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Summary
Item Identification
Keywords
Physical Location
Data Set Info
Support Roles
Extents
Access Info
Distribution Info
Tech Environment
Data Quality
Data Management
Lineage
Catalog Details

Summary

Short Citation
Alaska Fisheries Science Center, 2024: AFSC/RACE/EcoFOCI - Genetics analyses performed in support of FOCI assessment surveys and ecosystem observations in the Bering Sea and the Gulf of Alaska 2009 - 2010, https://www.fisheries.noaa.gov/inport/item/26576.
Full Citation Examples

Abstract

The datasets contain nucleotide sequence data that is in text format and each line of sequence has a unique sample code (combination of letters and numbers).

Distribution Information

Access Constraints:

User must read and fully comprehend the metadata prior to use. Applications or inferences derived from the data should be carefully considered for accuracy.

Use Constraints:

Acknowledgement of NOAA/NMFS/AFSC, as the source from which these data were obtained in any publications and/or other representations of these, data is suggested.

Child Items

No Child Items for this record.

Contact Information

Point of Contact
Melanie Paquin
melanie.paquin@noaa.gov

Metadata Contact
Kimberly Bahl
kimberly.bahl@noaa.gov
206 526 4314

Extents

Geographic Area 1

-180° W, -150° E, 60° N, 50° S

Time Frame 1
2009 - 2010

Item Identification

Title: AFSC/RACE/EcoFOCI - Genetics analyses performed in support of FOCI assessment surveys and ecosystem observations in the Bering Sea and the Gulf of Alaska 2009 - 2010
Short Name: EcoFOCI genetics analyses in the Bering Sea and the Gulf of Alaska 2009 - 2010
Status: Completed
Publication Date: 2014
Abstract:

The datasets contain nucleotide sequence data that is in text format and each line of sequence has a unique sample code (combination of letters and numbers).

Purpose:

These datasets were developed to fulfill two NPRB funded projects, one to determine the utility of simple, low-cost genetic methods for identifying species of prey fish in the diets of groundfish and the other to collect sequence data from common and rare species of sculpins that would likely be present in groundfish stomach contents. These data are for research purposes.

Supplemental Information:

Supplemental Information - Data Parameters and Units - Descriptive Information about the Data Parameters and Units.

The data itself is descriptive providing a unique string of DNA sequence and presented in this raw form. The data are archival species references for later post-processing. No parameters were measured or included.

Supplemental Information – Methods - Descriptive Information about the methods used.

[Are you sure you want methods starting with the DNA extraction? The paper that this passage was taken from is written for scientists who would like to repeat the genetic methods at the bench so is written as a laboratory protocol. Seems like you might just limit this section to how the sequence data was generated in very abbreviated terms such as the following:

PCR products from fish samples were sequenced using ABI Big Dye chemistry version 3.1 (Applied Biosystems, Inc) and run on an ABI 3730 automated sequencer. KB BASECALLER quality scores were generated using ABI data collection software version 3.0, and bidirectional sequences were aligned in the computer program SEQUENCHER version 4.9 (Gene Codes Corp.). Both directions were sequenced and aligned for reference specimen samples that showed intraspecific variation in RFLP banding patterns; otherwise, sequence from one direction was analyzed for PCR-RFLP assay development. Likewise, DNA sequence from one direction was analyzed for prey samples not assigned to one of the target fish groups (i.e. that could not be identified using the PCR-RFLP protocols), or were classified as unknown teleosts. Replicate DNA extractions of 12 prey items were sequenced in order to verify consistency of sequence data between replicates and to test for contamination from other prey species. Unique COI haplotypes from reference specimens were deposited in BOLD (DNA barcodes of marine fishes from the Northeast Pacific Ocean and Bering Sea, Proj. Code WXYZ http://www.boldsystems.org/). Sequences from samples that could not be identified using the PCR-RFLP protocols, or that were classified as unknown teleosts, were compared to the database of reference sequences in GenBank using the BLAST (Basic Local Alignment Search Tool) query algorithm.]

Supplemental Information – Instruments - Descriptive Information about the instruments and equipment used.

PCR products from fish samples were run on an ABI 3730 automated sequencer (Applied Biosystems, Inc).

Supplemental Information - Sampling Scales and Rates - Descriptive Information about the sampling spatial and temporal scales and rates.

Sampling included the Northeast Pacific and was conducted opportunistically over multiple years.

Supplemental Information - Error Analysis - Descriptive Information about the error analysis.

PCR products from fish samples were run on an ABI 3730 automated sequencer and KB BASECALLER quality scores were generated using ABI data collection software version 3.0. Bidirectional sequences were aligned in the computer program SEQUENCHER version 4.9 (Gene Codes Corp.). Matching haplotypes among samples confirmed correct species identification of voucher specimens.

Supplemental Information - Provenance and Historical References -

Descriptive Information about the provenance, historical data, key information packaged elsewhere.

Paquin, M.M., Buckley, T.W., Hibpshman, R. E., and Canino, M.F. (2014) DNA-based identification methods of prey fish from stomach contents of 12 species of eastern North Pacific groundfish. Deep Sea Research I 85:110-117.

Paquin, M.M., Kagley, A.N., Fresh K.L., and Orr, J.W. (2014) First Records of the Night Smelt, Spirinchus starksi, in the Salish Sea, Washington. Northwestern Naturalist, 95:40-43. 2014.

Keywords

Theme Keywords

Thesaurus Keyword
UNCONTROLLED
PARR Exclusion Non-Federal Funding
None genetics

Spatial Keywords

Thesaurus Keyword
UNCONTROLLED
None Aleutian Islands
None Gulf of Alaska

Physical Location

Organization: Alaska Fisheries Science Center
City: Seattle
State/Province: WA
Country: USA

Data Set Information

Data Set Scope Code: Data Set
Data Set Type: Other
Maintenance Frequency: As Needed
Data Presentation Form: Table (digital)

Support Roles

Data Steward

CC ID: 235234
Date Effective From: 2014
Date Effective To:
Contact (Person): Paquin, Melanie
Email Address: melanie.paquin@noaa.gov

Distributor

CC ID: 235233
Date Effective From: 2014
Date Effective To:
Contact (Person): Duffy-Anderson, Janet
Email Address: janet.duffy-anderson@noaa.gov

Metadata Contact

CC ID: 214041
Date Effective From: 2019
Date Effective To:
Contact (Person): Bahl, Kimberly
Email Address: kimberly.bahl@noaa.gov
Phone: 206 526 4314
Contact Instructions:

email

Originator

CC ID: 214040
Date Effective From: 2014
Date Effective To:
Contact (Person): Paquin, Melanie
Email Address: melanie.paquin@noaa.gov
Contact Instructions:

email

Point of Contact

CC ID: 214042
Date Effective From: 2014
Date Effective To:
Contact (Person): Paquin, Melanie
Email Address: melanie.paquin@noaa.gov
Contact Instructions:

email

Extents

Currentness Reference: Publication Date

Extent Group 1

Extent Group 1 / Geographic Area 1

CC ID: 214043
W° Bound: -180
E° Bound: -150
N° Bound: 60
S° Bound: 50

Extent Group 1 / Time Frame 1

CC ID: 214044
Time Frame Type: Range
Start: 2009
End: 2010

Access Information

Security Class: Unclassified
Data Access Policy:

There are no legal restrictions on access to the data. They reside in public domain and can be freely distributed.

Data Access Procedure:

Unique COI haplotypes from reference specimens were deposited in BOLD (DNA barcodes of marine fishes from the Northeast Pacific Ocean and Bering Sea, Proj. Code WXYZ http://www.boldsystems.org/).

Data Access Constraints:

User must read and fully comprehend the metadata prior to use. Applications or inferences derived from the data should be carefully considered for accuracy.

Data Use Constraints:

Acknowledgement of NOAA/NMFS/AFSC, as the source from which these data were obtained in any publications and/or other representations of these, data is suggested.

Metadata Access Constraints:

None

Metadata Use Constraints:

None

Distribution Information

Distribution 1

CC ID: 235235
Download URL: http://www.boldsystems.org/
Distributor:

Technical Environment

Description:

See methods.

Data Quality

Representativeness:

NA

Accuracy:

NA

Analytical Accuracy:

NA

Quantitation Limits:

NA

Bias:

NA

Comparability:

NA

Completeness Measure:

NA

Precision:

See methods

Analytical Precision:

See methods

Field Precision:

NA

Sensitivity:

NA

Detection Limit:

NA

Completeness Report:

See methods

Conceptual Consistency:

NA

Quality Control Procedures Employed:

See methods

Data Management

Have Resources for Management of these Data Been Identified?: No
Approximate Percentage of Budget for these Data Devoted to Data Management: 0
Do these Data Comply with the Data Access Directive?: No
Is Access to the Data Limited Based on an Approved Waiver?: No
If Distributor (Data Hosting Service) is Needed, Please Indicate: N/A
Approximate Delay Between Data Collection and Dissemination: varies
Actual or Planned Long-Term Data Archive Location: Other
If World Data Center or Other, Specify: A portion of the nucleotide sequence data are housed on the public genetic sequence database GenBank http://www.ncbi.nlm.nih.gov/ and BOLD http://www.boldsystems.org/ in the ‘DNA barcodes of marine fishes from the Northeast Pacific Ocean and Bering Sea’ (Proj. Code WXYZ.
Approximate Delay Between Data Collection and Archiving: varies
How Will the Data Be Protected from Accidental or Malicious Modification or Deletion Prior to Receipt by the Archive?:

Yes

Lineage

Lineage Statement:

PCR products from fish samples were sequenced using ABI Big Dye chemistry version 3.1 (Applied Biosystems, Inc) and run on an ABI 3730 automated sequencer. KB BASECALLER quality scores were generated using ABI data collection software version 3.0, and bidirectional sequences were aligned in the computer program SEQUENCHER version 4.9 (Gene Codes Corp.). Both directions were sequenced and aligned for reference specimen samples that showed intraspecific variation in RFLP banding patterns; otherwise, sequence from one direction was analyzed for PCR-RFLP assay development. Likewise, DNA sequence from one direction was analyzed for prey samples not assigned to one of the target fish groups (i.e. that could not be identified using the PCR-RFLP protocols), or were classified as unknown teleosts. Replicate DNA extractions of 12 prey items were sequenced in order to verify consistency of sequence data between replicates and to test for contamination from other prey species. Unique COI haplotypes from reference specimens were deposited in BOLD (DNA barcodes of marine fishes from the Northeast Pacific Ocean and Bering Sea, Proj. Code WXYZ http://www.boldsystems.org/). Sequences from samples that could not be identified using the PCR-RFLP protocols, or that were classified as unknown teleosts, were compared to the database of reference sequences in GenBank using the BLAST (Basic Local Alignment Search Tool) query algorithm.]

Catalog Details

Catalog Item ID: 26576
GUID: gov.noaa.nmfs.inport:26576
Metadata Record Created By: Tiffany C Vance
Metadata Record Created: 2015-08-24 16:18+0000
Metadata Record Last Modified By: SysAdmin InPortAdmin
Metadata Record Last Modified: 2022-08-09 17:11+0000
Metadata Record Published: 2016-05-18
Owner Org: AFSC
Metadata Publication Status: Published Externally
Do Not Publish?: N
Metadata Last Review Date: 2016-05-18
Metadata Review Frequency: 1 Year
Metadata Next Review Date: 2017-05-18