http://lod.bco-dmo.org/id/dataset/988253
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)
Single-cell transcriptomic data from ciliates isolated in New England waters between 2019 and 2023
2025-11-04
publication
2025-11-04
revision
BCO-DMO Linked Data URI
2025-11-04
creation
http://lod.bco-dmo.org/id/dataset/988253
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) Single-cell transcriptomic data from ciliates isolated in New England waters between 2019 and 2023. 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/988253 [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;marine metabarcoding data).</p> Methods and Sampling: <p>Data were collected near UConn Avery Point and on a research cruise. Data were&nbsp;deposited by George McManus.<br />
<br />
Sample type:<br />
Transcriptomes:&nbsp; single-cell amplification of polyA transcripts as described in Shazib et al. (2025, doi: 10.1016/j.ympev.2024.108239).<br />
<br />
Single-cell transcriptomes were based on poly-A selected gene sequences from individual ciliates that had been washed after isolation.&nbsp;<br />
<br />
Raw sequences are available in the Sequence Read Archive (SRA) at the National Center for Biotechnology Information (NCBI) under two BioProjects:<br />
<br />
<strong>https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1026950</strong><br />
<strong>* BioProject Title:</strong> "Phylogenomic pipeline for uncultivable microbial eukaryotes using single cell RNA sequencing data - A case study with planktonic ciliates (Protista, Ciliophora, Oligotrichea)."<br />
<strong>* BioProject Description: </strong>"We collected marine planktonic ciliates from a dock located in Groton, Connecticut, USA. The collection was made on multiple dates from July 2020 to January 2022. After isolating the single cell, we performed single-cell RNA sequencing. We created a phylogenomic pipeline relying on PhyloTol to construct single gene trees from the transcriptomic data. Our pipeline produced well-curated data, which we used to estimate species trees. Overall this project provides a guideline to infer species tree of uncultivable microbial eukaryotes using single cell RNA sequencing data."<br />
<br />
<strong>https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1223830</strong><br />
* <strong>BioProject Title:&nbsp;</strong>Whole transcriptome and genome data from several marine ciliates<br />
* <strong>BioProject Description:&nbsp;</strong>Single-cell whole transcriptome amplification and whole genome amplification; and subseqeunt Illumina NovaSeq 6000 reads from three marine ciliates species (Helicostemella sp., Stenosemella sp., and Tintinnopsis cylindrica), sampled in the northern US coast (from Maine to Connecticut); including one conjugating Tintinnopsis cylindrica.</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
BioProject
SRA_Experiment
SRA_study
SRA_Run
BioSample
sample_name
library_ID
title
Isolate
Isolation_source
Tissue
Collection_Date
geo_loc_name
Lat
Lon
description
Organism_label
Organism_NCBI
library_strategy
library_source
library_selection
library_layout
platform
instrument_model
design_description
Illumina NovaSeq 6000
Illumina HiSeq 2500
theme
None, User defined
NCBI BioProject accession
NCBI SRA experiment accession (SRX)
NCBI SRA study accession (SRP)
NCBI SRA run accession (SRR)
NCBI BioSample accession
sample description
tide
site description
date
site
latitude
longitude
verbatim identification
species scientific name (binomial)
instrument
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
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
-72.062171
-68.311088
41.316018
44.87
2019-05-22
2023-05-22
New England continental shelf
0
BCO-DMO catalogue of parameters from Single-cell transcriptomic data from ciliates isolated in New England waters between 2019 and 2023
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/988317.rdf
Name: BioProject
Units: unitless
Description: <p>NCBI BioProject accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/988318.rdf
Name: SRA_Experiment
Units: unitless
Description: <p>NCBI Sequence Read Archive (SRA) Study accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/988319.rdf
Name: SRA_study
Units: unitless
Description: <p>NCBI Sequence Read Archive (SRA) Study accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/988320.rdf
Name: SRA_Run
Units: unitless
Description: <p>NCBI Sequence Read Archive (SRA) Run accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/988322.rdf
Name: BioSample
Units: unitless
Description: <p>NCBI BioSample accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/988323.rdf
Name: sample_name
Units: unitless
Description: <p>Sample name. Uses in house tracking system sample identifier referred to as LKH Number""</p>
http://lod.bco-dmo.org/id/dataset-parameter/988324.rdf
Name: library_ID
Units: unitless
Description: <p>library identifier. Uses in house tracking system sample identifier referred to as LKH Number""</p>
http://lod.bco-dmo.org/id/dataset-parameter/988325.rdf
Name: title
Units: unitless
Description: <p>title of accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/988326.rdf
Name: Isolate
Units: unitless
Description: <p>Isolate (Not applicable)</p>
http://lod.bco-dmo.org/id/dataset-parameter/988327.rdf
Name: Isolation_source
Units: unitless
Description: <p>Isolation source (Not applicable)</p>
http://lod.bco-dmo.org/id/dataset-parameter/988328.rdf
Name: Tissue
Units: unitless
Description: <p>Tissue (not applicable)</p>
http://lod.bco-dmo.org/id/dataset-parameter/988329.rdf
Name: Collection_Date
Units: unitless
Description: <p>Collection date in format mm/dd/YY</p>
http://lod.bco-dmo.org/id/dataset-parameter/988330.rdf
Name: geo_loc_name
Units: unitless
Description: <p>geolocation name</p>
http://lod.bco-dmo.org/id/dataset-parameter/988331.rdf
Name: Lat
Units: decimal degrees
Description: <p>Latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/988332.rdf
Name: Lon
Units: decimal degrees
Description: <p>Longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/988333.rdf
Name: description
Units: unitless
Description: <p>Not used</p>
http://lod.bco-dmo.org/id/dataset-parameter/988334.rdf
Name: Organism_label
Units: unitless
Description: <p>Organism taxonomic name (full or abbreviated). May include additional descriptors in the label.</p>
http://lod.bco-dmo.org/id/dataset-parameter/988335.rdf
Name: Organism_NCBI
Units: unitless
Description: <p>Organism scientific name. This is the organism included in the NCBI metadata. See supplemental species list for more information and identifiers for this name.</p>
http://lod.bco-dmo.org/id/dataset-parameter/988336.rdf
Name: library_strategy
Units: unitless
Description: <p>Library strategy</p>
http://lod.bco-dmo.org/id/dataset-parameter/988337.rdf
Name: library_source
Units: unitless
Description: <p>Library source</p>
http://lod.bco-dmo.org/id/dataset-parameter/988338.rdf
Name: library_selection
Units: unitless
Description: <p>Library selection</p>
http://lod.bco-dmo.org/id/dataset-parameter/988339.rdf
Name: library_layout
Units: unitless
Description: <p>Library layout</p>
http://lod.bco-dmo.org/id/dataset-parameter/988340.rdf
Name: platform
Units: unitless
Description: <p>platform (ILLUMINA)</p>
http://lod.bco-dmo.org/id/dataset-parameter/988341.rdf
Name: instrument_model
Units: unitless
Description: <p>Instrument model</p>
http://lod.bco-dmo.org/id/dataset-parameter/988342.rdf
Name: design_description
Units: unitless
Description: <p>Design description</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/988253/data/download
download
onLine
dataset
<p>Data were collected near UConn Avery Point and on a research cruise. Data were&nbsp;deposited by George McManus.<br />
<br />
Sample type:<br />
Transcriptomes:&nbsp; single-cell amplification of polyA transcripts as described in Shazib et al. (2025, doi: 10.1016/j.ympev.2024.108239).<br />
<br />
Single-cell transcriptomes were based on poly-A selected gene sequences from individual ciliates that had been washed after isolation.&nbsp;<br />
<br />
Raw sequences are available in the Sequence Read Archive (SRA) at the National Center for Biotechnology Information (NCBI) under two BioProjects:<br />
<br />
<strong>https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1026950</strong><br />
<strong>* BioProject Title:</strong> "Phylogenomic pipeline for uncultivable microbial eukaryotes using single cell RNA sequencing data - A case study with planktonic ciliates (Protista, Ciliophora, Oligotrichea)."<br />
<strong>* BioProject Description: </strong>"We collected marine planktonic ciliates from a dock located in Groton, Connecticut, USA. The collection was made on multiple dates from July 2020 to January 2022. After isolating the single cell, we performed single-cell RNA sequencing. We created a phylogenomic pipeline relying on PhyloTol to construct single gene trees from the transcriptomic data. Our pipeline produced well-curated data, which we used to estimate species trees. Overall this project provides a guideline to infer species tree of uncultivable microbial eukaryotes using single cell RNA sequencing data."<br />
<br />
<strong>https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1223830</strong><br />
* <strong>BioProject Title:&nbsp;</strong>Whole transcriptome and genome data from several marine ciliates<br />
* <strong>BioProject Description:&nbsp;</strong>Single-cell whole transcriptome amplification and whole genome amplification; and subseqeunt Illumina NovaSeq 6000 reads from three marine ciliates species (Helicostemella sp., Stenosemella sp., and Tintinnopsis cylindrica), sampled in the northern US coast (from Maine to Connecticut); including one conjugating Tintinnopsis cylindrica.</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_transcriptomes.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: 988253_v1_ciliate_transcriptomes.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]
* Additional data at NCBI (PRJNA1223830) was made public after Katz_transcriptomes.xlsx was submitted to BCO-DMO so the new accession identifiers for the SRA, BioProject, and BioSample holdings were merged into this dataset using the SRA_Run as the join key to data extracted from the NCBI Run Selector (run 2025-11-04).
* NCBI Run Selector data were also extracted from the other BioProject PRJNA1026950 since the submitter indicated the Organism column had been updated there. The "Organism" column from the NCBI metadata were added to this dataset as column Organism_NCBI.
* The "Organism" column from the provided file Katz_transcriptomes.xlsx was also kept but renamed "Organism_label" since it included other information (example "Tintinnopsis sp_LIS-Tintinnina-11").
* SRA_sample for BioProject PRJNA1223830 was not included in the SRA run selector metadata so this column was not included here. The BioSample is included and sample information can be found from that.
* The names in the "Organism_NCBI" column were matched to ncbi_txid identifiers using the Global Names Verifier. NCBI advises consulting authoritative sources for taxonomic name information. To this end, the World Register of Marine Species taxon match tool was used to match the names on 2025-11-04 and the Life Science Identifiers (LSIDs) were added along with the accepted spelling of the names.
** Note: "Stenosemella steini" (ncbi_txid:1594485) was a phonetic (not exact) match to the currently accepted name "Stenosemella steinii" LSID (urn:lsid:marinespecies.org:taxname:178827).
* Column lat_lon separated into Lat,Lon columns in decimal degrees. Some lacked a negative for lon to be W so that was corrected.
* Instrument column in the dataset updated. The model number was sequentially increasing each row in the original excel file. Corrected so all models for Illumina HiSeq say "Illumina HiSeq 2500"
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.
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.