Name: Metatranscriptomic (RNA-seq) taxonomy data from an iron incubation experiment during the PUPCYCLE II cruise (R/V Sally Ride) within the California Current System in May and June of 2023
Published: 2026-08-12
Keywords: upwelling, phytoplankton, iron incubation, metatranscriptomics, biota, oceans

Data File(s)	Type	Description	Action
1003525_v1_rna_metatranscriptomic_taxonomy_pupcycle2.csv (19.72 KB)	Comma Separated Values (.csv)	RNA metatranscriptomic taxonomy results from an iron incubation experiment using upwelled waters sampled in the California Current System (CCS) during the PUPCYCLE II cruise; Primary data file for dataset ID 1003525, version 1	1003525_v1_rna_metatranscriptomic_taxonomy_pupcycle2.csv View Table

Files

Filename: 1003525_v1_rna_metatranscriptomic_taxonomy_pupcycle2.csv (19.72 KB)
Type: Comma Separated Values (.csv)

Description:

RNA metatranscriptomic taxonomy results from an iron incubation experiment using upwelled waters sampled in the California Current System (CCS) during the PUPCYCLE II cruise; Primary data file for dataset ID 1003525, version 1

1003525_v1_rna_metatranscriptomic_taxonomy_pupcycle2.csv View Table

This dataset is one of many generated from an iron incubation experiment conducted as part of the PUPCYCLE II cruise in May and June 2023. The different analyses are listed here, with links to other datasets from this study in the Related Datasets section.

Analyses include:

Physiology (dataset 994607)
- Dissolved inorganic nutrients (nitrate, phosphate, silicic acid)
- Size-fractionated chlorophyll a
- Size-fractionated isotope uptake rates (nitrate and DIC)
- Flow cytometry
- FlowCAM analysis
- FLP experiments for mixotroph cell-specific grazing rates
RNA taxonomy data for normalized reads (this dataset 1003525)
Differential expression for +Fe versus DFB treatments at T1 and T2: Pfam
- Mixotroph Pfam (dataset 1004659)
- Diatom Pfam (dataset 1004674)
Differential expression for +Fe versus DFB treatments at T1 and T2 for mixotrophs and diatoms: KEGG gene (dataset 1004689)
Differential expression for +Fe versus DFB treatments at T1 and T2 for mixotrophs and diatoms: KEGG pathways (dataset 1004704)
Dissolved iron concentrations (dataset 1004007)

See Related Datasets section below for links to the above mentioned datasets.

Speciale, E., Lim, P., Jeong, Y., Cook, C., Cohen, N., McClure, W., Schnetzer, A., Marchetti, A. (2026) KEGG gene differential expression data for mixotrophs and diatoms from an iron incubation experiment during the PUPCYCLE II R/V Sally Ride cruise within the California Current System in May and June of 2023. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-08-13 http://lod.bco-dmo.org/id/dataset/1004689

Speciale, E., Lim, P., Jeong, Y., Cook, C., Cohen, N., McClure, W., Schnetzer, A., Marchetti, A. (2026) KEGG pathway differential expression data for mixotrophs and diatoms from an iron incubation experiment during the PUPCYCLE II R/V Sally Ride cruise within the California Current System in May and June of 2023. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-08-14 http://lod.bco-dmo.org/id/dataset/1004704

Speciale, E., Lim, P., Jeong, Y., Cook, C., Cohen, N., McClure, W., Schnetzer, A., Marchetti, A. (2026) Pfam differential expression data for diatoms from an iron incubation experiment aboard the R/V Sally Ride during the PUPCYCLE II cruise within the California Current System in May-June 2023. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-09-13 http://lod.bco-dmo.org/id/dataset/1004674

Speciale, E., Lim, P., Jeong, Y., Cook, C., Cohen, N., McClure, W., Schnetzer, A., Marchetti, A. (2026) Pfam differential expression data for mixotrophs from an iron incubation experiment aboard the R/V Sally Ride during the PUPCYCLE II cruise within the California Current System in May-June 2023. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-09-11 http://lod.bco-dmo.org/id/dataset/1004659

Speciale, E., Lim, P., Jeong, Y., Cook, C., Cohen, N., McClure, W., Schnetzer, A., Marchetti, A. (2026) Physiological measurements from an iron incubation experiment using upwelled waters in the California Current System during the PUPCYCLE II cruise in May and June 2023. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-08-12 http://lod.bco-dmo.org/id/dataset/994607

Results

Speciale, E. V., Lim, P., Jeong, Y., Cook, C. C. Z., Cohen, N. R., McClure, W., Schnetzer, A., Till, C. P., Till, R. C., & Marchetti, A. (in review). Mixotrophy as an alternative strategy under iron-limited upwelling conditions. Manuscript submitted for publication.

Results

Speciale, Emily. (2025). THE MOLECULAR PHYSIOLOGY OF MIXOTROPHIC PHYTOPLANKTON UNDER IRON-LIMITED UPWELLING CONDITIONS. The University of North Carolina at Chapel Hill University Libraries. https://doi.org/10.17615/C0G7-RP52

General

Guillou, L., Bachar, D., Audic, S., Bass, D., Berney, C., Bittner, L., ... & Christen, R. (2012). The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy. Nucleic acids research, 41(D1), D597-D604.

Methods

Cook, C. C. Z., Ewton, E. M., Marchetti, A., Menden-Deuer, S., Millette, N. C., Slomka, S., Speciale, E. V., Wilken, S., & Cohen, N. R. (2025). Evaluating acidotropic dyes for detecting mixotrophy in protists: Insights from cultures and field communities. https://doi.org/10.1101/2025.09.29.679303

Methods

Kanehisa, M. (2000). KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Research, 28(1), 27–30. doi:10.1093/nar/28.1.27

Data File(s)	Type	Description	Action
1003525_v1_rna_metatranscriptomic_taxonomy_pupcycle2.csv (19.72 KB)	Comma Separated Values (.csv)	RNA metatranscriptomic taxonomy results from an iron incubation experiment using upwelled waters sampled in the California Current System (CCS) during the PUPCYCLE II cruise; Primary data file for dataset ID 1003525, version 1	1003525_v1_rna_metatranscriptomic_taxonomy_pupcycle2.csv View Table

Files

Filename: 1003525_v1_rna_metatranscriptomic_taxonomy_pupcycle2.csv (19.72 KB)
Type: Comma Separated Values (.csv)

Description:

1003525_v1_rna_metatranscriptomic_taxonomy_pupcycle2.csv View Table

Analyses include:

Physiology (dataset 994607)
- Dissolved inorganic nutrients (nitrate, phosphate, silicic acid)
- Size-fractionated chlorophyll a
- Size-fractionated isotope uptake rates (nitrate and DIC)
- Flow cytometry
- FlowCAM analysis
- FLP experiments for mixotroph cell-specific grazing rates
RNA taxonomy data for normalized reads (this dataset 1003525)
Differential expression for +Fe versus DFB treatments at T1 and T2: Pfam
- Mixotroph Pfam (dataset 1004659)
- Diatom Pfam (dataset 1004674)
Differential expression for +Fe versus DFB treatments at T1 and T2 for mixotrophs and diatoms: KEGG gene (dataset 1004689)
Differential expression for +Fe versus DFB treatments at T1 and T2 for mixotrophs and diatoms: KEGG pathways (dataset 1004704)
Dissolved iron concentrations (dataset 1004007)

See Related Datasets section below for links to the above mentioned datasets.

Results

General

Methods

Kanehisa, M. (2000). KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Research, 28(1), 27–30. doi:10.1093/nar/28.1.27

Dataset: Metatranscriptomic (RNA-seq) taxonomy data from an iron incubation experiment during the PUPCYCLE II cruise (R/V Sally Ride) within the California Current System in May and June of 2023

Principal Investigator: Adrian Marchetti (University of North Carolina at Chapel Hill)

Scientist: Natalie Cohen (University of Georgia)

Scientist: Astrid Schnetzer (North Carolina State University)

Student: Claire Cook (University of Georgia)

Student: Yubeen Jeong (University of North Carolina at Chapel Hill)

Student: Prisca Lim (University of North Carolina at Chapel Hill)

Student: Will McClure (North Carolina State University)

Student: Emily Speciale (University of North Carolina at Chapel Hill)

BCO-DMO Data Manager: Dana Stuart Gerlach (Woods Hole Oceanographic Institution)

Project: CAREER: An integrated molecular and physiological approach to examining the dynamics of upwelled phytoplankton in current and changing oceans (Upwelled Phytoplankton Dynamics)

Abstract

66

31

Files

Related Datasets

Related Publications

Dataset: Metatranscriptomic (RNA-seq) taxonomy data from an iron incubation experiment during the PUPCYCLE II cruise (R/V Sally Ride) within the California Current System in May and June of 2023

Principal Investigator: Adrian Marchetti (University of North Carolina at Chapel Hill)

Scientist: Natalie Cohen (University of Georgia)

Scientist: Astrid Schnetzer (North Carolina State University)

Student: Claire Cook (University of Georgia)

Student: Yubeen Jeong (University of North Carolina at Chapel Hill)

Student: Prisca Lim (University of North Carolina at Chapel Hill)

Student: Will McClure (North Carolina State University)

Student: Emily Speciale (University of North Carolina at Chapel Hill)

BCO-DMO Data Manager: Dana Stuart Gerlach (Woods Hole Oceanographic Institution)

Project: CAREER: An integrated molecular and physiological approach to examining the dynamics of upwelled phytoplankton in current and changing oceans (Upwelled Phytoplankton Dynamics)

Abstract

66

31

Files

Related Datasets

Related Publications

Dataset: Metatranscriptomic (RNA-seq) taxonomy data from an iron incubation experiment during the PUPCYCLE II cruise (R/V Sally Ride) within the California Current System in May and June of 2023

Principal Investigator: Adrian Marchetti (University of North Carolina at Chapel Hill)

Scientist: Natalie Cohen (University of Georgia)

Scientist: Astrid Schnetzer (North Carolina State University)

Student: Claire Cook (University of Georgia)

Student: Yubeen Jeong (University of North Carolina at Chapel Hill)

Student: Prisca Lim (University of North Carolina at Chapel Hill)

Student: Will McClure (North Carolina State University)

Student: Emily Speciale (University of North Carolina at Chapel Hill)

BCO-DMO Data Manager: Dana Stuart Gerlach (Woods Hole Oceanographic Institution)

Project: CAREER: An integrated molecular and physiological approach to examining the dynamics of upwelled phytoplankton in current and changing oceans (Upwelled Phytoplankton Dynamics)

Abstract

Metadata

66

31

Files

Related Datasets

Related Publications

Dataset: Metatranscriptomic (RNA-seq) taxonomy data from an iron incubation experiment during the PUPCYCLE II cruise (R/V Sally Ride) within the California Current System in May and June of 2023

Principal Investigator: Adrian Marchetti (University of North Carolina at Chapel Hill)

Scientist: Natalie Cohen (University of Georgia)

Scientist: Astrid Schnetzer (North Carolina State University)

Student: Claire Cook (University of Georgia)

Student: Yubeen Jeong (University of North Carolina at Chapel Hill)

Student: Prisca Lim (University of North Carolina at Chapel Hill)

Student: Will McClure (North Carolina State University)

Student: Emily Speciale (University of North Carolina at Chapel Hill)

BCO-DMO Data Manager: Dana Stuart Gerlach (Woods Hole Oceanographic Institution)

Project: CAREER: An integrated molecular and physiological approach to examining the dynamics of upwelled phytoplankton in current and changing oceans (Upwelled Phytoplankton Dynamics)

Abstract

Metadata

66

31

Files

Related Datasets

Related Publications