Dataset: Annotated de novo transcriptomes generated from six co-occurring species of calanoid copepods from the R/V Tiglax TXF18, TXS19, TXF15, TXF17 in the Gulf of Alaska from 2015-2019

Name: Annotated de novo transcriptomes generated from six co-occurring species of calanoid copepods from the R/V Tiglax TXF18, TXS19, TXF15, TXF17 in the Gulf of Alaska from 2015-2019
Published: 2024-07-02
Keywords: Neocalanus flemingeri, Eucalanus bungii, Calanus marshallae, Metridia pacifica, Neocalanus cristatus, Neocalanus plumchrus, oceans

ValidatedFinal no updates expectedDOI: 10.26008/1912/bco-dmo.908689.1Version 1 (2024-07-02)Dataset Type:experimentalDataset Type:Cruise Results

Principal Investigator: Daniel K. Hartline (University of Hawaiʻi at Mānoa)

Scientist, Contact: Petra H. Lenz (University of Hawaiʻi at Mānoa)

Technician, Data Manager: Matthew C. Cieslak (University of Hawaiʻi at Mānoa)

BCO-DMO Data Manager: Lynne M. Merchant (Woods Hole Oceanographic Institution)

Project: Collaborative Proposal: Optimizing Recruitment of Neocalanus copepods through Strategic Timing of Reproduction and Growth in the Gulf of Alaska (Neocalanus Gulf of Alaska)

Project: Collaborative Research: Molecular profiling of the ecophysiology of dormancy induction in calanid copepods of the Northern Gulf of Alaska LTER site (Diapause preparation)

Abstract

The dataset includes the annotation files of nine high-quality de novo transcriptomes generated from shotgun assemblies of short-sequence reads. The species are ecologically-important members of sub-arctic North Pacific marine zooplankton communities. The de novo assemblies included one generated several years ago plus eight new ones generated from six co-occurring species of calanoid copepods in the Gulf of Alaska. The transcriptomes include the first published ones for Neocalanus plumchrus, Ne...

Cite Dataset

Spatial Extent: N:60.67 E:-147.67 S:59.84 W:-149.47
Temporal Extent: 2015-05-10 - 2019-04-30

Data File(s)	Type	Description	Action
908689_v1_annotated_transcriptomes.csv (611.74 MB)	Comma Separated Values (.csv)	Primary data file for dataset ID 908689, version 1 Combined file of the following supplemental annotated transcriptome files: Neocalanus flemingeri 2015 stage CV annotated transcriptome Neocalanus flemingeri 2018 stage CV annotated transcriptome Neocalanus flemingeri 2019 stage CV annotated transcriptome Neocalanus cristatus 2017 stage CV annotated transcriptome Neocalanus plumchrus 2015 stage adult male annotated transcriptome Calanus marshallae 2017 stage CV annotated transcriptome Calanus marshallae 2018 stage CV annotated transcriptome Eucalanus bungii 2017 stage CV annotated transcriptome Metridia pacifica 2017 stage adult female annotated transcriptome	Download View Table What is ERDDAP? SUBSET DATA VIEW TABLE CSV TSV GeoJSON MATLAB netCDF

Supplemental File(s)	Type	Description	Action
supplemental_files/calanus_marshallae_stage_cv_2017_annotated_transcriptome.csv (66.50 MB)	Comma Separated Values (.csv)	Parameter names and definitions are the same as the main combined dataset file.	Download
supplemental_files/calanus_marshallae_stage_cv_2018_annotated_transcriptome.csv (76.30 MB)	Comma Separated Values (.csv)	Parameter names and definitions are the same as the main combined dataset file.	Download
supplemental_files/eucalanus_bungii_stage_cv_2017_annotated_transcriptome.csv (34.28 MB)	Comma Separated Values (.csv)	Parameter names and definitions are the same as the main combined dataset file.	Download
supplemental_files/metadata_table_with_ncbi_accessions.csv (2.23 KB)	Comma Separated Values (.csv)	Metadata table including NCBI accession values for all the supplemental annotated transcriptome files. Columns are: Species, Station, Latitude, Longitude, Collection_date, Depth_range, Life_stage, Sex, BioProject, TSA_Master_Accession, Study_Accession, Study_Title, Experiment_Accession, Experiment_Title, SRA_Accession, BioSample, Sample_Accession The parameter definitions are the same as the main dataset file and are described in the parameters section.	Download
supplemental_files/metridia_pacifica_stage_adult_female_2017_annotated_transcriptome.csv (103.88 MB)	Comma Separated Values (.csv)	Parameter names and definitions are the same as the main combined dataset file.	Download
supplemental_files/neocalanus_cristatus_stage_cv_2017_annotated_transcriptome.csv (80.95 MB)	Comma Separated Values (.csv)	Parameter names and definitions are the same as the main combined dataset file.	Download
supplemental_files/neocalanus_flemingeri_stage_cv_2015_annotated_transcriptome.csv (49.92 MB)	Comma Separated Values (.csv)	Parameter names and definitions are the same as the main combined dataset file.	Download
supplemental_files/neocalanus_flemingeri_stage_cv_2018_annotated_transcriptome.csv (75.87 MB)	Comma Separated Values (.csv)	Parameter names and definitions are the same as the main combined dataset file.	Download
supplemental_files/neocalanus_flemingeri_stage_cv_2019_annotated_transcriptome.csv (60.02 MB)	Comma Separated Values (.csv)	Parameter names and definitions are the same as the main combined dataset file.	Download
supplemental_files/neocalanus_plumchrus_stage_adult_male_2015_annotated_transcriptome.csv (64.02 MB)	Comma Separated Values (.csv)	Parameter names and definitions are the same as the main combined dataset file.	Download
species_list.csv (889.00 B)	Comma Separated Values (.csv)	Taxonomic identifiers AphiaID and LSID for the species of the annotated transcriptomes	Download View Table

Files

Filename: 908689_v1_annotated_transcriptomes.csv (611.74 MB)
Type: Comma Separated Values (.csv)
Description: Primary data file for dataset ID 908689, version 1 Combined file of the following supplemental annotated transcriptome files: Neocalanus flemingeri 2015 stage CV annotated transcriptome Neocalanus flemingeri 2018 stage CV annotated transcriptome Neocalanus flemingeri 2019 stage CV annotated transcriptome Neocalanus cristatus 2017 stage CV annotated transcriptome Neocalanus plumchrus 2015 stage adult male annotated transcriptome Calanus marshallae 2017 stage CV annotated transcriptome Calanus marshallae 2018 stage CV annotated transcriptome Eucalanus bungii 2017 stage CV annotated transcriptome Metridia pacifica 2017 stage adult female annotated transcriptome

Download View Table

Supplemental Files

Filename: supplemental_files/calanus_marshallae_stage_cv_2017_annotated_transcriptome.csv (66.50 MB)
Type: Comma Separated Values (.csv)
Description: Parameter names and definitions are the same as the main combined dataset file.

Download

Filename: supplemental_files/calanus_marshallae_stage_cv_2018_annotated_transcriptome.csv (76.30 MB)
Type: Comma Separated Values (.csv)
Description: Parameter names and definitions are the same as the main combined dataset file.

Download

Filename: supplemental_files/eucalanus_bungii_stage_cv_2017_annotated_transcriptome.csv (34.28 MB)
Type: Comma Separated Values (.csv)
Description: Parameter names and definitions are the same as the main combined dataset file.

Download

Filename: supplemental_files/metadata_table_with_ncbi_accessions.csv (2.23 KB)
Type: Comma Separated Values (.csv)
Description: Metadata table including NCBI accession values for all the supplemental annotated transcriptome files. Columns are: Species, Station, Latitude, Longitude, Collection_date, Depth_range, Life_stage, Sex, BioProject, TSA_Master_Accession, Study_Accession, Study_Title, Experiment_Accession, Experiment_Title, SRA_Accession, BioSample, Sample_Accession The parameter definitions are the same as the main dataset file and are described in the parameters section.

Download

Filename: supplemental_files/metridia_pacifica_stage_adult_female_2017_annotated_transcriptome.csv (103.88 MB)
Type: Comma Separated Values (.csv)
Description: Parameter names and definitions are the same as the main combined dataset file.

Download

Filename: supplemental_files/neocalanus_cristatus_stage_cv_2017_annotated_transcriptome.csv (80.95 MB)
Type: Comma Separated Values (.csv)
Description: Parameter names and definitions are the same as the main combined dataset file.

Download

Filename: supplemental_files/neocalanus_flemingeri_stage_cv_2015_annotated_transcriptome.csv (49.92 MB)
Type: Comma Separated Values (.csv)
Description: Parameter names and definitions are the same as the main combined dataset file.

Download

Filename: supplemental_files/neocalanus_flemingeri_stage_cv_2018_annotated_transcriptome.csv (75.87 MB)
Type: Comma Separated Values (.csv)
Description: Parameter names and definitions are the same as the main combined dataset file.

Download

Filename: supplemental_files/neocalanus_flemingeri_stage_cv_2019_annotated_transcriptome.csv (60.02 MB)
Type: Comma Separated Values (.csv)
Description: Parameter names and definitions are the same as the main combined dataset file.

Download

Filename: supplemental_files/neocalanus_plumchrus_stage_adult_male_2015_annotated_transcriptome.csv (64.02 MB)
Type: Comma Separated Values (.csv)
Description: Parameter names and definitions are the same as the main combined dataset file.

Download

Filename: species_list.csv (889.00 B)
Type: Comma Separated Values (.csv)
Description: Taxonomic identifiers AphiaID and LSID for the species of the annotated transcriptomes

Download View Table

These data are further described in the following publications:

Hartline, D. K., Cieslak, M. C., Castelfranco, A. M., Lieberman, B., Roncalli, V., & Lenz, P. H. (2023). De novo transcriptomes of six calanoid copepods (Crustacea): a resource for the discovery of novel genes. Scientific Data, 10(1). https://doi.org/10.1038/s41597-023-02130-1

Roncalli, V., Niestroy, J., Cieslak, M. C., Castelfranco, A. M., Hopcroft, R. R., & Lenz, P. H. (2022). Physiological acclimatization in high‐latitude zooplankton. Molecular Ecology, 31(6), 1753–1765. Portico. https://doi.org/10.1111/mec.16354

Roncalli, V., Cieslak, M. C., Germano, M., Hopcroft, R. R., & Lenz, P. H. (2019). Regional heterogeneity impacts gene expression in the subarctic zooplankter Neocalanus flemingeri in the northern Gulf of Alaska. Communications Biology, 2(1). https://doi.org/10.1038/s42003-019-0565-5

Related Datasets

IsRelatedTo

Dataset: Molecular identification of genetic variants of Neocalanus flemingeri
Relationship Description: This dataset (908689) was cited in the methods of another dataset (954181) "...The reference consisted of consensus sequences obtained by comparing sequences downloaded from NCBI and from de novo assemblies (Hartline et al., 2023; Hartline et al., 2024 [BCO-DMO dataset 908689]). "

Block, L. N., Lenz, P. H. (2025) Molecular identification of genetic variants of Neocalanus flemingeri in the Gulf of Alaska from samples collected from 2015 to 2023. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-02-21 http://lod.bco-dmo.org/id/dataset/954181

Lenz, P. H., Hartline, D. K., Roncalli, V., Block, L. N., Niestroy, J. L., Cieslak, M. C. (2024) Gene expression profiles for Neocalanus flemingeri pre adults (CV) exposed to four different experimental food conditions collected from the M/V Dora in the Gulf of Alaska at station GAK1 from April 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-05-30 doi:10.26008/1912/bco-dmo.914459.1

University of Hawaii at Manoa (2018). Neocalanus flemingeri, Neocalanus flemingeri pre adult (CV). 2018/10. NCBI:BioProject: PRJNA496596 [Internet]. Bethesda, MD: National Library of Medicine (US), National Center for Biotechnology Information; Available from: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA496596.

University of Hawaii at Manoa (2018). Neocalanus plumchrus, Neocalanus cristatus, Calanus marshallae, Eucalanus bungii, Metridia pacifica, Ocean ZOOP-Zooplankton transcriptomes. 2020/09. NCBI:BioProject: PRJNA662858.[Internet]. Bethesda, MD: National Library of Medicine (US), National Center for Biotechnology Information; Available from: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA662858

Related Publications

Results

Hartline, D. K., Cieslak, M. C., Castelfranco, A. M., Lieberman, B., Roncalli, V., & Lenz, P. H. (2023). De novo transcriptomes of six calanoid copepods (Crustacea): a resource for the discovery of novel genes. Scientific Data, 10(1). https://doi.org/10.1038/s41597-023-02130-1

Results

Roncalli, V., Cieslak, M. C., Germano, M., Hopcroft, R. R., & Lenz, P. H. (2019). Regional heterogeneity impacts gene expression in the subarctic zooplankter Neocalanus flemingeri in the northern Gulf of Alaska. Communications Biology, 2(1). https://doi.org/10.1038/s42003-019-0565-5

Results

Roncalli, V., Niestroy, J., Cieslak, M. C., Castelfranco, A. M., Hopcroft, R. R., & Lenz, P. H. (2022). Physiological acclimatization in high‐latitude zooplankton. Molecular Ecology, 31(6), 1753–1765. Portico. https://doi.org/10.1111/mec.16354

Methods

Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., Harris, M. A., Hill, D. P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J. C., Richardson, J. E., Ringwald, M., Rubin, G. M., & Sherlock, G. (2000). Gene Ontology: tool for the unification of biology. Nature Genetics, 25(1), 25–29. https://doi.org/10.1038/75556

Methods

Bateman, A., Martin, M.-J., Orchard, S., Magrane, M., Agivetova, R., Ahmad, S., Alpi, E., Bowler-Barnett, E. H., Britto, R., Bursteinas, B., Bye-A-Jee, H., Coetzee, R., Cukura, A., Da Silva, A., Denny, P., Dogan, T., Ebenezer, T., Fan, J., … Teodoro, D. (2020). UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Research, 49(D1), D480–D489. https://doi.org/10.1093/nar/gkaa1100

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Dataset: Annotated de novo transcriptomes generated from six co-occurring species of calanoid copepods from the R/V Tiglax TXF18, TXS19, TXF15, TXF17 in the Gulf of Alaska from 2015-2019

ValidatedFinal no updates expectedDOI: 10.26008/1912/bco-dmo.908689.1Version 1 (2024-07-02)Dataset Type:experimentalDataset Type:Cruise Results

Principal Investigator: Daniel K. Hartline (University of Hawaiʻi at Mānoa)

Scientist, Contact: Petra H. Lenz (University of Hawaiʻi at Mānoa)

Technician, Data Manager: Matthew C. Cieslak (University of Hawaiʻi at Mānoa)

BCO-DMO Data Manager: Lynne M. Merchant (Woods Hole Oceanographic Institution)

Project: Collaborative Proposal: Optimizing Recruitment of Neocalanus copepods through Strategic Timing of Reproduction and Growth in the Gulf of Alaska (Neocalanus Gulf of Alaska)

Project: Collaborative Research: Molecular profiling of the ecophysiology of dormancy induction in calanid copepods of the Northern Gulf of Alaska LTER site (Diapause preparation)

Abstract

Cite Dataset

Spatial Extent: N:60.67 E:-147.67 S:59.84 W:-149.47
Temporal Extent: 2015-05-10 - 2019-04-30

Data File(s)	Type	Description	Action
908689_v1_annotated_transcriptomes.csv (611.74 MB)	Comma Separated Values (.csv)	Primary data file for dataset ID 908689, version 1 Combined file of the following supplemental annotated transcriptome files: Neocalanus flemingeri 2015 stage CV annotated transcriptome Neocalanus flemingeri 2018 stage CV annotated transcriptome Neocalanus flemingeri 2019 stage CV annotated transcriptome Neocalanus cristatus 2017 stage CV annotated transcriptome Neocalanus plumchrus 2015 stage adult male annotated transcriptome Calanus marshallae 2017 stage CV annotated transcriptome Calanus marshallae 2018 stage CV annotated transcriptome Eucalanus bungii 2017 stage CV annotated transcriptome Metridia pacifica 2017 stage adult female annotated transcriptome	Download View Table What is ERDDAP? SUBSET DATA VIEW TABLE CSV TSV GeoJSON MATLAB netCDF

Supplemental File(s)	Type	Description	Action
supplemental_files/calanus_marshallae_stage_cv_2017_annotated_transcriptome.csv (66.50 MB)	Comma Separated Values (.csv)	Parameter names and definitions are the same as the main combined dataset file.	Download
supplemental_files/calanus_marshallae_stage_cv_2018_annotated_transcriptome.csv (76.30 MB)	Comma Separated Values (.csv)	Parameter names and definitions are the same as the main combined dataset file.	Download
supplemental_files/eucalanus_bungii_stage_cv_2017_annotated_transcriptome.csv (34.28 MB)	Comma Separated Values (.csv)	Parameter names and definitions are the same as the main combined dataset file.	Download
supplemental_files/metadata_table_with_ncbi_accessions.csv (2.23 KB)	Comma Separated Values (.csv)	Metadata table including NCBI accession values for all the supplemental annotated transcriptome files. Columns are: Species, Station, Latitude, Longitude, Collection_date, Depth_range, Life_stage, Sex, BioProject, TSA_Master_Accession, Study_Accession, Study_Title, Experiment_Accession, Experiment_Title, SRA_Accession, BioSample, Sample_Accession The parameter definitions are the same as the main dataset file and are described in the parameters section.	Download
supplemental_files/metridia_pacifica_stage_adult_female_2017_annotated_transcriptome.csv (103.88 MB)	Comma Separated Values (.csv)	Parameter names and definitions are the same as the main combined dataset file.	Download
supplemental_files/neocalanus_cristatus_stage_cv_2017_annotated_transcriptome.csv (80.95 MB)	Comma Separated Values (.csv)	Parameter names and definitions are the same as the main combined dataset file.	Download
supplemental_files/neocalanus_flemingeri_stage_cv_2015_annotated_transcriptome.csv (49.92 MB)	Comma Separated Values (.csv)	Parameter names and definitions are the same as the main combined dataset file.	Download
supplemental_files/neocalanus_flemingeri_stage_cv_2018_annotated_transcriptome.csv (75.87 MB)	Comma Separated Values (.csv)	Parameter names and definitions are the same as the main combined dataset file.	Download
supplemental_files/neocalanus_flemingeri_stage_cv_2019_annotated_transcriptome.csv (60.02 MB)	Comma Separated Values (.csv)	Parameter names and definitions are the same as the main combined dataset file.	Download
supplemental_files/neocalanus_plumchrus_stage_adult_male_2015_annotated_transcriptome.csv (64.02 MB)	Comma Separated Values (.csv)	Parameter names and definitions are the same as the main combined dataset file.	Download
species_list.csv (889.00 B)	Comma Separated Values (.csv)	Taxonomic identifiers AphiaID and LSID for the species of the annotated transcriptomes	Download View Table

Files

Download View Table

Supplemental Files

Download

Filename: species_list.csv (889.00 B)
Type: Comma Separated Values (.csv)
Description: Taxonomic identifiers AphiaID and LSID for the species of the annotated transcriptomes

Download View Table

These data are further described in the following publications:

Related Datasets

Related Publications

Results

Hartline, D. K., Cieslak, M. C., Castelfranco, A. M., Lieberman, B., Roncalli, V., & Lenz, P. H. (2023). De novo transcriptomes of six calanoid copepods (Crustacea): a resource for the discovery of novel genes. Scientific Data, 10(1). https://doi.org/10.1038/s41597-023-02130-1

Results

Roncalli, V., Cieslak, M. C., Germano, M., Hopcroft, R. R., & Lenz, P. H. (2019). Regional heterogeneity impacts gene expression in the subarctic zooplankter Neocalanus flemingeri in the northern Gulf of Alaska. Communications Biology, 2(1). https://doi.org/10.1038/s42003-019-0565-5

Results

Methods