DNA data
Data Set (DS) | Southwest Fisheries Science Center (SWFSC)GUID: gov.noaa.nmfs.inport:20689 | Updated: August 9, 2022 | Published / External
Summary
Short Citation
Southwest Fisheries Science Center, 2024: DNA data, https://www.fisheries.noaa.gov/inport/item/20689.
Full Citation Examples
Raw DNA chromatogram data produced by the ABI 373, 377, 3130 and 3730 automated sequencing machines in ABI format. These are from fish (primarily Sebastes spp., Seriola lalandi, and several shark species) and invertebrates (primarily Haliotis spp.). These data are in either of 2 formats, ".fsa" files containing chromatograms used for genotyping, and ".ab1" files containing chromatograms of DNA sequences. These data are used for studies on taxonomy, population connectivity, species identification, and studies of mating systems
Distribution Information
-
ABI raw chromatograms
There are no restrictions or prerequisites for accessing these data.
Child Items
| Type | Title |
|---|---|
| Entity | FRD DNA Data |
Contact Information
Point of Contact
John R Hyde
John.Hyde@noaa.gov
(858) 546-7086
Metadata Contact
John R Hyde
John.Hyde@noaa.gov
(858) 546-7086
Extents
-180° W,
180° E,
90° N,
-90° S
Global sample collections with primary area of focus in the northeast Pacific
1991 - Present
Item Identification
| Title: | DNA data |
|---|---|
| Short Name: | DNA data |
| Status: | In Work |
| Creation Date: | Unknown |
| Revision Date: | 2019-06-17 |
| Abstract: |
Raw DNA chromatogram data produced by the ABI 373, 377, 3130 and 3730 automated sequencing machines in ABI format. These are from fish (primarily Sebastes spp., Seriola lalandi, and several shark species) and invertebrates (primarily Haliotis spp.). These data are in either of 2 formats, ".fsa" files containing chromatograms used for genotyping, and ".ab1" files containing chromatograms of DNA sequences. These data are used for studies on taxonomy, population connectivity, species identification, and studies of mating systems |
| Purpose: |
Data are used in support of studies on taxonomy, population connectivity, species identification, and studies of mating systems of fish and invertebrates. |
Keywords
Theme Keywords
| Thesaurus | Keyword |
|---|---|
| UNCONTROLLED | |
| None | abalone |
| None | anchovy |
| None | DNA sequence |
| None | genotyping |
| None | opah |
| None | sardine |
| None | shark |
| None | yellowtail |
Physical Location
| Organization: | Southwest Fisheries Science Center |
|---|---|
| City: | La Jolla |
| State/Province: | CA |
| Country: | USA |
Data Set Information
| Data Set Scope Code: | Data Set |
|---|---|
| Data Set Type: | Mixed |
| Maintenance Frequency: | As Needed |
| Data Presentation Form: | Raw sequence output files |
Support Roles
Data Steward
| Date Effective From: | 2015 |
|---|---|
| Date Effective To: | |
| Contact (Person): | Hyde, John R |
| Address: |
8901 La Jolla Shores Dr La Jolla, CA 92037 USA |
| Email Address: | John.Hyde@noaa.gov |
| Phone: | (858) 546-7086 |
| Fax: | (858) 546-7003 |
| Business Hours: | 8:00 AM - 4:30 PM |
Distributor
| Date Effective From: | 2015 |
|---|---|
| Date Effective To: | |
| Contact (Organization): | Southwest Fisheries Science Center (SWFSC) |
| Address: |
8901 La Jolla Shores Dr. La Jolla, CA 92037 USA |
| Phone: | (858)546-7000 |
| URL: | http://swfsc.noaa.gov/ |
| Business Hours: | 8:00-16:30 |
Metadata Contact
| Date Effective From: | 2015 |
|---|---|
| Date Effective To: | |
| Contact (Person): | Hyde, John R |
| Address: |
8901 La Jolla Shores Dr La Jolla, CA 92037 USA |
| Email Address: | John.Hyde@noaa.gov |
| Phone: | (858) 546-7086 |
| Fax: | (858) 546-7003 |
| Business Hours: | 8:00 AM - 4:30 PM |
Point of Contact
| Date Effective From: | 2015 |
|---|---|
| Date Effective To: | |
| Contact (Person): | Hyde, John R |
| Address: |
8901 La Jolla Shores Dr La Jolla, CA 92037 USA |
| Email Address: | John.Hyde@noaa.gov |
| Phone: | (858) 546-7086 |
| Fax: | (858) 546-7003 |
| Business Hours: | 8:00 AM - 4:30 PM |
Extents
Extent Group 1
Extent Group 1 / Geographic Area 1
| W° Bound: | -180 | |
|---|---|---|
| E° Bound: | 180 | |
| N° Bound: | 90 | |
| S° Bound: | -90 | |
| Description |
Global sample collections with primary area of focus in the northeast Pacific |
|
Extent Group 1 / Time Frame 1
| Time Frame Type: | Continuing |
|---|---|
| Start: | 1991 |
Access Information
| Security Class: | Unclassified |
|---|---|
| Data Access Policy: |
There are no restrictions on access to these data. |
| Data Access Procedure: |
Contact John Hyde at John.Hyde@noaa.gov |
| Data Access Constraints: |
There are no restrictions or prerequisites for accessing these data. |
Distribution Information
Distribution 1
| Start Date: | 1997 |
|---|---|
| End Date: | Present |
| Download URL: | https://swfsc.noaa.gov/ |
| Distributor: | Southwest Fisheries Science Center (SWFSC) (2015 - Present) |
| Description: |
ABI raw chromatograms |
| File Type (Deprecated): | AB1 |
Data Quality
| Completeness Measure: |
Contains 100% of files generated. |
|---|---|
| Quality Control Procedures Employed: |
DNA sequences are manually edited to remove low-quality data. |
Data Management
| Have Resources for Management of these Data Been Identified?: | No |
|---|---|
| Approximate Percentage of Budget for these Data Devoted to Data Management: | Unknown |
| Do these Data Comply with the Data Access Directive?: | No |
| Is Access to the Data Limited Based on an Approved Waiver?: | No |
| Approximate Delay Between Data Collection and Dissemination: | 1 year |
| Actual or Planned Long-Term Data Archive Location: | NCEI-MD |
| Approximate Delay Between Data Collection and Archiving: | 1 year |
| How Will the Data Be Protected from Accidental or Malicious Modification or Deletion Prior to Receipt by the Archive?: |
Data are stored on a server at the Southwest Fisheries Science Center which has all appropriate access controls. |
Lineage
| Lineage Statement: |
Samples are collected from a variety of gears, processed and sequenced in the laboratory. |
|---|
Sources
DNA Data
| Contact Role Type: | Originator |
|---|---|
| Contact Type: | Organization |
| Contact Name: | Southwest Fisheries Science Center |
| Extent Type: | Continuing |
| Extent Start Date/Time: | 1997 |
| Citation URL: | https://swfsc.noaa.gov/ |
| Citation URL Name: | SWFSC |
| Citation URL Description: |
SWFSC Home page |
Process Steps
Process Step 1
| Description: |
Organism collected. |
|---|---|
| Process Contact: | Hyde, John R |
| Phone (Voice): | (858) 546-7086 |
| Email Address: | John.Hyde@noaa.gov |
| Source: | DNA Data |
Process Step 2
| Description: |
Tissue subsample taken. |
|---|---|
| Process Contact: | Hyde, John R |
| Phone (Voice): | (858) 546-7086 |
| Email Address: | John.Hyde@noaa.gov |
| Source: | DNA Data |
Process Step 3
| Description: |
DNA extracted, PCR, and sequencing |
|---|---|
| Process Contact: | Hyde, John R |
| Phone (Voice): | (858) 546-7086 |
| Email Address: | John.Hyde@noaa.gov |
| Source: | DNA Data |
Child Items
Rubric scores updated every 15m
|
Type | Title |
|---|---|---|
| Entity | FRD DNA Data |
Catalog Details
| Catalog Item ID: | 20689 |
|---|---|
| GUID: | gov.noaa.nmfs.inport:20689 |
| Metadata Record Created By: | Edward D Weber |
| Metadata Record Created: | 2013-09-26 17:10+0000 |
| Metadata Record Last Modified By: | SysAdmin InPortAdmin |
| Metadata Record Last Modified: | 2022-08-09 17:11+0000 |
| Metadata Record Published: | 2019-06-19 |
| Owner Org: | SWFSC |
| Metadata Publication Status: | Published Externally |
| Do Not Publish?: | N |
| Metadata Last Review Date: | 2019-06-19 |
| Metadata Review Frequency: | 1 Year |
| Metadata Next Review Date: | 2020-06-19 |