TITLE: PCR Protocol Template
AUTHORS: Kathleen Pitz, Raïssa Meyer

[DESCRIPTION]

A protocol template created through the BeBOP project for PCR.

Main protocol steps begin below the "Standard Operating Procedure" section.
A detailed description of the BeBOP project and these templates is available here: https://github.com/BeBOP-OBON/



[GUIDELINES]
test

[STEPS]
SECTION: MIOP: Minimum Information about an Omics Protocol
1. 
  
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: AUTHORS
2. 
  
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
 
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yyyy-mm-dd
  

SECTION: RELATED PROTOCOLS
3. 
  
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: ACRONYMS AND ABBREVIATIONS
23. 
  
ACRONYM / ABBREVIATION
DEFINITION
   
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SECTION: GLOSSARY
24. 
  
SPECIALISED TERM
DEFINITION
   
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SECTION: BACKGROUND
4. 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: BACKGROUND
5. 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: BACKGROUND
6. 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.
https://www.ebi.ac.uk/ols/ontologies/envo
SECTION: BACKGROUND
7. Personnel Required

Insert the number of technicians, data managers, and scientists required for the good execution of the procedure
SECTION: BACKGROUND
8. Safety

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

Specify technical training required for the good execution of the procedure.
SECTION: BACKGROUND
10. Time needed to execute the procedure

Specify how much time is necessary to execute the procedure.
SECTION: EQUIPMENT
11. 
  
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: STANDARD OPERATING PROCEDURE
12. In the following SOP, please use the exact names of equipment as noted in the table above.

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.
SECTION: PREPARATION
13. 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
SECTION: PCR
16. 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)

Primers: PCR primer name, direction, and sequence
  
PCR Primer Name
Direction
Sequence (5’ -> 3’)
   
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forward
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reverse
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SECTION: PCR clean-up
20. 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).
SECTION: QUALITY CONTROL
21. Describe and explain criteria used to validate results of the standard operating procedure.
SECTION: BASIC TROUBLESHOOTING GUIDE
22. Identify known issues associated with the procedure, if any.

Provide troubleshooting guidelines when available.
SECTION: REFERENCES
25. 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: APPENDIX A: DATASHEETS
26. 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.
SECTION: PREPARATION
15. Step
SECTION: PREPARATION
14. Step
SECTION: PCR
17. PCR Cycling Program: PCR step, temperature, duration, and number of cycles
  
PCR step
Temperature
Duration
Repetition
   
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SECTION: PCR
18. Reaction Mixture: PCR reagents, volumes, initial and final concentrations
 

SECTION: PCR
19. Step