Which, do you think, can be the most time-consuming and difficult part of genome editing protocols? Design (oligos, shRNAs, KO, KI, etc.), cloning/construct preparation, screening, etc.?
With genome editing, it all depends on what you are doing (Knockout versus knockin), what design you are using, if the lab has previous experience using such techniques, etc. So there is no simple answer, the variety of tools available makes it so there is no ideal method and no quick method versus slow time consuming method. It depends on alot of factors.
When I used to do this a lot my bottleneck would usually be gel running/gel extraction and recombinant protein expression (from lysing to FPLC). You can usually do designing, screening, DNA amplification/extraction, RNA extraction, etc, fairly quickly and efficiency if you're employing a solid technique and are mindful of time vs productivity. Doing the dishes also takes a while, although it isn't nearly as bad compared with dish washing as an organic chemist!
I agree with Shawn on this, it really depends on what tools you have at your disposal, and how much experience you (or your lab) have with them.
If you are developing an assay from scratch it's essentially like any other experiment, its difficult to predict how long it will take to troubleshoot. On the other hand, if it's an established assay, in my experience the screening and validation bit usually takes the longest.
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