TITLE: PCR Protocol Template
AUTHORS: Andreas Novotny

[DESCRIPTION]
A protocol template created through the BeBOP project for PCR.


[BEFORE_START]
Read background information, MIOP and BePOP-OBON information under the "Guidelines" tab.

[GUIDELINES]
MIOP: Minimum Information about an Omics Protocol
 
 
AUTHORS
 
 
 
RELATED PROTOCOLS
 
 
 
ACRONYMS AND ABBREVIATIONS

 

GLOSSARY

 

BACKGROUND

This document describes the required protocol to conduct insert name of the method/protocol.

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.

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….).

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.

Personnel Required

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

Safety

Identify hazards associated with the procedure and specify protective equipment and safety training required to safely execute the procedure

Training requirements

Specify technical training required for the good execution of the procedure.

Time needed to execute the procedure

Specify how much time is necessary to execute the procedure.

[STEPS]
SECTION: PREPARATION
1. 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
4. 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’)
   
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reverse
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SECTION: PCR clean-up
7. 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
8. Describe and explain criteria used to validate results of the standard operating procedure.
SECTION: BASIC TROUBLESHOOTING GUIDE
9. Identify known issues associated with the procedure, if any.

Provide troubleshooting guidelines when available.
SECTION: APPENDIX A: DATASHEETS
10. 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
3. Step
SECTION: PREPARATION
2. Step
SECTION: PCR
5. 
  
PCR step
Temperature
Duration
Repetition
   
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SECTION: PCR
6. Step