless
Description: <p>Sampling location description (e.g. ANP)</p>
http://lod.bco-dmo.org/id/dataset-parameter/988308.rdf
Name: Sample_Site_Type
Units: unitless
Description: <p>Sample site description (e.g. Ocean, middle pool)</p>
http://lod.bco-dmo.org/id/dataset-parameter/988309.rdf
Name: Location_Details
Units: unitless
Description: <p>Location description (geolocation)</p>
http://lod.bco-dmo.org/id/dataset-parameter/988310.rdf
Name: GPS_Lat
Units: decimal degrees
Description: <p>Latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/988311.rdf
Name: GPS_Lon
Units: decimal degrees
Description: <p>Longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/988312.rdf
Name: Water_Temperature
Units: degrees Celsius
Description: <p>Water temperature</p>
http://lod.bco-dmo.org/id/dataset-parameter/988313.rdf
Name: Salinity
Units: parts per thousand (ppt)
Description: <p>Salinity</p>
http://lod.bco-dmo.org/id/dataset-parameter/988314.rdf
Name: pH
Units: pH scale
Description: <p>pH</p>
http://lod.bco-dmo.org/id/dataset-parameter/988315.rdf
Name: Depth
Units: meters (m)
Description: <p>Depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/988316.rdf
Name: Instrument
Units: unitless
Description: <p>Instrument name</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/988266/data/download
download
onLine
dataset
<p>Sample type: Amplicon = communities collected on filters at varying sizes and amplified using primers as described in Grow et al. (2023, doi:10.3354/ame02003).</p>
<p>Metabarcoding relied on taxon-specifc primers to characters ciliates and close relatives.&nbsp;&nbsp;<br />
<br />
Raw sequences are available in the Sequence Read Archive (SRA) at the National Center for Biotechnology Information (NCBI) under BioProject https://www.ncbi.nlm.nih.gov/bioproject/<strong>PRJNA952215</strong><br />
<strong>* BioProject Title: "</strong>Exploring the diversity of microeukaryotic communities in New England tide pools"<br />
<strong>* BioProject Description:&nbsp;</strong> "Extraction of community DNA &amp; RNA from Acadia National Park, ME tide pool and ocean samples, amplification of SSU rRNA using SAR (Stramenopila, Alveolata, Rhizaria) primers, metabarcoding sequencing of amplified DNA."</p>
Specified by the Principal Investigator(s)
<p>Scripts developed under this study to analyze the NCBI data can be found at the GitHub (see Wiki https://github.com/Katzlab/EukPhylo/wiki), with versions of scripts developed through this project from 2020-2024. A full version of EukPhylo version 1 is published on Zenodo (doi: 10.5281/ZENODO.15866075). The parent DOI for all versions of the github repository, including past releases of PhyloTol is doi:10.5281/ZENODO.13323347.&nbsp;</p>
Specified by the Principal Investigator(s)
* Sheet 1 of submitted file "Katz_metabarcoding.xlsx" was imported into the BCO-DMO data system for this dataset. Values "NA" imported as missing data values. Table will appear as Data File: 988266_v1_marine-metabarcoding.csv (along with other download format options).
Missing Data Identifiers:
* In the BCO-DMO data system missing data identifiers are displayed according to the format of data you access. For example, in csv files it will be blank (null) values. In Matlab .mat files it will be NaN values. When viewing data online at BCO-DMO, the missing value will be shown as blank (null) values.
* Column names adjusted to conform to BCO-DMO naming conventions designed to support broad re-use by a variety of research tools and scripting languages. [Only numbers, letters, and underscores. Can not start with a number]
* NCBI Run Selector data were used to extract data from BioProject PRJNA952215. The Date, Instrument, and Depth columns were added from the NCBI metadata as the dates matched the provided excel data but were in a consistent (ISO) format.
* Time column renamed Time_local
* Additional column added: ISO_DateTime_UTC (ISO datetime with timezone) in UTC. Converted from Date and Time_Local (US Eastern EST/EDT).
* Column lat_lon separated into Lat,Lon columns in decimal degrees.
* Second "Sample_Type" column renamed Sample_Site_Type. The other Sample_Type contained RNA or DNA indication.
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 NovaSeq 6000
Illumina NovaSeq 6000
PI Supplied Instrument Name: Illumina NovaSeq 6000 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.