Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • Data Processing Description
  • BCO-DMO Processing Description
• Related Publications
• Related Datasets
• Parameters
• Instruments
• Project Information
• Funding

See the "Related Datasets" section for methods and data from additional datasets from this study (CTD profile data and marine metabarcoding data).

Data were collected near UConn Avery Point and on a research cruise. Data were deposited by George McManus.

Sample type:
Transcriptomes:  single-cell amplification of polyA transcripts as described in Shazib et al. (2025, doi: 10.1016/j.ympev.2024.108239).

Single-cell transcriptomes were based on poly-A selected gene sequences from individual ciliates that had been washed after isolation. 

Raw sequences are available in the Sequence Read Archive (SRA) at the National Center for Biotechnology Information (NCBI) under two BioProjects:

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1026950
* BioProject Title: "Phylogenomic pipeline for uncultivable microbial eukaryotes using single cell RNA sequencing data - A case study with planktonic ciliates (Protista, Ciliophora, Oligotrichea)."
* BioProject Description: "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."

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1223830
* BioProject Title: Whole transcriptome and genome data from several marine ciliates
* BioProject Description: 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.

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. 

* 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"

NSF Award Abstract:
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.

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.

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.