
Getting Started with CRISPR Experiments – Part 1 - akarve
http://genomics.quiltdata.com/2016/01/26/getting-started-with-crispr-experiments-part-i/
======
akarve
Hi HN. I'm one of the founders of Quilt Data. We've started a blog series on
how to run CRISPR experiments. Let us know what you'd like to see in future
parts of the series.

------
redwood
What is the iteration latency today? Eg I do this test described, learn
something (maybe something as small as what I tried didn't work) and now I
want to try something else.

It looks like each run requires a new order with suppliers. They may take time
to produce and send. So how long from "I want to try this other approach
requiring nee supplies" to "new approach is laid down for testing"? And when
something gets laid down for testing, how long might a test take?

(FYI I'm personally very excited about these developments and trying to grok
the real world experience a bit more. Haven't done a day in a wet lab since
high school! )

~~~
jeegnomejeff
Great question. In almost all cases, you have an actionable lead after doing a
screen experiment. The problem is typically that you have learned too many,
not too few things. And those things need to be backed with more experimental
evidence.

But more generally, the iteration latency is about a week to order & receive
reagents for another targeted screen. Or if you want to do a single gene
CRISPR experiment, you can get the single oligo reagents the next day.

Then the cloning, virus production, cell infection, etc. will be about another
week if you are rushing. We in genomics are still a far cry from the iteration
latency in software dev, but given that many of our scientific
forefathers/mothers in the previous generation counted on making a whole
genetically engineered mouse (which could take a year+) for an experiment,
we're making solid progress.

More questions about the real world lab experience are always welcome!

~~~
redwood
love it thank you so much. A back of the envelope calculations suggest 8 - 14
days per cycle so 25-50 cycles per year. Assuming no vacation. I can see how
we just face an incredible amount of work to do. Parallelism of course will
help. But it must be so amazing to be like a blind man wandering around in a
dark room with a sense that there might be something warm in the distance but
that's about it. At least you're doing real work.

------
dnautics
What would be more powerful instead of "comment out" debugging is if you could
have println debugging.

~~~
jeegnomejeff
Something like this is possible with CRISPR by tagging endogenous genes with
fluorescent proteins. In this way, the output of that particular genetic line
of code can be traced. It's not a perfect metaphor, and the method doesn't
scale genome-wide, but its a clever thought.

~~~
daveguy
Also, iirc, there are several studies under way to permit in vivo
activation/deactivation of specific genes. CRISPR the switch in place and
subject it to the stimulus (magnetic, light, sound). Changing the phenotype on
the fly.

