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

[DESCRIPTION]

A protocol template created through the BeBOP project for PCR.




[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
   
Content Cell
Content Cell
Content Cell
yyyy-mm-dd
 
Content Cell
Content Cell
Content Cell
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
   
Content Cell
Content Cell
yyyy-mm-dd
 
Content Cell
Content Cell
yyyy-mm-dd
  

SECTION: ACRONYMS AND ABBREVIATIONS
4. 
  
ACRONYM / ABBREVIATION
DEFINITION
   
Content Cell
Content Cell
  

SECTION: GLOSSARY
5. 
  
SPECIALISED TERM
DEFINITION
   
Content Cell
Content Cell
 
Content Cell
Content Cell
  

SECTION: BACKGROUND
6. 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
7. 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
8. 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
9. Personnel Required

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

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

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

Specify how much time is necessary to execute the procedure.
SECTION: EQUIPMENT
13. 
  
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




 
Content Cell
Content Cell
Content Cell
Content Cell
Content Cell
 
Content Cell
Content Cell
Content Cell
Content Cell
Content Cell
 
Consumable equipment




 
Content Cell
Content Cell
Content Cell
Content Cell
Content Cell
 
Content Cell
Content Cell
Content Cell
Content Cell
Content Cell
 
Chemicals




 
Content Cell
Content Cell
Content Cell
Content Cell
Content Cell
 
Content Cell
Content Cell
Content Cell
Content Cell
Content Cell
  

SECTION: STANDARD OPERATING PROCEDURE
14. 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
15. 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
18. 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)

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



SECTION: PCR clean-up
21. 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
22. Describe and explain criteria used to validate results of the standard operating procedure.
SECTION: BASIC TROUBLESHOOTING GUIDE
23. Identify known issues associated with the procedure, if any.

Provide troubleshooting guidelines when available.
SECTION: REFERENCES
24. 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
25. 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
17. Step
SECTION: PREPARATION
16. Step
SECTION: PCR
19. 
  
PCR step
Temperature
Duration
Repetition
   
content
content
content
content
 
content
content
content
content
  

SECTION: PCR
20. Step