Aug 23, 2024
Version 3
PCR Protocol Template V.3
This protocol is a draft, published without a DOI.
- 1Monterey Bay Aquarium Research Institute;
- 2AWI
- Better Biomolecular Ocean Practices (BeBOP)
Protocol Citation: Kathleen Pitz, Raïssa Meyer 2024. PCR Protocol Template. Protocol exchange https://protocols.io/view/pcr-protocol-template-c89tzz6nVersion created by Kathleen Pitz
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: February 14, 2024
Last Modified: August 23, 2024
Protocol Integer ID: 95251
Abstract
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
Materials
test
MIOP: Minimum Information about an Omics Protocol
MIOP: Minimum Information about an Omics Protocol
| 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 |
See MIOP_definition.md for term definitions. The terms "methodology category" and "maturity level" have controlled vocabulary.
AUTHORS
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 | |
| Content Cell | Content Cell | Content Cell | yyyy-mm-dd | |
| Content Cell | Content Cell | Content Cell | yyyy-mm-dd |
RELATED PROTOCOLS
RELATED PROTOCOLS
| PROTOCOL NAME AND LINK | ISSUER / AUTHOR | 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 |
This is a list of other protocols which should be known to users of this protocol. Please include the link to each related protocol.
BACKGROUND
BACKGROUND
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.
EQUIPMENT
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 | |||||
| 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 |
STANDARD OPERATING PROCEDURE
STANDARD OPERATING PROCEDURE
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.
PREPARATION
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
Step
Step
PCR
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)
Primers: PCR primer name, direction, and sequence
| PCR Primer Name | Direction | Sequence (5’ -> 3’) | |
| content | forward | content | |
| content | reverse | content |
PCR Cycling Program: PCR step, temperature, duration, and number of cycles
| PCR step | Temperature | Duration | Repetition | |
| content | content | content | content | |
| content | content | content | content |
Reaction Mixture: PCR reagents, volumes, initial and final concentrations
| reagent | volume | initial concentration | final concentration | |
| content | content | content | content | |
| content | content | content | content | |
| content | content | content | content | |
| content | content | content | content |
Step
PCR clean-up
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).
QUALITY CONTROL
QUALITY CONTROL
Describe and explain criteria used to validate results of the standard operating procedure.
BASIC TROUBLESHOOTING GUIDE
BASIC TROUBLESHOOTING GUIDE
Identify known issues associated with the procedure, if any.
Provide troubleshooting guidelines when available.
ACRONYMS AND ABBREVIATIONS
ACRONYMS AND ABBREVIATIONS
| ACRONYM / ABBREVIATION | DEFINITION | |
| Content Cell | Content Cell |
GLOSSARY
GLOSSARY
| SPECIALISED TERM | DEFINITION | |
| Content Cell | Content Cell | |
| Content Cell | Content Cell |
REFERENCES
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
APPENDIX A: DATASHEETS
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.