TITLE: PCR Protocol Template
AUTHORS: Kathleen Pitz, Raissa.meyer

[DESCRIPTION]

A protocol template created through the BeBOP project for PCR.




[STEPS]
SECTION: Protocol Template
1. Minimum Information about an Omics Protocol (MIOP)

See https://github.com/BeBOP-OBON/miop/blob/main/model/schema/terms.yaml for list and definitions.



  
MIOP Term
Value
   
methodology category

 
project

 
purpose

 
analyses

 
geographic location

 
broad-scale environmental context

 
local environmental context

 
environmental medium

 
target

 
creator

 
materials required

 
skills required

 
time required

 
personnel required

 
language

 
issued

 
audience

 
publisher

 
hasVersion

 
license

 
maturity level

  

SECTION: Protocol Template
2. AUTHORS


  
PREPARED BY All authors known to have contributed to the preparation of this protocol, including those who filled in the template.
AFFILIATION
ORCID (visit https://orcid.org/ to register)
DATE
   
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yyyy-mm-dd
  

SECTION: Protocol Template
3. PROTOCOL REVISION RECORD

Version numbers start at “1.0.0” when the protocol is first completed and will increase when changes that impact the outcome of the procedure are made (patches: 1.0.1; minor changes: 1.1.0; major changes: 2.0.0). Please store all versions in the gDrive folder designated to your institute.



  
VERSION
RELEASE DATE This is the date when a given protocol version was finalised
DESCRIPTION OF REVISIONS Please include a brief description of what was changed relative to the previous version
   
1.0.0
yyyy-mm-dd
Initial release
 
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SECTION: Protocol Template
4. RELATED PROTOCOLS IN YOUR FOLDER

This is a list of other protocols deposited in your folder which should be known to users of this protocol. For example, if you create a derivative or altered protocol, you would link to the original protocol in the section below. Please include the link to each related protocol. Also include the version number of that protocol when you linked to it.



  
PROTOCOL NAME AND LINK
VERSION The version of the protocol you linked to
RELEASE DATE This is the date corresponding to the version listed to the left
   
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yyyy-mm-dd
 
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yyyy-mm-dd
  

SECTION: Protocol Template
5. RELATED EXTERNAL PROTOCOLS

This is a list of other protocols that are not in your folder which should be known to users of this protocol. These include, e.g., kit manuals. Please upload all relevant external protocols to Appendix A and link to them here.



  
EXTERNAL PROTOCOL NAME AND LINK
ISSUER / AUTHOR Please note who authored the protocol (this may also be a company name)
ACCESS DATE This is the date you downloaded or scanned the protocol and uploaded it.
   
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yyyy-mm-dd
 
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yyyy-mm-dd
  

SECTION: Protocol Template
6. ACRONYMS AND ABBREVIATIONS


  
ACRONYM / ABBREVIATION
DEFINITION
   
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7. GLOSSARY


  
SPECIALISED TERM
DEFINITION
   
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SECTION: Protocol Template
8. BACKGROUND

This document describes the required protocol to conduct insert name of the method/protocol.
SECTION: Protocol Template
9. Summary

Insert a short description of the background for the method/protocol (e.g. why and for which purpose do you perform water sampling).

Please provide a brief summary of your method including, as appropriate, a brief description of what techniques your best practice is about, which ocean environments or regions it targets, the primary sensors covered, what type of data/measurements/observing platform it covers, limits to its applicability.
SECTION: Protocol Template
10. Method description and rationale

Insert a short description of the functioning principal of the methodology used in the protocol (i.e. how does the method work?). Please note that this is different from the step-by-step description of the protocol procedure.

Insert a short statement explaining why the specific methodology used in the protocol has been selected (e.g. it is highly reproducible, highly accurate, procedures are easy to execute etc….).
SECTION: Protocol Template
11. Spatial coverage and environment(s) of relevance

If applicable, please specify the region where the protocol is applied. For regional term guidance see here. If applicable, please indicate here the environment(s) of relevance for the protocol, e.g. Abyssal plain. Select from the ENVO terminology.
SECTION: Protocol Template
12. PERSONNEL REQUIRED

Insert the number of technicians, data managers, and scientists required for the good execution of the procedure
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13. Safety

Identify hazards associated with the procedure and specify protective equipment and safety training required to safely execute the procedure
SECTION: Protocol Template
14. Training requirements

Specify technical training required for the good execution of the procedure.
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15. Time needed to execute the procedure

Specify how much time is necessary to execute the procedure.
SECTION: Protocol Template
16. EQUIPMENT


  
DESCRIPTION e.g. filter
PRODUCT NAME AND MODEL Provide the official name of the product
MANUFACTURER Provide the name of the manufacturer of the product.
QUANTITY Provide quantities necessary for one application of the standard operating procedure (e.g. number of filters).
REMARK For example, some of the consumable may need to be sterilized, some commercial solution may need to be diluted or shielded from light during the operating procedure.
   
Durable equipment




 
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Consumable equipment




 
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Chemicals




 
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SECTION: Protocol Template
17. STANDARD OPERATING PROCEDURE

In the following SOP, please use the exact names of equipment as noted in the table above.
SECTION: Protocol Template
18. Protocol

Provide a step-by-step description of the protocol. The identification of difficult steps in the protocol and the provision of recommendations for the execution of those steps are encouraged.


Preparation


Please specify the preparatory actions you took before you collected the samples and note what equipment was needed to do so (e.g. disinfection of work surfaces, preparations to the equipment you intend to use later on).



Step 1


Step 2


SECTION: Protocol Template
19. PCR

Please specify the actions you took to amplify the previously extracted DNA and the equipment and primers you used (ingredients for the PCR reaction, number of triplicates, PCR cycle parameter)



Step 1




  
PCR Primer Name
Direction
Sequence (5’ -> 3’)
   
content
forward
content
 
content
reverse
content
  





Step 2





Step 3






  
PCR step
Temperature
Duration
Repetition
   
content
content
content
content
 
content
content
content
content
  

SECTION: Protocol Template
20. Quality control, PCR clean-up

Please specify the actions you took to confirm the quality of the PCR output, to clean up the PCR output and the equipment you used (e.g. agarose gel to confirm quality, purification of PCR products).




Step 1





Step 2




SECTION: Protocol Template
21. Quality control

Describe and explain criteria used to validate results of the standard operating procedure.
SECTION: Protocol Template
22. Basic troubleshooting guide

Identify known issues associated with the procedure, if any.

Provide troubleshooting guidelines when available.
SECTION: Protocol Template
23. REFERENCES

Insert all references cited in the document.

Please insert full DOI address when available, e.g. http://doi.dx.org/10.1007/s11258-014-0404-1
SECTION: Protocol Template
24. APPENDIX A: DATASHEETS

Link templates (e.g. preformatted spreadsheets) used to record measurements and report on the quality of the data as well as any documents such as manufacturer specifications, images, etc that support this protocol. Please include a short note describing the document’s relevance.