Difference between revisions of "Team:Oxford/Protocols"

 
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<h1 class="text-center">Protocols</h1>
 
<h1 class="text-center">Protocols</h1>
  
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<p> This page includes all our protocols that we made when we were cloning initially, as well as being a repository for protocols we made for experiments that did or didn't work to characterise our parts. Although a lot of them are simple protocols, and probably do not vary much from other teams', we have left them as we used them, so that other teams can get an indication of the sort of things we feel are important to include when you make protocols for your team. We used Benchling to write them, and it meant that demonstrators only had to explain things to one member of our team, rather than 12 different times! <p>
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<p>This page includes all our protocols that we made when we were cloning initially, as well as being a repository for protocols we made for experiments that did or didn't work to characterise our parts. Although a lot of them are simple protocols, and probably do not vary much from other teams', we have left them as we used them, so that other teams can get an indication of the sort of things we feel are important to include when you make protocols for your team. We used Benchling to write them, and it meant that demonstrators only had to explain things to one member of our team, rather than 12 different times!</p>
  
 
<h2> Protocols for Initial Cloning </h2>  
 
<h2> Protocols for Initial Cloning </h2>  
  
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<p> We wanted part of this page to summarise the steps that we took from designing our parts all the way through to sending them to iGEM to add to the registry. It is the sort of overview we would have found useful when we first started, and we hope it will help other teams. </p>  
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<p> We wanted part of this page to summarise the steps that we took from designing our parts all the way through to sending them to iGEM to add to the registry. It is the sort of overview we would have found useful when we first started, and we hope it will help other teams.</p>  
  
 
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<h3>Create DNA in Snapgene</h3> <br/>
 
<h3>Create DNA in Snapgene</h3> <br/>
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<h3>Order DNA from IDT</h3> <br/>
 
<h3>Order DNA from IDT</h3> <br/>
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<h3>PCR from G-Blocks</h3> <br/>
 
<h3>PCR from G-Blocks</h3> <br/>
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<h3>Run a Gel of the PCR</h3><br/>
 
<h3>Run a Gel of the PCR</h3><br/>
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       <span> Digest and Ligate </span>
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         <h3>Digest and Ligate Into Shipping Vector</h3><br/>
 
         <h3>Digest and Ligate Into Shipping Vector</h3><br/>
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<h3>Transform and Plate</h3> <br/>
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     <span id="caption"> Inoculate</span>
 
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<h3>Test Digest and Sequence</h3><br/>
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<h2>Other Protocols</h2>
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<p>Below we have listed all the other protocols we used over the summer, they are linked to from throughout the wiki, and we hope other teams find them useful.</p>
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<li><a href="https://static.igem.org/mediawiki/2017/b/b6/T--Oxford--Protocols--bap1.pdf">gBlock Resuspending</a> </li>
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<li><a href="https://static.igem.org/mediawiki/2017/b/b7/T--Oxford--Protocols--bap2.pdf">Making Loading Dye</a> </li>
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<li><a href="https://static.igem.org/mediawiki/2017/9/90/T--Oxford--Protocols--bap3.pdf">Making 1kb+ Ladder</a> </li>
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<li><a href="https://static.igem.org/mediawiki/2017/8/8a/T--Oxford--Protocols--bap4.pdf">Making Plates</a> </li>
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<li><a href="https://static.igem.org/mediawiki/2017/f/f1/T--Oxford--Protocols--bap5.pdf">Making Competent Cells</a> </li>
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<li><a href="https://static.igem.org/mediawiki/2017/2/27/T--Oxford--Protocols--bap6.pdf">Making Antibiotics</a> </li>
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</ul>
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<a href="#demoa" class="btn btn-info" data-toggle="collapse">Various Types of PCR</a>
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<li><a href="https://static.igem.org/mediawiki/2017/5/5b/T--Oxford--Protocols--pcr1.pdf">Normal PCR</a> </li>
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<li><a href="https://static.igem.org/mediawiki/2017/f/ff/T--Oxford--Protocols--pcr2.pdf">Colony PCR</a> </li>
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<li><a href="https://static.igem.org/mediawiki/2017/4/4f/T--Oxford--Protocols--pcr3.pdf">Quick-change PCR</a> </li>
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<li><a href="https://static.igem.org/mediawiki/2017/9/96/T--Oxford--Protocols--pcr4.pdf">Phusion PCR</a> </li>
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<li><a href="https://static.igem.org/mediawiki/2017/a/a3/T--Oxford--Protocols--pcr5.pdf">Overlap Extension PCR</a></li>
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<li><a href="https://static.igem.org/mediawiki/2017/2/2e/T--Oxford--Protocols--purification1.pdf">Making Buffers for Purification</a> </li>
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<li><a href="https://static.igem.org/mediawiki/2017/4/4a/T--Oxford--Protocols--purification2.pdf">Using the Avanti Centrifuge</a> </li>
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<li><a href="https://static.igem.org/mediawiki/2017/a/aa/T--Oxford--Protocols--purification3.pdf">Using the Berks Cell Disruptor</a> </li>
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<li><a href="https://static.igem.org/mediawiki/2017/c/cf/T--Oxford--Protocols--purification4.pdf">E.g. of a Purification TEV-mCherry-His</a> </li>
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<a href="#democ" class="btn btn-info" data-toggle="collapse">Microscopy</a>
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<!--<p>In brief, mid-log phase cells were immobilised on a thin layer of 1% w/v agarose in water on a slide with a cover slip. Microscopy was carried out using a Nikon TE200 inverted microscope with filter sets for CFP, GFP, YFP and mCherry from Chroma. Images were acquired on a Hamamatsu Orca ER CCD camera and processed using SimplePCI software. All biological samples to be compared were grown simultaneously and the microscope settings, exposure times and post processing of each image were identical.</p>-->
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<ul>
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<li><a href="https://static.igem.org/mediawiki/2017/9/90/T--Oxford--Protocols--microscopy1.pdf">Making Slides</a> </li>
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<li><a href="https://static.igem.org/mediawiki/2017/d/d4/T--Oxford--Protocols--microscopy2.pdf">Using the Fluorescence Microscope</a> </li>
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<a href="#demod" class="btn btn-info" data-toggle="collapse">OMVs</a>
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<ul>
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<li><a href="https://static.igem.org/mediawiki/2017/1/1a/T--Oxford--Protocols--OMV.pdf">OMV Extraction</a> </li>
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Latest revision as of 03:06, 2 November 2017


Protocols


This page includes all our protocols that we made when we were cloning initially, as well as being a repository for protocols we made for experiments that did or didn't work to characterise our parts. Although a lot of them are simple protocols, and probably do not vary much from other teams', we have left them as we used them, so that other teams can get an indication of the sort of things we feel are important to include when you make protocols for your team. We used Benchling to write them, and it meant that demonstrators only had to explain things to one member of our team, rather than 12 different times!

Protocols for Initial Cloning

We wanted part of this page to summarise the steps that we took from designing our parts all the way through to sending them to iGEM to add to the registry. It is the sort of overview we would have found useful when we first started, and we hope it will help other teams.

Create DNA in Snapgene
Order DNA from IDT
PCR from G-Blocks
Run a Gel of the PCR
Digest and Ligate


Transform and Plate
Inoculate
Miniprep
Test Digest and Sequence
Send DNA to iGEM


Other Protocols

Below we have listed all the other protocols we used over the summer, they are linked to from throughout the wiki, and we hope other teams find them useful.


Bits and Pieces
Various Types of PCR
Protein Purification
Microscopy
OMVs