| Data File(s) | Type | Description | Action |
|---|---|---|---|
954181_v1_bowtie-mapping-results.csv (19.69 KB) | Comma Separated Values (.csv) | Mapping results for RNA-Seq data showing short-sequence read counts aligned to mtCOI sequences from six different species. This is the primary data table of this BCO-DMO dataset (953181 version 1). | |
| Supplemental File(s) | Type | Description | Action |
collections_regional_map.png (192.85 KB)  | Portable Network Graphics (.png) | A regional map of the eastern Pacific and locates the collection area. These locations were previously published as part of Figure 1 of Pinchuk, et al. (2008). | |
species_list_copepods.csv (687.00 B) | Comma Separated Values (.csv) | Copepod ScientificNames and taxnomic identifiers. Columns: Name_in_Dataset, Category name as it appears in 954181_v1_copepod_species_filter.csv column "Species" ScientificName, The scientific name within "Species" column. AphiaID, World Register of Marine Species identifier (AphiaID) for the ScientificName LSID, Life Science Identifier (LSID) for the ScientificName | |
954181_v1_sra-run-table.csv (238.83 KB) | Comma Separated Values (.csv) | Supplemental table containing additional information related to the SRA accessions and BioSamples referenced in this dataset. These tables are the results of the NCBI SRA Run Selector for each of the BioProjects referenced in this dataset (PRJNA324453, PRJNA662858, PRJNA496596, PRJNA807352). See https://www.ncbi.nlm.nih.gov/Traces/study/# | |
954181_v1_suitos-blast-data.csv (6.84 KB) | Comma Separated Values (.csv) | Search results and identification to genetic variant of mtCOI sequences obtained from a ca. 600 bp amplicon from DNA extracted from individual Neocalanus flemingeri. Column (parameter) information Station,GAK = numbering on Seward Line; PWS & KIP2 = Prince William Sound,Unitless, Sample,Sample sequence number; gaps in numbering due to failed sequencing reaction,Unitless, Date,Collection date,Day-Month-Year, Query Cover,Column label for NCBI BLAST indicating how much of the Query sequence was represented in the Subject,Percent, E-Value,Column label for NCBI BLAST indicating the E-value for the Query-to-Subject matrch (0 for E < 1e-180),Probability, Ident,Identity between Query and Subject in aligned portion,Percent, Base Pairs,Length in nucleotide bases of aligned portion,Integer, Accession,Accession number for the best-match Subject,Unitless, Species,Species of the bast-match Subject,Unitless, Form,Identified variety of bast-match Subject Large or Small,Unitless, | |
954181_v1_copepod_species_filter.csv (12.34 KB) | Comma Separated Values (.csv) | Reference mtCOI sequences and their source used in the species identification using Bowtie mapping. Sequences are provided in FASTA format. Column (parameter) information: Identifier,COI sequence identifier description ,Unitless, NCBI Accession,NCBI Accession number available at the National Center for Biotechnology Information,Unitless, COI location,The location of the reference sequence in relation to the entire sequence in the NCBI accession,integer range, Species,Genus and species,Unitless, Notes,Special note on entry,Unitless, Sequence,Nucleotide sequence in fasta format,Unitless, ScientificName, The Genus and species within the "Species" column LSID, The Life Science Identifier (LSID) for the ScientificName |
Files
Filename: 954181_v1_bowtie-mapping-results.csv (19.69 KB)
Type: Comma Separated Values (.csv)
Description: Mapping results for RNA-Seq data showing short-sequence read counts aligned to mtCOI sequences from six different species. This is the primary data table of this BCO-DMO dataset (953181 version 1).
Type: Comma Separated Values (.csv)
Description: Mapping results for RNA-Seq data showing short-sequence read counts aligned to mtCOI sequences from six different species. This is the primary data table of this BCO-DMO dataset (953181 version 1).
Supplemental Files
Filename: collections_regional_map.png (192.85 KB)
Type: Portable Network Graphics (.png)
Description: A regional map of the eastern Pacific and locates the collection area. These locations were previously published as part of Figure 1 of Pinchuk, et al. (2008).
Type: Portable Network Graphics (.png)
Description: A regional map of the eastern Pacific and locates the collection area. These locations were previously published as part of Figure 1 of Pinchuk, et al. (2008).
Filename: species_list_copepods.csv (687.00 B)
Type: Comma Separated Values (.csv)
Description: Copepod ScientificNames and taxnomic identifiers. Columns: Name_in_Dataset, Category name as it appears in 954181_v1_copepod_species_filter.csv column "Species" ScientificName, The scientific name within "Species" column. AphiaID, World Register of Marine Species identifier (AphiaID) for the ScientificName LSID, Life Science Identifier (LSID) for the ScientificName
Type: Comma Separated Values (.csv)
Description: Copepod ScientificNames and taxnomic identifiers. Columns: Name_in_Dataset, Category name as it appears in 954181_v1_copepod_species_filter.csv column "Species" ScientificName, The scientific name within "Species" column. AphiaID, World Register of Marine Species identifier (AphiaID) for the ScientificName LSID, Life Science Identifier (LSID) for the ScientificName
Filename: 954181_v1_sra-run-table.csv (238.83 KB)
Type: Comma Separated Values (.csv)
Description: Supplemental table containing additional information related to the SRA accessions and BioSamples referenced in this dataset. These tables are the results of the NCBI SRA Run Selector for each of the BioProjects referenced in this dataset (PRJNA324453, PRJNA662858, PRJNA496596, PRJNA807352). See https://www.ncbi.nlm.nih.gov/Traces/study/#
Type: Comma Separated Values (.csv)
Description: Supplemental table containing additional information related to the SRA accessions and BioSamples referenced in this dataset. These tables are the results of the NCBI SRA Run Selector for each of the BioProjects referenced in this dataset (PRJNA324453, PRJNA662858, PRJNA496596, PRJNA807352). See https://www.ncbi.nlm.nih.gov/Traces/study/#
Filename: 954181_v1_suitos-blast-data.csv (6.84 KB)
Type: Comma Separated Values (.csv)
Description: Search results and identification to genetic variant of mtCOI sequences obtained from a ca. 600 bp amplicon from DNA extracted from individual Neocalanus flemingeri. Column (parameter) information Station,GAK = numbering on Seward Line; PWS & KIP2 = Prince William Sound,Unitless, Sample,Sample sequence number; gaps in numbering due to failed sequencing reaction,Unitless, Date,Collection date,Day-Month-Year, Query Cover,Column label for NCBI BLAST indicating how much of the Query sequence was represented in the Subject,Percent, E-Value,Column label for NCBI BLAST indicating the E-value for the Query-to-Subject matrch (0 for E < 1e-180),Probability, Ident,Identity between Query and Subject in aligned portion,Percent, Base Pairs,Length in nucleotide bases of aligned portion,Integer, Accession,Accession number for the best-match Subject,Unitless, Species,Species of the bast-match Subject,Unitless, Form,Identified variety of bast-match Subject Large or Small,Unitless,
Type: Comma Separated Values (.csv)
Description: Search results and identification to genetic variant of mtCOI sequences obtained from a ca. 600 bp amplicon from DNA extracted from individual Neocalanus flemingeri. Column (parameter) information Station,GAK = numbering on Seward Line; PWS & KIP2 = Prince William Sound,Unitless, Sample,Sample sequence number; gaps in numbering due to failed sequencing reaction,Unitless, Date,Collection date,Day-Month-Year, Query Cover,Column label for NCBI BLAST indicating how much of the Query sequence was represented in the Subject,Percent, E-Value,Column label for NCBI BLAST indicating the E-value for the Query-to-Subject matrch (0 for E < 1e-180),Probability, Ident,Identity between Query and Subject in aligned portion,Percent, Base Pairs,Length in nucleotide bases of aligned portion,Integer, Accession,Accession number for the best-match Subject,Unitless, Species,Species of the bast-match Subject,Unitless, Form,Identified variety of bast-match Subject Large or Small,Unitless,
Filename: 954181_v1_copepod_species_filter.csv (12.34 KB)
Type: Comma Separated Values (.csv)
Description: Reference mtCOI sequences and their source used in the species identification using Bowtie mapping. Sequences are provided in FASTA format. Column (parameter) information: Identifier,COI sequence identifier description ,Unitless, NCBI Accession,NCBI Accession number available at the National Center for Biotechnology Information,Unitless, COI location,The location of the reference sequence in relation to the entire sequence in the NCBI accession,integer range, Species,Genus and species,Unitless, Notes,Special note on entry,Unitless, Sequence,Nucleotide sequence in fasta format,Unitless, ScientificName, The Genus and species within the "Species" column LSID, The Life Science Identifier (LSID) for the ScientificName
Type: Comma Separated Values (.csv)
Description: Reference mtCOI sequences and their source used in the species identification using Bowtie mapping. Sequences are provided in FASTA format. Column (parameter) information: Identifier,COI sequence identifier description ,Unitless, NCBI Accession,NCBI Accession number available at the National Center for Biotechnology Information,Unitless, COI location,The location of the reference sequence in relation to the entire sequence in the NCBI accession,integer range, Species,Genus and species,Unitless, Notes,Special note on entry,Unitless, Sequence,Nucleotide sequence in fasta format,Unitless, ScientificName, The Genus and species within the "Species" column LSID, The Life Science Identifier (LSID) for the ScientificName