Difference between revisions of "Team:Oxford/Protocols"
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<h1 class="text-center">Protocols</h1> | <h1 class="text-center">Protocols</h1> | ||
| − | + | <img class="img-responsive img-center" width="200px;" src="https://static.igem.org/mediawiki/2017/4/44/T--Oxford--Protocols--Logo.png"> | |
| − | < | + | <br> |
<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> | <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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<div class="col-sm-2"> | <div class="col-sm-2"> | ||
<img class="img-responsive img-circle team-member-img helen_open" src="https://static.igem.org/mediawiki/2017/0/09/T--Oxford--Protocols--Figure_6.png"> | <img class="img-responsive img-circle team-member-img helen_open" src="https://static.igem.org/mediawiki/2017/0/09/T--Oxford--Protocols--Figure_6.png"> | ||
| − | <span> Digest and Ligate </span> | + | <span id="caption"> Digest and Ligate </span> |
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<div id="helen" class="popup_box"> | <div id="helen" class="popup_box"> | ||
<button type="button" class="helen_close close_button"><span class="glyphicon glyphicon-remove"></span></button> | <button type="button" class="helen_close close_button"><span class="glyphicon glyphicon-remove"></span></button> | ||
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<h3>Digest and Ligate Into Shipping Vector</h3><br/> | <h3>Digest and Ligate Into Shipping Vector</h3><br/> | ||
<object data="https://static.igem.org/mediawiki/2017/9/9f/T--Oxford--Protocols--Figure_6_pdf.pdf" type="application/pdf" width="900px" height="900px"></object> | <object data="https://static.igem.org/mediawiki/2017/9/9f/T--Oxford--Protocols--Figure_6_pdf.pdf" type="application/pdf" width="900px" height="900px"></object> | ||
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<h3>Inoculate</h3><br/> | <h3>Inoculate</h3><br/> | ||
| − | <object data="https://static.igem.org/mediawiki/2017/ | + | <object data="https://static.igem.org/mediawiki/2017/7/79/T--Oxford--Protocols--Figure_8_pdf.pdf" type="application/pdf" width="900px" height="900px"></object> |
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<br/> | <br/> | ||
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<div class="col-sm-1"> | <div class="col-sm-1"> | ||
</div> | </div> | ||
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| − | < | + | <br> |
| − | + | <br> | |
| − | < | + | <h2> Other Protocols </h2> <br> |
| − | <h2> Other Protocols </h2> < | + | |
<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> | <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> | ||
| − | < | + | <br> |
<div class="container"> | <div class="container"> | ||
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</div> | </div> | ||
<div class="col-sm-2"> | <div class="col-sm-2"> | ||
| − | <a href="#demo" class="btn btn-info" data-toggle="collapse | + | <a href="#demo" class="btn btn-info" data-toggle="collapse">Bits and Pieces</a> |
<div id="demo" class="collapse"> | <div id="demo" class="collapse"> | ||
<ul> | <ul> | ||
| − | <li><a href="https://static.igem.org/mediawiki/2017/b/b6/T--Oxford--Protocols--bap1.pdf">gBlock Resuspending</a> </li | + | <li><a href="https://static.igem.org/mediawiki/2017/b/b6/T--Oxford--Protocols--bap1.pdf">gBlock Resuspending</a> </li> |
| − | <li><a href="https://static.igem.org/mediawiki/2017/b/b7/T--Oxford--Protocols--bap2.pdf">Making Loading Dye</a> </li | + | <li><a href="https://static.igem.org/mediawiki/2017/b/b7/T--Oxford--Protocols--bap2.pdf">Making Loading Dye</a> </li> |
| − | <li><a href="https://static.igem.org/mediawiki/2017/9/90/T--Oxford--Protocols--bap3.pdf">Making 1kb+ Ladder/a> </li | + | <li><a href="https://static.igem.org/mediawiki/2017/9/90/T--Oxford--Protocols--bap3.pdf">Making 1kb+ Ladder</a> </li> |
| − | <li><a href="https://static.igem.org/mediawiki/2017/8/8a/T--Oxford--Protocols--bap4.pdf">Making Plates</a> </li | + | <li><a href="https://static.igem.org/mediawiki/2017/8/8a/T--Oxford--Protocols--bap4.pdf">Making Plates</a> </li> |
| − | <li><a href="https://static.igem.org/mediawiki/2017/f/f1/T--Oxford--Protocols--bap5.pdf">Making Competent Cells</a> </li | + | <li><a href="https://static.igem.org/mediawiki/2017/f/f1/T--Oxford--Protocols--bap5.pdf">Making Competent Cells</a> </li> |
| − | <li><a href="https://static.igem.org/mediawiki/2017/2/27/T--Oxford--Protocols--bap6.pdf">Making Antibiotics</a> </li></ | + | <li><a href="https://static.igem.org/mediawiki/2017/2/27/T--Oxford--Protocols--bap6.pdf">Making Antibiotics</a> </li> |
| + | </ul> | ||
</div> | </div> | ||
</div> | </div> | ||
<div class="col-sm-2"> | <div class="col-sm-2"> | ||
| − | <a href="#demo" class="btn btn-info" data-toggle="collapse | + | <a href="#demo" class="btn btn-info" data-toggle="collapse">Various Types of PCR</a> |
<div id="demo" class="collapse"> | <div id="demo" class="collapse"> | ||
<ul> | <ul> | ||
| − | <li><a href="https://static.igem.org/mediawiki/2017/5/5b/T--Oxford--Protocols--pcr1.pdf">Normal PCR</a> </li | + | <li><a href="https://static.igem.org/mediawiki/2017/5/5b/T--Oxford--Protocols--pcr1.pdf">Normal PCR</a> </li> |
| − | <li><a href="https://static.igem.org/mediawiki/2017/f/ff/T--Oxford--Protocols--pcr2.pdf">Colony PCR</a> </li | + | <li><a href="https://static.igem.org/mediawiki/2017/f/ff/T--Oxford--Protocols--pcr2.pdf">Colony PCR</a> </li> |
| − | <li><a href="https://static.igem.org/mediawiki/2017/4/4f/T--Oxford--Protocols--pcr3.pdf">Quick-change PCR/a> </li | + | <li><a href="https://static.igem.org/mediawiki/2017/4/4f/T--Oxford--Protocols--pcr3.pdf">Quick-change PCR</a> </li> |
| − | <li><a href="https://static.igem.org/mediawiki/2017/9/96/T--Oxford--Protocols--pcr4.pdf">Phusion PCR</a> </li | + | <li><a href="https://static.igem.org/mediawiki/2017/9/96/T--Oxford--Protocols--pcr4.pdf">Phusion PCR</a> </li> |
| − | <li><a href="https://static.igem.org/mediawiki/2017/a/a3/T--Oxford--Protocols--pcr5.pdf">Overlap Extension PCR</a> </li></ | + | <li><a href="https://static.igem.org/mediawiki/2017/a/a3/T--Oxford--Protocols--pcr5.pdf">Overlap Extension PCR</a></li> |
| + | </ul> | ||
</div> | </div> | ||
</div> | </div> | ||
<div class="col-sm-2"> | <div class="col-sm-2"> | ||
| − | <a href="#demo" class="btn btn-info" data-toggle="collapse | + | <a href="#demo" class="btn btn-info" data-toggle="collapse">Protein Purification</a> |
<div id="demo" class="collapse"> | <div id="demo" class="collapse"> | ||
<ul> | <ul> | ||
| − | <li><a href="https://static.igem.org/mediawiki/2017/2/2e/T--Oxford--Protocols--purification1.pdf">Making Buffers for Purification</a> </li | + | <li><a href="https://static.igem.org/mediawiki/2017/2/2e/T--Oxford--Protocols--purification1.pdf">Making Buffers for Purification</a> </li> |
| − | <li><a href="https://static.igem.org/mediawiki/2017/4/4a/T--Oxford--Protocols--purification2.pdf">Using the Avanti Centrifuge</a> </li | + | <li><a href="https://static.igem.org/mediawiki/2017/4/4a/T--Oxford--Protocols--purification2.pdf">Using the Avanti Centrifuge</a> </li> |
| − | <li><a href="https://static.igem.org/mediawiki/2017/a/aa/T--Oxford--Protocols--purification3.pdf">Using the Berks Cell Disruptor/a> </li | + | <li><a href="https://static.igem.org/mediawiki/2017/a/aa/T--Oxford--Protocols--purification3.pdf">Using the Berks Cell Disruptor</a> </li> |
| − | <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></ | + | <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> |
| + | </ul> | ||
</div> | </div> | ||
</div> | </div> | ||
<div class="col-sm-2"> | <div class="col-sm-2"> | ||
| − | Microscopy | + | <h2>Microscopy</h2> |
| − | 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>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> |
<ul> | <ul> | ||
| − | <li><a href="https://static.igem.org/mediawiki/2017/9/90/T--Oxford--Protocols--microscopy1.pdf">Making Slides</a> </li | + | <li><a href="https://static.igem.org/mediawiki/2017/9/90/T--Oxford--Protocols--microscopy1.pdf">Making Slides</a> </li> |
| − | <li><a href="https://static.igem.org/mediawiki/2017/d/d4/T--Oxford--Protocols--microscopy2.pdf">Using the Fluorescence Microscope</a> </li | + | <li><a href="https://static.igem.org/mediawiki/2017/d/d4/T--Oxford--Protocols--microscopy2.pdf">Using the Fluorescence Microscope</a> </li> |
| − | + | </ul> | |
| − | + | ||
| − | </ | + | |
</div> | </div> | ||
| + | <br> | ||
| + | <br> | ||
<div class="col-sm-2"> | <div class="col-sm-2"> | ||
| − | <a href="#demo" class="btn btn-info" data-toggle="collapse | + | <a href="#demo" class="btn btn-info" data-toggle="collapse">OMVs</a> |
<div id="demo" class="collapse"> | <div id="demo" class="collapse"> | ||
<ul> | <ul> | ||
| − | <li><a href="https://static.igem.org/mediawiki/2017/1/1a/T--Oxford--Protocols--OMV.pdf">OMV Extraction</a> </li> </ | + | <li><a href="https://static.igem.org/mediawiki/2017/1/1a/T--Oxford--Protocols--OMV.pdf">OMV Extraction</a> </li> |
| + | </ul> | ||
</div> | </div> | ||
| − | < | + | <br> |
</div> | </div> | ||
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</body> | </body> | ||
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</html> | </html> | ||
{{Oxford/footer}} | {{Oxford/footer}} | ||
Revision as of 02:44, 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
Create DNA in Snapgene
Order DNA from IDT
Order DNA from IDT
PCR from G-Blocks
PCR from G-Blocks
Run a Gel of the PCR
Run a Gel of the PCR
Digest and Ligate
Digest and Ligate Into Shipping Vector
Transform and Plate
Transform and Plate
Inoculate
Inoculate
Miniprep
Miniprep
Test Digest and Sequence
Test Digest and Sequence
Send DNA to iGEM
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.
Microscopy
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.
Sponsors
