Accessing BCO-DMO data
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BCO-DMO ERDDAP
Accessing BCO-DMO data |
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| Dataset Title: | [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) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_914459_v1) |
| Information: | Summary
| License
| FGDC
| ISO 19115
| Metadata
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Attributes {
s {
seq_id {
String long_name "Seq_id";
String units "unitless";
}
Genbank_accession {
String long_name "Genbank_accession";
String units "unitless";
}
Organism_Name {
String long_name "Organism_name";
String units "unitless";
}
Station {
String long_name "Station";
String units "unitless";
}
latitude {
String _CoordinateAxisType "Lat";
Float32 actual_range 59.8443, 59.8443;
String axis "Y";
String ioos_category "Location";
String long_name "Latitude";
String standard_name "latitude";
String units "degrees_north";
}
longitude {
String _CoordinateAxisType "Lon";
Float32 actual_range -149.4838, -149.4838;
String axis "X";
String ioos_category "Location";
String long_name "Longitude";
String standard_name "longitude";
String units "degrees_east";
}
Collection_date {
String long_name "Collection_date";
String units "unitless";
}
Year {
Int32 actual_range 2019, 2019;
String long_name "Year";
String units "unitless";
}
Month {
Int32 actual_range 4, 4;
String long_name "Month";
String units "unitless";
}
Day {
Int32 actual_range 15, 15;
String long_name "Day";
String units "unitless";
}
Depth_range {
String long_name "Depth_range";
String units "meters (m)";
}
T0_1 {
Float32 actual_range 0.0, 14.11;
String long_name "T0_1";
String units "Log2[RPKM+1]";
}
T0_2 {
Float32 actual_range 0.0, 14.4;
String long_name "T0_2";
String units "Log2[RPKM+1]";
}
T0_3 {
Float32 actual_range 0.0, 13.87;
String long_name "T0_3";
String units "Log2[RPKM+1]";
}
NF_1 {
Float32 actual_range 0.0, 15.2;
String long_name "Nf_1";
String units "Log2[RPKM+1]";
}
NF_2 {
Float32 actual_range 0.0, 14.48;
String long_name "Nf_2";
String units "Log2[RPKM+1]";
}
NF_3 {
Float32 actual_range 0.0, 14.25;
String long_name "Nf_3";
String units "Log2[RPKM+1]";
}
BW1_1 {
Float32 actual_range 0.0, 14.7;
String long_name "Bw1_1";
String units "Log2[RPKM+1]";
}
BW1_2 {
Float32 actual_range 0.0, 15.45;
String long_name "Bw1_2";
String units "Log2[RPKM+1]";
}
BW1_3 {
Float32 actual_range 0.0, 15.63;
String long_name "Bw1_3";
String units "Log2[RPKM+1]";
}
GW1_1 {
Float32 actual_range 0.0, 15.81;
String long_name "Gw1_1";
String units "Log2[RPKM+1]";
}
GW1_2 {
Float32 actual_range 0.0, 15.29;
String long_name "Gw1_2";
String units "Log2[RPKM+1]";
}
GW1_3 {
Float32 actual_range 0.0, 15.14;
String long_name "Gw1_3";
String units "Log2[RPKM+1]";
}
YW1_1 {
Float32 actual_range 0.0, 15.63;
String long_name "Yw1_1";
String units "Log2[RPKM+1]";
}
YW1_2 {
Float32 actual_range 0.0, 15.4;
String long_name "Yw1_2";
String units "Log2[RPKM+1]";
}
YW1_3 {
Float32 actual_range 0.0, 15.54;
String long_name "Yw1_3";
String units "Log2[RPKM+1]";
}
BW2_1 {
Float32 actual_range 0.0, 15.49;
String long_name "Bw2_1";
String units "Log2[RPKM+1]";
}
BW2_2 {
Float32 actual_range 0.0, 13.54;
String long_name "Bw2_2";
String units "Log2[RPKM+1]";
}
BW2_3 {
Float32 actual_range 0.0, 15.51;
String long_name "Bw2_3";
String units "Log2[RPKM+1]";
}
GW2_1 {
Float32 actual_range 0.0, 14.51;
String long_name "Gw2_1";
String units "Log2[RPKM+1]";
}
GW2_2 {
Float32 actual_range 0.0, 14.8;
String long_name "Gw2_2";
String units "Log2[RPKM+1]";
}
GW2_3 {
Float32 actual_range 0.0, 13.47;
String long_name "Gw2_3";
String units "Log2[RPKM+1]";
}
YW2_1 {
Float32 actual_range 0.0, 14.92;
String long_name "Yw2_1";
String units "Log2[RPKM+1]";
}
YW2_2 {
Float32 actual_range 0.0, 14.96;
String long_name "Yw2_2";
String units "Log2[RPKM+1]";
}
YW2_3 {
Float32 actual_range 0.0, 14.91;
String long_name "Yw2_3";
String units "Log2[RPKM+1]";
}
BW3_1 {
Float32 actual_range 0.0, 15.72;
String long_name "Bw3_1";
String units "Log2[RPKM+1]";
}
BW3_2 {
Float32 actual_range 0.0, 15.51;
String long_name "Bw3_2";
String units "Log2[RPKM+1]";
}
BW3_3 {
Float32 actual_range 0.0, 15.04;
String long_name "Bw3_3";
String units "Log2[RPKM+1]";
}
GW3_1 {
Float32 actual_range 0.0, 15.39;
String long_name "Gw3_1";
String units "Log2[RPKM+1]";
}
GW3_2 {
Float32 actual_range 0.0, 14.89;
String long_name "Gw3_2";
String units "Log2[RPKM+1]";
}
GW3_3 {
Float32 actual_range 0.0, 14.67;
String long_name "Gw3_3";
String units "Log2[RPKM+1]";
}
YW3_1 {
Float32 actual_range 0.0, 14.28;
String long_name "Yw3_1";
String units "Log2[RPKM+1]";
}
YW3_2 {
Float32 actual_range 0.0, 15.01;
String long_name "Yw3_2";
String units "Log2[RPKM+1]";
}
YW3_3 {
Float32 actual_range 0.0, 15.39;
String long_name "Yw3_3";
String units "Log2[RPKM+1]";
}
}
NC_GLOBAL {
String cdm_data_type "Other";
String Conventions "COARDS, CF-1.6, ACDD-1.3";
String creator_email "info@bco-dmo.org";
String creator_name "BCO-DMO";
String creator_url "https://www.bco-dmo.org/";
String doi "10.26008/1912/bco-dmo.914459.1";
Float64 Easternmost_Easting -149.4838;
Float64 geospatial_lat_max 59.8443;
Float64 geospatial_lat_min 59.8443;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max -149.4838;
Float64 geospatial_lon_min -149.4838;
String geospatial_lon_units "degrees_east";
String history
"2024-11-21T12:07:38Z (local files)
2024-11-21T12:07:38Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_914459_v1.html";
String infoUrl "https://www.bco-dmo.org/dataset/914459";
String institution "BCO-DMO";
String 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.";
Float64 Northernmost_Northing 59.8443;
String sourceUrl "(local files)";
Float64 Southernmost_Northing 59.8443;
String summary
"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)";
String title "[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)";
Float64 Westernmost_Easting -149.4838;
}
}
Data Access Protocol (DAP) and its
selection constraints.
The URL specifies what you want: the dataset, a description of the graph or the subset of the data, and the file type for the response.
Tabledap request URLs must be in the form
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/datasetID.fileType{?query}
For example,
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/pmelTaoDySst.htmlTable?longitude,latitude,time,station,wmo_platform_code,T_25&time>=2015-05-23T12:00:00Z&time<=2015-05-31T12:00:00Z
Thus, the query is often a comma-separated list of desired variable names,
followed by a collection of
constraints (e.g., variable<value),
each preceded by '&' (which is interpreted as "AND").
For details, see the tabledap Documentation.