bcodmo_dataset_908689_v1

Name: [Gulf of Alaska copepods: annotated transcriptomes] - 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 (Collaborative Proposal: Optimizing Recruitment of Neocalanus copepods through Strategic Timing of Reproduction and Growth in the Gulf of Alaska)
Creator: BCO-DMO
License: The data may be used and redistributed for free but is not intended for legal use, since it may contain inaccuracies. Neither the data Contributor, ERD, NOAA, nor the United States Government, nor any of their employees or contractors, makes any warranty, express or implied, including warranties of merchantability and fitness for a particular purpose, or assumes any legal liability for the accuracy, completeness, or usefulness, of this information.

Grid DAP Data	Sub- set	Table DAP Data	Make A Graph	W M S	Source Data Files	Acces- sible	Title	Sum- mary	FGDC, ISO, Metadata	Back- ground Info	RSS	E mail	Institution	Dataset ID
		data	graph		files	public	[Gulf of Alaska copepods: annotated transcriptomes] - 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 (Collaborative Proposal: Optimizing Recruitment of Neocalanus copepods through Strategic Timing of Reproduction and Growth in the Gulf of Alaska)		F I M	background			BCO-DMO	bcodmo_dataset_908689_v1

The Dataset's Variables and Attributes

Row Type	Variable Name	Attribute Name	Data Type	Value
attribute	NC_GLOBAL	cdm_data_type	String	Other
attribute	NC_GLOBAL	Conventions	String	COARDS, CF-1.6, ACDD-1.3
attribute	NC_GLOBAL	creator_email	String	info at bco-dmo.org
attribute	NC_GLOBAL	creator_name	String	BCO-DMO
attribute	NC_GLOBAL	creator_url	String	https://www.bco-dmo.org/
attribute	NC_GLOBAL	doi	String	10.26008/1912/bco-dmo.908689.1
attribute	NC_GLOBAL	Easternmost_Easting	double	-147.6667
attribute	NC_GLOBAL	geospatial_lat_max	double	60.6667
attribute	NC_GLOBAL	geospatial_lat_min	double	59.845
attribute	NC_GLOBAL	geospatial_lat_units	String	degrees_north
attribute	NC_GLOBAL	geospatial_lon_max	double	-147.6667
attribute	NC_GLOBAL	geospatial_lon_min	double	-149.4667
attribute	NC_GLOBAL	geospatial_lon_units	String	degrees_east
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/908689
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	license	String	The data may be used and redistributed for free but is not intended for legal use, since it may contain inaccuracies. Neither the data Contributor, ERD, NOAA, nor the United States Government, nor any of their employees or contractors, makes any warranty, express or implied, including warranties of merchantability and fitness for a particular purpose, or assumes any legal liability for the accuracy, completeness, or usefulness, of this information.
attribute	NC_GLOBAL	Northernmost_Northing	double	60.6667
attribute	NC_GLOBAL	sourceUrl	String	(local files)
attribute	NC_GLOBAL	Southernmost_Northing	double	59.845
attribute	NC_GLOBAL	summary	String	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, Neocalanus cristatus, Eucalanus bungii and Metridia pacifica and three for Neocalanus flemingeri and two for Calanus marshallae. Total RNA from single individuals was used to construct gene libraries that were sequenced on an Illumina Next-Seq platform. Short-sequence reads were assembled with Trinity software and resulting transcripts were annotated using the SwissProt database with additional functional annotation using gene ontology terms and enzyme function. The annotations files are the first ones published for these species. The integrated dataset can be used for quantitative inter- and intra-species comparisons of gene expression patterns across biological processes using the annotations. These data are further described in the following publications: Hartline, et al. (2023) (DOI: 10.1038/s41597-023-02130-1), Roncalli, et al. (2022) (DOI: 10.1111/mec.16354), and Roncalli, et al. (2019) (DOI: 10.1038/s42003-019-0565-5)
attribute	NC_GLOBAL	title	String	[Gulf of Alaska copepods: annotated transcriptomes] - 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 (Collaborative Proposal: Optimizing Recruitment of Neocalanus copepods through Strategic Timing of Reproduction and Growth in the Gulf of Alaska)
attribute	NC_GLOBAL	Westernmost_Easting	double	-149.4667
variable	seq_id		String
attribute	seq_id	long_name	String	Seq_id
attribute	seq_id	units	String	unitless
variable	Genbank_accession		String
attribute	Genbank_accession	long_name	String	Genbank_accession
attribute	Genbank_accession	units	String	unitless
variable	Species		String
attribute	Species	long_name	String	Species
attribute	Species	units	String	unitless
variable	Station		String
attribute	Station	long_name	String	Station
attribute	Station	units	String	unitless
variable	latitude		float
attribute	latitude	_CoordinateAxisType	String	Lat
attribute	latitude	actual_range	float	59.845, 60.6667
attribute	latitude	axis	String	Y
attribute	latitude	ioos_category	String	Location
attribute	latitude	long_name	String	Latitude
attribute	latitude	standard_name	String	latitude
attribute	latitude	units	String	degrees_north
variable	longitude		float
attribute	longitude	_CoordinateAxisType	String	Lon
attribute	longitude	actual_range	float	-149.4667, -147.6667
attribute	longitude	axis	String	X
attribute	longitude	ioos_category	String	Location
attribute	longitude	long_name	String	Longitude
attribute	longitude	standard_name	String	longitude
attribute	longitude	units	String	degrees_east
variable	Collection_date		String
attribute	Collection_date	long_name	String	Collection_date
attribute	Collection_date	units	String	unitless
variable	Depth_range		String
attribute	Depth_range	long_name	String	Depth_range
attribute	Depth_range	units	String	meters (m)
variable	Life_stage		String
attribute	Life_stage	long_name	String	Life_stage
attribute	Life_stage	units	String	unitless
variable	Sex		String
attribute	Sex	long_name	String	Sex
attribute	Sex	units	String	unitless
variable	Entry		String
attribute	Entry	long_name	String	Entry
attribute	Entry	units	String	unitless
variable	Entry_name		String
attribute	Entry_name	long_name	String	Entry_name
attribute	Entry_name	units	String	unitless
variable	evalue		String
attribute	evalue	long_name	String	Evalue
attribute	evalue	units	String	unitless
variable	Protein_names		String
attribute	Protein_names	long_name	String	Protein_names
attribute	Protein_names	units	String	unitless
variable	Gene_names		String
attribute	Gene_names	long_name	String	Gene_names
attribute	Gene_names	units	String	unitless
variable	Organism		String
attribute	Organism	long_name	String	Organism
attribute	Organism	units	String	unitless
variable	Cross_reference_KEGG		String
attribute	Cross_reference_KEGG	long_name	String	Cross_reference_kegg
attribute	Cross_reference_KEGG	units	String	unitless
variable	Gene_ontology_IDs		String
attribute	Gene_ontology_IDs	long_name	String	Gene_ontology_ids
attribute	Gene_ontology_IDs	units	String	unitless
variable	Gene_ontology_GO		String
attribute	Gene_ontology_GO	long_name	String	Gene_ontology_go
attribute	Gene_ontology_GO	units	String	unitless
variable	Gene_ontology_biological_process		String
attribute	Gene_ontology_biological_process	long_name	String	Gene_ontology_biological_process
attribute	Gene_ontology_biological_process	units	String	unitless
variable	Gene_ontology_cellular_component		String
attribute	Gene_ontology_cellular_component	long_name	String	Gene_ontology_cellular_component
attribute	Gene_ontology_cellular_component	units	String	unitless
variable	Gene_ontology_molecular_function		String
attribute	Gene_ontology_molecular_function	long_name	String	Gene_ontology_molecular_function
attribute	Gene_ontology_molecular_function	units	String	unitless
variable	BioProject		String
attribute	BioProject	long_name	String	Bioproject
attribute	BioProject	units	String	unitless
variable	TSA_Master_Accession		String
attribute	TSA_Master_Accession	long_name	String	Tsa_master_accession
attribute	TSA_Master_Accession	units	String	unitless
variable	Study_Accession		String
attribute	Study_Accession	long_name	String	Study_accession
attribute	Study_Accession	units	String	unitless
variable	Study_Title		String
attribute	Study_Title	long_name	String	Study_title
attribute	Study_Title	units	String	unitless
variable	Experiement_Accession		String
attribute	Experiement_Accession	long_name	String	Experiement_accession
attribute	Experiement_Accession	units	String	unitless
variable	Experiment_Title		String
attribute	Experiment_Title	long_name	String	Experiment_title
attribute	Experiment_Title	units	String	unitless
variable	SRA_Accession		String
attribute	SRA_Accession	long_name	String	Sra_accession
attribute	SRA_Accession	units	String	unitless
variable	BioSample		String
attribute	BioSample	long_name	String	Biosample
attribute	BioSample	units	String	unitless
variable	Sample_Accession		String
attribute	Sample_Accession	long_name	String	Sample_accession
attribute	Sample_Accession	units	String	unitless

The information in the table above is also available in other file formats (.csv, .htmlTable, .itx, .json, .jsonlCSV1, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.