Data File(s)	Type	Description	Action
914459_v1_relative_gene_expression.csv (13.06 MB)	Comma Separated Values (.csv)	Primary data file for dataset ID 914459, version 1 Relative gene expression given in log2(RPKM +1) for all transcripts based on RNA-Seq data mapped against a reference transcriptome.	Download View Table What is ERDDAP? SUBSET DATA VIEW TABLE CSV TSV GeoJSON MATLAB netCDF

Supplemental File(s)	Type	Description	Action
differentially_expressed_genes.csv (477.77 KB)	Comma Separated Values (.csv)	List of differentially expressed genes (DEGs) calculated using EdgeR GLM analysis. Columns: seq_id, Genbank_accession See the parameters section of this dataset for definitions of seq_id and Genbank_accession parameters used in this file. Blank values in Genbank_accession represent no corresponding value for seq_id	Download View Table
supplemental_files/metadata_table_with_ncbi_accessions.csv (10.55 KB)	Comma Separated Values (.csv)	See the supplemental file "Metadata table parameter definitions", metadata_table_parameter_definitions.csv, for definitions of parameters included in this metadata table. Columns: Replicate, Organism_Name, Station, Latitude, Longitude, Collection_date, Year, Month, Day, Depth_range, week_after_molting_to_CV, feeding_protocol, BioProject, Study_Accession, Study_Title, Experiment_Accession, Experiment_Title, BioSample, Sample_Accession	Download
metadata_table_parameter_definitions.csv (1.54 KB)	Comma Separated Values (.csv)	This file contains parameter definitions for the supplemental file "Metadata table including NCBI accessions", metadata_table_with_ncbi_accessions.csv Columns: suppliedName, description, suppliedUnits, no_data_value, bcodmo_standard_parameter_name, Datatype, Format suppliedName = Supplied Name description = parameter description suppliedUnits = parameter units no_data_value = fill value for no data bcodmo_standard_parameter_name = BCO-DMO standard parameter name DataType = parameter data type Format = date format if the parameter data type is date	Download
seq_id_genbank_accession_cross_reference.csv (1.96 MB)	Comma Separated Values (.csv)	Cross-reference between Trinity IDs and Genbank accession numbers Columns: seq_id, Genbank_accession See the parameters section of this dataset for definitions of seq_id and Genbank_accession parameters used in this file.	Download View Table
species_list.csv (211.00 B)	Comma Separated Values (.csv)	Species WoRMS taxonomy table with columns: ScientificName, AphiaID, LSID, Authority, Class, Order, Family, Genus, Species	Download View Table
supplemental_files/unpivoted_relative_gene_expression.csv (230.86 MB)	Comma Separated Values (.csv)	See the supplemental file "Metadata table parameter definitions", metadata_table_parameter_definitions.csv, for definitions of parameters included in this file that are not listed as parameters on this dataset page. Columns: seq_id, Genbank_Accession, Organism_Name, Station, Latitude, Longitude, Collection_date, Year, Month, Day, Depth_range, Replicate, relative_expression, week_after_molting_to_CV, feeding_protocol	Download

Files

Filename: 914459_v1_relative_gene_expression.csv (13.06 MB)
Type: Comma Separated Values (.csv)
Description: Primary data file for dataset ID 914459, version 1 Relative gene expression given in log2(RPKM +1) for all transcripts based on RNA-Seq data mapped against a reference transcriptome.

Download View Table

Supplemental Files

Filename: differentially_expressed_genes.csv (477.77 KB)
Type: Comma Separated Values (.csv)
Description: List of differentially expressed genes (DEGs) calculated using EdgeR GLM analysis. Columns: seq_id, Genbank_accession See the parameters section of this dataset for definitions of seq_id and Genbank_accession parameters used in this file. Blank values in Genbank_accession represent no corresponding value for seq_id

Download View Table

Filename: supplemental_files/metadata_table_with_ncbi_accessions.csv (10.55 KB)
Type: Comma Separated Values (.csv)
Description: See the supplemental file "Metadata table parameter definitions", metadata_table_parameter_definitions.csv, for definitions of parameters included in this metadata table. Columns: Replicate, Organism_Name, Station, Latitude, Longitude, Collection_date, Year, Month, Day, Depth_range, week_after_molting_to_CV, feeding_protocol, BioProject, Study_Accession, Study_Title, Experiment_Accession, Experiment_Title, BioSample, Sample_Accession

Download

Filename: metadata_table_parameter_definitions.csv (1.54 KB)
Type: Comma Separated Values (.csv)
Description: This file contains parameter definitions for the supplemental file "Metadata table including NCBI accessions", metadata_table_with_ncbi_accessions.csv Columns: suppliedName, description, suppliedUnits, no_data_value, bcodmo_standard_parameter_name, Datatype, Format suppliedName = Supplied Name description = parameter description suppliedUnits = parameter units no_data_value = fill value for no data bcodmo_standard_parameter_name = BCO-DMO standard parameter name DataType = parameter data type Format = date format if the parameter data type is date

Download

Filename: seq_id_genbank_accession_cross_reference.csv (1.96 MB)
Type: Comma Separated Values (.csv)
Description: Cross-reference between Trinity IDs and Genbank accession numbers Columns: seq_id, Genbank_accession See the parameters section of this dataset for definitions of seq_id and Genbank_accession parameters used in this file.

Download View Table

Filename: species_list.csv (211.00 B)
Type: Comma Separated Values (.csv)
Description: Species WoRMS taxonomy table with columns: ScientificName, AphiaID, LSID, Authority, Class, Order, Family, Genus, Species

Download View Table

Filename: supplemental_files/unpivoted_relative_gene_expression.csv (230.86 MB)
Type: Comma Separated Values (.csv)
Description: See the supplemental file "Metadata table parameter definitions", metadata_table_parameter_definitions.csv, for definitions of parameters included in this file that are not listed as parameters on this dataset page. Columns: seq_id, Genbank_Accession, Organism_Name, Station, Latitude, Longitude, Collection_date, Year, Month, Day, Depth_range, Replicate, relative_expression, week_after_molting_to_CV, feeding_protocol

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These data are further described in the following publications:

Roncalli, V., Block, L. N., Niestroy, J. L., Cieslak, M. C., Castelfranco, A. M., Hartline, D. K., & Lenz, P. H. (2023). Experimental analysis of development, lipid accumulation and gene expression in a high-latitude marine copepod. Journal of Plankton Research, 45(6), 885–898. https://doi.org/10.1093/plankt/fbad045

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. Commun 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 was cited in metadata of dataset (954181) as a related dataset that provides additional information to National Center for Biotechnology Information raw sequences.

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

Hartline, D. K., Lenz, P. H., Cieslak, M. C. (2024) 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. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-07-02 doi:10.26008/1912/bco-dmo.908689.1

IsRelatedTo

Dataset: Multiyear RNA-Seq of Neocalanus flemingeri stages CV and Adult Female
Relationship Description: Related datasets to raw sequence accessions at the National Center for Biotechnology Information.

Lenz, P. H., Roncalli, V., Cieslak, M. C. (2024) Multiyear RNA-Seq of Neocalanus flemingeri stages CV and Adult Female from the R/V Tiglax and R/V Sikuliaq in the Northern Gulf of Alaska from 2015-2022. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-07-26 doi:10.26008/1912/bco-dmo.922330.1

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 (2022). Neocalanus flemingeri, Response to food availability in pre-adult Neocalanus flemingeri. 2022/02. NCBI:BioProject: PRJNA807352.[Internet]. Bethesda, MD: National Library of Medicine (US), National Center for Biotechnology Information; Available from: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA807352.

Related Publications

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

Methods

Bray, N. L., Pimentel, H., Melsted, P., & Pachter, L. (2016). Near-optimal probabilistic RNA-seq quantification. Nature Biotechnology, 34(5), 525–527. https://doi.org/10.1038/nbt.3519

Methods

Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology, 10(3), R25. https://doi.org/10.1186/gb-2009-10-3-r25

Methods

Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008). Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods, 5(7), 621–628. https://doi.org/10.1038/nmeth.1226

Methods

Robinson, M. D., & Oshlack, A. (2010). A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biology, 11(3), R25. https://doi.org/10.1186/gb-2010-11-3-r25

Dataset: 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

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

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

Scientist: Jeanette L. Niestroy (University of Hawaiʻi at Mānoa)

Scientist: Vittoria Roncalli (University of Hawaiʻi at Mānoa)

Student: Lauren N Block (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 Research: Molecular profiling of the ecophysiology of dormancy induction in calanid copepods of the Northern Gulf of Alaska LTER site (Diapause preparation)

Abstract

Files

Supplemental Files

Related Datasets

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