bcodmo_dataset_914459_v1

Name: [Neocalanus flemingeri incubation experiment: gene expression] - 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 (Collaborative Research: Molecular profiling of the ecophysiology of dormancy induction in calanid copepods of the Northern Gulf of Alaska LTER site)
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	[Neocalanus flemingeri incubation experiment: gene expression] - 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 (Collaborative Research: Molecular profiling of the ecophysiology of dormancy induction in calanid copepods of the Northern Gulf of Alaska LTER site)		F I M	background			BCO-DMO	bcodmo_dataset_914459_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.914459.1
attribute	NC_GLOBAL	Easternmost_Easting	double	-149.4838
attribute	NC_GLOBAL	geospatial_lat_max	double	59.8443
attribute	NC_GLOBAL	geospatial_lat_min	double	59.8443
attribute	NC_GLOBAL	geospatial_lat_units	String	degrees_north
attribute	NC_GLOBAL	geospatial_lon_max	double	-149.4838
attribute	NC_GLOBAL	geospatial_lon_min	double	-149.4838
attribute	NC_GLOBAL	geospatial_lon_units	String	degrees_east
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/914459
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	59.8443
attribute	NC_GLOBAL	sourceUrl	String	(local files)
attribute	NC_GLOBAL	Southernmost_Northing	double	59.8443
attribute	NC_GLOBAL	summary	String	This experimental dataset includes relative expression of individual Neocalanus flemingeri stage CV individuals incubated for different lengths of time and four different food treatments. The experimental protocol and results are described in detail in Roncalli et al., 2023. Briefly, field-collected N. flemingeri were allowed to molt into stage CV and then sorted into four different treatments: no food, low carbon, high carbon and high carbon with diatoms. After a one-week incubation, individuals from all four treatments were processed individually for RNA-Seq. In addition, following two and three-week incubations, copepods from the three fed treatments were processed individually for RNA-Seq. Short-sequence reads were mapped against a reference transcriptome and normalized gene expression was computed for each transcript. The dataset includes log-transformed relative gene expression in reads per kilobase per million reads (RPKM) (log2[RPKM+1]). The dataset also includes a list of differentially expressed genes and a look-up table that cross-references the hierarchical identifications of transcripts generated by the Trinity assembly software and the corresponding National Center for Biotechnology Information (NCBI) accession number. These data are further described in the following publications: Roncalli, et al. (2023) (DOI: 10.1093/plankt/fbad045) and Roncalli, et al. (2019) (DOI: 10.1038/s42003-019-0565-5)
attribute	NC_GLOBAL	title	String	[Neocalanus flemingeri incubation experiment: gene expression] - 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 (Collaborative Research: Molecular profiling of the ecophysiology of dormancy induction in calanid copepods of the Northern Gulf of Alaska LTER site)
attribute	NC_GLOBAL	Westernmost_Easting	double	-149.4838
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	Organism_Name		String
attribute	Organism_Name	long_name	String	Organism_name
attribute	Organism_Name	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	59.8443, 59.8443
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	-149.4838, -149.4838
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	Year		int
attribute	Year	actual_range	int	2019, 2019
attribute	Year	long_name	String	Year
attribute	Year	units	String	unitless
variable	Month		int
attribute	Month	actual_range	int	4, 4
attribute	Month	long_name	String	Month
attribute	Month	units	String	unitless
variable	Day		int
attribute	Day	actual_range	int	15, 15
attribute	Day	long_name	String	Day
attribute	Day	units	String	unitless
variable	Depth_range		String
attribute	Depth_range	long_name	String	Depth_range
attribute	Depth_range	units	String	meters (m)
variable	T0_1		float
attribute	T0_1	actual_range	float	0.0, 14.11
attribute	T0_1	long_name	String	T0_1
attribute	T0_1	units	String	Log2[RPKM+1]
variable	T0_2		float
attribute	T0_2	actual_range	float	0.0, 14.4
attribute	T0_2	long_name	String	T0_2
attribute	T0_2	units	String	Log2[RPKM+1]
variable	T0_3		float
attribute	T0_3	actual_range	float	0.0, 13.87
attribute	T0_3	long_name	String	T0_3
attribute	T0_3	units	String	Log2[RPKM+1]
variable	NF_1		float
attribute	NF_1	actual_range	float	0.0, 15.2
attribute	NF_1	long_name	String	Nf_1
attribute	NF_1	units	String	Log2[RPKM+1]
variable	NF_2		float
attribute	NF_2	actual_range	float	0.0, 14.48
attribute	NF_2	long_name	String	Nf_2
attribute	NF_2	units	String	Log2[RPKM+1]
variable	NF_3		float
attribute	NF_3	actual_range	float	0.0, 14.25
attribute	NF_3	long_name	String	Nf_3
attribute	NF_3	units	String	Log2[RPKM+1]
variable	BW1_1		float
attribute	BW1_1	actual_range	float	0.0, 14.7
attribute	BW1_1	long_name	String	Bw1_1
attribute	BW1_1	units	String	Log2[RPKM+1]
variable	BW1_2		float
attribute	BW1_2	actual_range	float	0.0, 15.45
attribute	BW1_2	long_name	String	Bw1_2
attribute	BW1_2	units	String	Log2[RPKM+1]
variable	BW1_3		float
attribute	BW1_3	actual_range	float	0.0, 15.63
attribute	BW1_3	long_name	String	Bw1_3
attribute	BW1_3	units	String	Log2[RPKM+1]
variable	GW1_1		float
attribute	GW1_1	actual_range	float	0.0, 15.81
attribute	GW1_1	long_name	String	Gw1_1
attribute	GW1_1	units	String	Log2[RPKM+1]
variable	GW1_2		float
attribute	GW1_2	actual_range	float	0.0, 15.29
attribute	GW1_2	long_name	String	Gw1_2
attribute	GW1_2	units	String	Log2[RPKM+1]
variable	GW1_3		float
attribute	GW1_3	actual_range	float	0.0, 15.14
attribute	GW1_3	long_name	String	Gw1_3
attribute	GW1_3	units	String	Log2[RPKM+1]
variable	YW1_1		float
attribute	YW1_1	actual_range	float	0.0, 15.63
attribute	YW1_1	long_name	String	Yw1_1
attribute	YW1_1	units	String	Log2[RPKM+1]
variable	YW1_2		float
attribute	YW1_2	actual_range	float	0.0, 15.4
attribute	YW1_2	long_name	String	Yw1_2
attribute	YW1_2	units	String	Log2[RPKM+1]
variable	YW1_3		float
attribute	YW1_3	actual_range	float	0.0, 15.54
attribute	YW1_3	long_name	String	Yw1_3
attribute	YW1_3	units	String	Log2[RPKM+1]
variable	BW2_1		float
attribute	BW2_1	actual_range	float	0.0, 15.49
attribute	BW2_1	long_name	String	Bw2_1
attribute	BW2_1	units	String	Log2[RPKM+1]
variable	BW2_2		float
attribute	BW2_2	actual_range	float	0.0, 13.54
attribute	BW2_2	long_name	String	Bw2_2
attribute	BW2_2	units	String	Log2[RPKM+1]
variable	BW2_3		float
attribute	BW2_3	actual_range	float	0.0, 15.51
attribute	BW2_3	long_name	String	Bw2_3
attribute	BW2_3	units	String	Log2[RPKM+1]
variable	GW2_1		float
attribute	GW2_1	actual_range	float	0.0, 14.51
attribute	GW2_1	long_name	String	Gw2_1
attribute	GW2_1	units	String	Log2[RPKM+1]
variable	GW2_2		float
attribute	GW2_2	actual_range	float	0.0, 14.8
attribute	GW2_2	long_name	String	Gw2_2
attribute	GW2_2	units	String	Log2[RPKM+1]
variable	GW2_3		float
attribute	GW2_3	actual_range	float	0.0, 13.47
attribute	GW2_3	long_name	String	Gw2_3
attribute	GW2_3	units	String	Log2[RPKM+1]
variable	YW2_1		float
attribute	YW2_1	actual_range	float	0.0, 14.92
attribute	YW2_1	long_name	String	Yw2_1
attribute	YW2_1	units	String	Log2[RPKM+1]
variable	YW2_2		float
attribute	YW2_2	actual_range	float	0.0, 14.96
attribute	YW2_2	long_name	String	Yw2_2
attribute	YW2_2	units	String	Log2[RPKM+1]
variable	YW2_3		float
attribute	YW2_3	actual_range	float	0.0, 14.91
attribute	YW2_3	long_name	String	Yw2_3
attribute	YW2_3	units	String	Log2[RPKM+1]
variable	BW3_1		float
attribute	BW3_1	actual_range	float	0.0, 15.72
attribute	BW3_1	long_name	String	Bw3_1
attribute	BW3_1	units	String	Log2[RPKM+1]
variable	BW3_2		float
attribute	BW3_2	actual_range	float	0.0, 15.51
attribute	BW3_2	long_name	String	Bw3_2
attribute	BW3_2	units	String	Log2[RPKM+1]
variable	BW3_3		float
attribute	BW3_3	actual_range	float	0.0, 15.04
attribute	BW3_3	long_name	String	Bw3_3
attribute	BW3_3	units	String	Log2[RPKM+1]
variable	GW3_1		float
attribute	GW3_1	actual_range	float	0.0, 15.39
attribute	GW3_1	long_name	String	Gw3_1
attribute	GW3_1	units	String	Log2[RPKM+1]
variable	GW3_2		float
attribute	GW3_2	actual_range	float	0.0, 14.89
attribute	GW3_2	long_name	String	Gw3_2
attribute	GW3_2	units	String	Log2[RPKM+1]
variable	GW3_3		float
attribute	GW3_3	actual_range	float	0.0, 14.67
attribute	GW3_3	long_name	String	Gw3_3
attribute	GW3_3	units	String	Log2[RPKM+1]
variable	YW3_1		float
attribute	YW3_1	actual_range	float	0.0, 14.28
attribute	YW3_1	long_name	String	Yw3_1
attribute	YW3_1	units	String	Log2[RPKM+1]
variable	YW3_2		float
attribute	YW3_2	actual_range	float	0.0, 15.01
attribute	YW3_2	long_name	String	Yw3_2
attribute	YW3_2	units	String	Log2[RPKM+1]
variable	YW3_3		float
attribute	YW3_3	actual_range	float	0.0, 15.39
attribute	YW3_3	long_name	String	Yw3_3
attribute	YW3_3	units	String	Log2[RPKM+1]

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.