AFSC/RACE/SAP/Shavey: DNA extraction from archived Giemsa-stained blood smears using polymerase chain reaction to detect host and parasitic DNA
Alaska Fisheries Science Center
Data Set
(DS)
| ID: 35937
| Published / External
Created: 2016-12-13
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Last Modified: 2024-01-15
Project (PRJ) | ID: 22354
ID: 35937
Data Set (DS)
* Discovery• First Pass
» Metadata Rubric
Item Identification
* » Title | AFSC/RACE/SAP/Shavey: DNA extraction from archived Giemsa-stained blood smears using polymerase chain reaction to detect host and parasitic DNA |
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Short Name | AFSC/RACE/SAP/Shavey: DNA extraction from archived Giemsa-stained blood smears using polymerase chain reaction to detect host and parasitic DNA |
* Status | Completed |
Creation Date | |
Revision Date | |
• Publication Date | |
* » Abstract |
These are the data from a laboratory experiment in which DNA content was removed from blood smears and extracted. The blood smears were either stained with Giemsa-stain or remained un-stained. Some of the un-stained smears were coverslipped. Host and parasitic DNA was amplified using conventional PCR. |
* Purpose |
To identify a new technique of removing contents from blood smears and to evalutate the effects of Giemsa-staining and coverslipping for DNA amplication. |
Notes |
Loaded by FGDC Metadata Uploader, batch 9574, 12-13-2016 12:44 The following FGDC sections are not currently supported in InPort, but were preserved and will be included in the FGDC export: - Taxonomy (FGDC:taxonomy) |
Other Citation Details | |
• Supplemental Information | |
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Keywords
Theme Keywords
Thesaurus | Keyword |
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ISO 19115 Topic Category | biota |
ISO 19115 Topic Category | oceans |
None | Blood Smear |
None | disease |
None | DNA Extraction |
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* Spatial Keywords
Thesaurus | Keyword |
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None | Alaska |
None | Bering Sea |
None | Gulf of Alaska |
None | Newfoundland, Canada |
None | SE Alaska |
None | Washington State Coast |
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Physical Location
• » Organization | Alaska Fisheries Science Center |
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• » City | Seattle |
• » State/Province | WA |
• Country | USA |
• » Location Description |
Data Set Information
* Data Set Scope Code | Data Set |
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• Data Set Type | MS Excel |
• Maintenance Frequency | None Planned |
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» Data Presentation Form | Table (digital) |
• Entity Attribute Overview | |
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Distribution Liability |
The user is responsible for the results of any application of this data for other than its intended purpose. NOAA denies liability if the data are misused. |
Data Set Credit |
Support Roles
* » Support Role | Data Steward |
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* » Date Effective From | 2016-12-13 |
Date Effective To | |
Person | Lang, Christie |
Email Address | christie.lang@noaa.gov |
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* » Support Role | Distributor |
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* » Date Effective From | 2016-12-13 |
Date Effective To | |
Person | Foy, Robert |
Email Address | robert.foy@noaa.gov |
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* » Support Role | Metadata Contact |
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* » Date Effective From | 2016-12-13 |
Date Effective To | |
Person | MC, Metadata Coordinators |
Email Address | AFSC.metadata@noaa.gov |
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* » Support Role | Originator |
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* » Date Effective From | 2016-12-13 |
Date Effective To | |
Organization | Alaska Fisheries Science Center (AFSC) |
Address |
7600 Sand Point Way N.E., Building 4 Seattle, WA 98115 USA |
Email Address | afsc.webmaster@noaa.gov |
Phone | (206) 526-4000 |
Fax | (206) 526-4004 |
Mobile | |
URL | https://www.fisheries.noaa.gov/about/alaska-fisheries-science-center |
Business Hours | 0700-1700 Pacific Time |
Contact Instructions |
* » Support Role | Point of Contact |
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* » Date Effective From | 2016-12-13 |
Date Effective To | |
Person | Lang, Christie |
Email Address | christie.lang@noaa.gov |
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Extents
Currentness Reference | Ground Condition |
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Extent Group 1
Extent Description |
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Extent Group 1 / Geographic Area 1
* » W° Bound | -178.51 |
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* » E° Bound | -53.11 |
* » N° Bound | 61.67 |
* » S° Bound | 49.63 |
* » Description |
Eastern Bering Sea, Alaska; Gulf of Alaska; Southeast Alaska, Washington State Coast, North Atlantic Coast |
Extent Group 1 / Vertical Extent
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Extent Group 1 / Time Frame 1
* » Time Frame Type | Range |
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* » Start | 1988 |
End | 2004 |
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Access Information
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Data License Statement | |
* » Security Class | Unclassified |
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Security Handling Description | |
• Data Access Policy | |
» Data Access Procedure |
unknown |
• » Data Access Constraints |
There are no legal restrictions on access to the data. They reside in public domain and can be freely distributed. |
• Data Use 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. Acknowledgementof NOAA/NMFS/AFSC, as the source from which these data were obtained in any publications and/or other representations of these, data is suggested. |
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Distribution Information
Start Date | |
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» Download URL | https://console.cloud.google.com/storage/browser/_details/nmfs_odp_afsc/RACE/SAP/Shavey%3B%20DNA%20extraction%20from%20archived%20Giemsa-stained%20blood%20smears%20using%20polymerase%20chain%20reaction%20to%20detect%20host%20and%20parasitic%20DNA.csv |
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Note: Dataset migrated by Dan Woodrich (AFSC data management coordinator) on 12/15/2021. Contact: Daniel.woodrich@noaa.gov |
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Completeness Report |
Due to small sample size, only blood smears with high parasite ratings were used in statistical analysis. Crab morphometrics are not available for some samples. BCS smears were rated with trophont stage. Two samples used in analysis had a trophont and prespore stage (thought to be advanced stage) and those samples were grouped as highest trophont stage (T5). |
Conceptual Consistency |
Data is checked for values outside range. |
» Quality Control Procedures Employed |
Data is checked for values outside range. |
Data Management
» Have Resources for Management of these Data Been Identified? | No |
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» 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 |
» If Distributor (Data Hosting Service) is Needed, Please Indicate | Yes |
» Approximate Delay Between Data Collection and Dissemination | no delay |
» If Delay is Longer than Latency of Automated Processing, Indicate Under What Authority Data Access is Delayed | |
» Actual or Planned Long-Term Data Archive Location | NCEI-MD |
» Approximate Delay Between Data Collection and Archiving | unknown |
» How Will the Data Be Protected from Accidental or Malicious Modification or Deletion Prior to Receipt by the Archive? |
IT Security and Contingency Plan for the system establishes procedures and applies to the functions, operations, and resources necessary to recover and restore data as hosted in the Western Regional Support Center in Seattle, Washington, following a disruption. |
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Process Steps
Process Step Number | 1 |
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» Description |
A subset of 76 blood smears that were prepared in the field from 1988 to 2004 were chosen based on smear preparation (Giemsa-stained vs. no stain and coverslipped vs no coverslip) and parasite status (parasite presence vs. no parasite). All content was removed from each smear using a pipette tip and sterile blade. DNA was extracted and amplified using crab host and parasite PCR primer sets. |
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Process Step Number | 2 |
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» Description |
SPNO is a number assigned to each collected crab. Duplicate numbers represent replicate smears taken from sample. The sex of the crab is identified as: 1) Male, 2) Female, 3) Unknown. Individual crab carapaces were measured (1 mm), excluding spines, and are reported as size. Null or blank fields in data represent no size information reported for crab specimen. Shell condition class serves as a semi-quantitative index of molt status and time in shell post-molt. Carapace shell condition was assessed for each Chionoecetes crab sampled and assigned to one of six classes according to specific criteria (0 = premolt or molting, 1 = soft and pliable, 2 = new hardshell both firm and clean, 3 = oldshell slightly worn, 4 = oldshell worn, 9 = no shell condition information reported for crab specimen). Collection location was not a factor, so only general location is listed. |
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Process Step Number | 3 |
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» Description |
Blood smears analyzed were either unstained (none), or fixed with methanol and Giemsa-stained for 30 minutes (Giemsa). Treatment of blood smears are identified as (0 = no cover slip, 1 = cover slip attached using mounting media). 30 fields at 250X were read to determine presence or absence of Hematodinium spp. parasite on blood smear. Results were documented as: (0 = Hematodinium parasite absent on smear, 1 = Hematodinium parasite present on smear). Hematodinium parasite presence on smear was identified as T-rating (0 = No rating due to parasite absence, T1 = Up to 10% Hematodinium parasite present on smear (trophont stage), T2 = 10 - 40% Hematodinium parasite present on smear (trophont stage), T3 = 40 - 60% Hematodinium parasite present on smear (trophont stage), T4 = 60 - 90% Hematodinium parasite present on smear (trophont stage), T4P1 = 60 - 90% Hematodinium parasite present on smear (trophont stage) and up to 10% Hematodium prespore stage, T5 = Above 90% Hematodinium parasite present on smear (trophont stage), T5P1 = Above 90% Hematodinium parasite present on smear (trophont stage) and up to 10% Hematodium prespore stage). |
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Process Step Number | 4 |
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» Description |
PCR assays: for 16S, COI, 18S and ITS Primer (0 = Did not use primer set on this sample, 1 = Used primer set on this sample). For 16S, COI, 18S and ITS Amplification (0 = No DNA amplification using this primer set, 1 = DNA was amplified using primer set, 9 = no amplification to report due to primer set not used in sample). Primer set descriptions: 16S = 16Sar-L (CgC CTg TTT ATC AAA AAC AT) & 16Sbr-H (CCg gTC TgA ACT CAg ATC ACg T) primer set used in PCR assay, targeting mitochondrial DNA 16S ribosomal RNA gene. COI = LCO1490 (ggT CAA CAA ATC ATA AAg ATA TTg g) & HCO2198 (TAA ACT TCA ggg TgA CCA AAA AAT CA) primer set used in PCR assay, targeting the mitochondrial cytochrome c oxidase subunit I gene. 18S = HF1487 (CCT ggC TCg ATA gAg TTg) & HR1654 (ggC TgC CgT CCg AAT TAT TCA C) primer set used in PCR assay, targeting the 18S ribosomal gene located at the small subunit 3'-end of the ribosomal RNA unit. ITS = HSP7f (AGT CAT CAG CTC GTG CTG A) & HSP9r (TTC ACG GAA TTC TGC AAT TCG) primer set used in PCR assay, targeting the first internal transcribed spacer of the ribosomal RNA unit. Statistical analysis: Blood smears were analyzed using two-sample t-test (0 = smear was not used in statistical analysis, 1 = smear was used in statistical analysis). |
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Acquisition Information
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Related Items
Item Type | Relationship Type | Title |
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Catalog Details
Catalog Item ID | 35937 |
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Metadata Record Created By | Christie Lang |
Metadata Record Created | 2016-12-13 11:56+0000 |
Metadata Record Last Modified By | SysAdmin InPortAdmin |
» Metadata Record Last Modified | 2024-01-15 12:08+0000 |
Metadata Record Published | 2016-12-16 |
Owner Org | AFSC |
Metadata Publication Status | Published Externally |
Do Not Publish? | N |
Metadata Workflow State | Published / External |
Metadata Last Review Date | 2016-12-16 |
Metadata Review Frequency | 1 Year |
Metadata Next Review Date | 2017-12-16 |
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