Hello,
I have come up with a new set of primers for the amplification of this one protein for a project. I am now writing, and I am not sure how I should describe the process in how I made them. I basically used different software, and evaluated them based of various primer design criteria. (Also I tested whether they work, and they do). What are some things I should include when describing this?
If someone could reference a good paper which does something like this, that would be great, or give any tips.
Thanks.
Is this for writing a paper? If for lab notebook useful information will include
1) How you prepared them (i.e. how much water you added/what concentration)
2) Rising point (the Ct when it reaches above background signal)
3) Tm of the melt curve.
4) Keep sequences on an excel tab sheet-will be useful if you have problems and need to reorder.
If you want to find out what information should be reported for a paper, google MIQE guideline Bustin.
Think about what message you're trying to communicate... Is the primer design process itself a major focus of your paper? Did you discover some unusual principle during the design process that you'd like the reader to know about? In that case, share the exciting story of your discovery process!
Or was the PCR used as a routine tool, in the course of asking some other interesting question? Did everything go by the book? Would you prefer the reader to focus on the story you're telling about your protein of interest? In that case just say what the primer sequence was, and don't elaborate. Focus on what you found out using it.
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