Switch Lab Intro

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Intro to Switch Labs

I have decided to start brew down some of the advice I have been giving on switch labs in the Switch Lab Guide and the later shorter version of the former: Different Types of Switches. Here it comes:



These are pointers towards what I think will work well for switch labs, from what data I have seen so far.

I wish you too, to watch out for how switches behave. What makes them work, what makes them move?


Being a citizen scientist

As encouragement, I want to share a fine article I found on being a citizen scientist. Enjoy!

Brian Cox’s guide to becoming a citizen scientist

Also check out my Lab Analysis Kit.
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Eli Fisker

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Posted 4 years ago

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salish99

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nice
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Eli Fisker

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MS2 Lab Intro

I am working on a continuation of my previous Switch Lab Intro.



Its still very much a work in progress. But the aim is to go more into details of how solve a switch lab puzzle in practice. I will add more pictures along the way. I just put it up now so it can be of help with the current round.

Omei has already made a fine Switch Lab Tutorial puzzle:

Intro to the Exclusion 3 lab

I have made a continuation

Intro to the Exclusion 3 lab: Simple


Go try them out and have fun getting started in lab! :)
(Edited)
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Astromon

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Thanks for the abundance of information! Great work!
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Eli Fisker

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I have started to collect some resources on microRNA and put them in a presentation. It is very much still a work in progress, but I'm putting it up in the hope it may still be of some help for this round.

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Eli Fisker

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My link to the guide appears to not be working, so I'm adding one here: 

https://docs.google.com/presentation/d/11pkK5JpyxrzN-GsFRhc8mWa5xf6zjIXS4gOVFBG42Os/edit#slide=id.p
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Astromon

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we need to be able to show a screen shot of our specs in chat so we can compare our data together . One could explain shape data and melting dot plot data to inquiring individuals if this were an option. Thanks! 
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Eli Fisker

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I am starting a guide on doing math with RNA.

This is thought as a helper for the [A]/[B] lab and future labs of that kind.

I think we already have a lot of the math tools needed, to make an increase of concentration of one microRNA over another. Just to mention a few things that can likely increase the presence and binding of one microRNA over the other:

  • Position of the microRNA in relation to the MS2 - before and after
  • MS2 gates - now they should come in really handy as a one way brake :)
  • MS2 turnoffs - and them being before and after the MS2
  • MicroRNA catching dangling stretches - and their length - also in relation to each other
  • How much of the microRNA that is targeted - length in total
Basically I think we can totally exploit even those things that have weighed down in past microRNA labs and slowed the switching, as the microRNA labs we have had so far have not had big problems with getting a good fold change. So things that in other labs have hurt the switching ability - like MS2 gates are now fair game for pushing the concentration of one microRNA up over the other. :) Especially since both the turnoff and turnoff microRNA labs have shown a good tolerance for MS2 gates.

My intro is not finished, but since I think it what is there may already be of help, I put it up. Bear with the mess - work in progress. :)

Doing math with RNApng
(Edited)
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whbob

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Attaching the oligo's to the main RNA sequence has started to appear straight forward, but where to place them and how they affect the MS2 hairpin still seems like an artform to me:)
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Eli Fisker

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Moved my answer to here.
(Edited)
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Eli Fisker

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I just want to highlight that Omei has started a fine guide with tutorials for the currently open [A]/[B] lab.

A Tutorial for A/B Ramp-up Puzzles
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Eli Fisker

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Here is an intro to one of the hard lab puzzles for the Open TB lab. I have written down the thought process that helped get me to a solve.


Open TB Labpng


Also I have been working on a intro to logic gate puzzles.


Logic gate imagepng

(Edited)
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Eli Fisker

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I have started writing an introduction to our lab data spreadsheets. Here is the beginning.


Reading EteRNA lab data spreadsheets
(Edited)
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Eli Fisker

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Switch graph intro

(Edited)
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Eli Fisker

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RNA - What have we learned so far?

A while back I put up an unfinished guide up as for helping with lab. The guide is still unfinished, but since a part of it deals with labs with inputs, I put it here as well.