Difference between revisions of "Team:Oxford/Protocols"

 
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<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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<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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<span id="header-lightbox-title">Protocols</span>
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     <img class="img-responsive img-circle team-member-img alissa_open" src="https://static.igem.org/mediawiki/2017/3/37/T--Oxford--Protocols--Figure_1.png">
 
     <img class="img-responsive img-circle team-member-img alissa_open" src="https://static.igem.org/mediawiki/2017/3/37/T--Oxford--Protocols--Figure_1.png">
   
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<span id="caption">Create DNA in Snapgene</span>
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<h3>Create DNA in Snapgene</h3> <br/>
<b>Alissa Hummer</b> (Biochemistry)<br/>
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<i>Co-leader<br/>
+
She. cruzi</i><br/>
+
 
+
Alissa spends most of her iGEM days split between the wet lab, working with the engineers on mathematical modelling, and doing organizational things because she loves pretty much everything. Her experience in other labs prior to iGEM is invaluable to the team, because she knows all of the tips and tricks for efficient research. Outside of iGEM she enjoys playing football, being in nature, and reading.
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     <img class="img-responsive img-circle team-member-img angela_open" src="https://static.igem.org/mediawiki/2017/a/a5/T--oxford--team--angela--circle.jpeg">
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     <img class="img-responsive img-circle team-member-img angela_open" src="https://static.igem.org/mediawiki/2017/f/f9/T--Oxford--Protocols--Figure_2.png">
    <span id="profile_caption"> Angela Hellyer </span>
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<span id="caption"> Order DNA from IDT </span>
    <div class="subject-icon bioch"></div>
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<h3>Order DNA from IDT</h3> <br/>
<b>Angela Hellyer</b> (Biochemistry)<br/>
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<i>Wet Lab Co-ordinator &amp; Safety<br/>
+
G. weazli</i><br/>
+
 
+
Angela doesn’t really know how she ended up being in charge of safety, it kind of just happened when she wasn’t looking. Creator of the cake rota, she likes to keep things light, and provides some moral support for when things inevitably go wrong; only to be fixed promptly of course! Outside of iGEM she enjoys food and all things astro-, along with being Zoe F’s main Hogwarts buddy.
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     <img class="img-responsive img-circle team-member-img arthur_open" src="https://static.igem.org/mediawiki/2017/7/79/T--Oxford--Protocols--Figure_4.png">
    <span id="profile_caption"> Arthur Norman </span>
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<span id="caption"> PCR from G-Blocks </span>
    <div class="subject-icon bioch"></div>
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<h3>PCR from G-Blocks</h3> <br/>
<b>Arthur Norman</b> (Biochemistry)<br/>
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<i>Co-leader<br/>
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T. freezi</i><br/>
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Arthur has been dubbed ‘freezer boy’, and his super powers include being able to organise freezer boxes without them thawing and the ability to tidy away everyone else’s eppendorfs. Arthur spends his time split between working in the lab and coming up with novel ideas for the project. When outside the lab he plays tennis, runs, and drinks pimms, sometimes all three at the same time.
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     <span id="profile_caption"> Chun Ngai Au </span>
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     <span id="caption"> Run a Gel of the PCR </span>
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<h3>Run a Gel of the PCR</h3><br/>
<b>Chun Ngai Au</b> (Engineering)<br/>
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<i>Dry Lab Co-ordinator<br/>
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T. snoozi</i><br/>
+
 
+
Chun likes creating colourful and cool looking graphs on Matlab, although he isn’t totally against putting on a lab coat and pipetting a couple of things every now and again. He put in a lot of work at the beginning of the project to catch up on the biochemistry, but is now as knowledgable as the rest of us. Outside of iGEM, he likes to play Ultimate, sleep, and eat spicy food - even his pizzas tend to have chillies on them.
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      <span id="caption"> Digest and Ligate </span>
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        <h3>Digest and Ligate Into Shipping Vector</h3><br/>
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    <span id="profile_caption"> Helen Siyu Ren </span>
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<b>Helen Siyu Ren</b> (Engineering)<br/>
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<i>Dry Lab Co-ordinator<br/>
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Si. yuzi</i><br/>
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+
As one of the few non-bio students, Helen is learning new things in the wet lab while spending the rest of time staring at her laptop doing wiki pages and trying to implement the complicated model that comes with all of our many parts. She is one of those people who really likes to sit on the floor, where her free time is spent reading, playing bridge, and eating delicious food she made earlier.
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     <span id="caption"> Transform and Plate </span>
     <span id="profile_caption"> Jei Diwakar </span>
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    <div class="subject-icon bioch"></div>
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<h3>Transform and Plate</h3> <br/>
<b>Jei Diwakar</b> (Biochemistry)<br/>
+
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<i>Wet Lab Co-ordinator &amp; Treasurer<br/>
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T. schmoozi</i><br/>
+
 
+
Jei’s role means that sending emails and adding SUM functions to Excel have become routine to him. He spends most of his time doing wet lab work, unless he is organising flights and hotels, then he is on the phone all day! Outside of the lab, Jei plays a lot of cricket for the Oxford University Cricket Club and also is a co-founder of the Oxford University Biotech Society.
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     <img class="img-responsive img-circle team-member-img john_open" src="https://static.igem.org/mediawiki/2017/6/69/T--oxford--team--john--circle.jpeg">
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     <img class="img-responsive img-circle team-member-img john_open" src="https://static.igem.org/mediawiki/2017/2/2c/T--Oxford--Protocols--Figure_8.png">
     <span id="profile_caption"> John Myers </span>
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     <span id="caption"> Inoculate</span>
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<h3>Inoculate</h3><br/>
<b>John Myers</b> (Biochemistry)<br/>
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<i>Secretary<br/>
+
Oui. cruzi</i><br/>
+
 
+
John keeps track of the team’s regular meetings and is enthusiastic about outreach. Often he can be found helping out in the lab, learning all of the protocols in detail. Outside of iGEM, he rows for his college, plays the violin, and cooks - very useful for the team’s weekly cake rota. He also introduced a large chunk of the team to Bridget Jones, for which we are all eternally grateful.
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     <span id="profile_caption"> Kushal Mansatta </span>
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     <span id="caption"> Miniprep </span>
 
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<img class="img-responsive img-circle" src="https://static.igem.org/mediawiki/2017/e/ea/T--oxford--team--kushal--circle.jpeg">
+
<h3>Miniprep</h3><br/>
<b>Kushal Mansatta</b> (Medicine)<br/>
+
<object data="https://static.igem.org/mediawiki/2017/1/17/T--Oxford--Protocols--Figure_9_pdf.pdf" type="application/pdf" width="900px" height="900px"></object>
<i>Wiki Co-ordinator &amp; Social Sec<br/>
+
He. cruzi</i><br/>
+
 
+
Kushal is a man of two lives. By day he can usually be found browsing older wikis for inspiration or reminding people to reference EVERYTHING they read; by night he makes sure everyone on the team has fun and eats well. His medical background has been invaluable for our diagnostic track. Outside of iGEM, he enjoys going to the gym, caring for patients at his job on a hospital ward, and switching off at the end of the day with trashy TV.
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     <img class="img-responsive img-circle team-member-img noah_open" src="https://static.igem.org/mediawiki/2017/e/e9/T--Oxford--Protocols--Figure_10.png">
     <img class="img-responsive img-circle team-member-img noah_open" src="https://static.igem.org/mediawiki/2017/1/12/T--oxford--team--noah--circle.jpeg">
+
     <span id="caption"> Test Digest and Sequence </span>
     <span id="profile_caption"> Noah Sprent </span>
+
    <div class="subject-icon bioch"></div>
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<img class="img-responsive img-circle" src="https://static.igem.org/mediawiki/2017/1/12/T--oxford--team--noah--circle.jpeg">
+
<h3>Test Digest and Sequence</h3><br/>
<b>Noah Sprent</b> (Biochemistry)<br/>
+
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<i>Co-leader<br/>
+
No. shoezi</i><br/>
+
 
+
Noah loves making agendas for meetings and reading about definitely-not-useless features on Benchling when he’s not keeping our lab beautifully clean. Although life outside of iGEM isn’t really life at all, Noah is a co-founder of the Oxford University Biotech Society, tries to do cool things with the Oxford University Gymnastics Club, and has confusing discussions with his philosopher housemates.
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     <img class="img-responsive img-circle team-member-img sumaera_open" src="https://static.igem.org/mediawiki/2017/2/2f/T--oxford--team--sumaera--circle.jpeg">
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     <img class="img-responsive img-circle team-member-img sumaera_open" src="https://static.igem.org/mediawiki/2017/1/1d/T--Oxford--Protocols--Figure_11.png">
     <span id="profile_caption"> Sumaera Rathore </span>
+
     <span id="caption"> Send DNA to iGEM </span>
    <div class="subject-icon bio"></div>
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<img class="img-responsive img-circle" src="https://static.igem.org/mediawiki/2017/2/2f/T--oxford--team--sumaera--circle.jpeg">
+
<h3>Send DNA to iGEM</h3><br/>
<b>Sumaera Rathore</b> (Biology)<br/>
+
<img class="img-responsive img-circle team-member-img sumaera_open" src="https://static.igem.org/mediawiki/2017/6/63/T--Oxford--Protocols--Figure_11_iGEM.png">
<i>iGEM Requirements Co-ordinator<br/>
+
Tea. Brewzi</i><br/>
+
 
+
Sumaera puts the 'bio' into 'biochem' and is responsible for ensuring our project ticks all the boxes in the judging booklet so we can really impress the judges with all our hard work. She also knows a lot more about parasites than the rest of us. Outside of iGEM, Sumaera enjoys anything to do with plants, tea, and chocolate. In fact, she brightened up our iGEM desks with a collection of aloe plants!
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    <span id="profile_caption"> Zoë Catchpole </span>
 
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<b>Zoë Catchpole</b> (Biochemistry)<br/>
 
<i>Outreach &amp; Human Practices<br/>
 
Cant. choozi</i><br/>
 
 
Zoe wants to show everyone that synbio is as cool as she thinks it is by designing ‘fun’ activities for outreach, and is key to co-ordinating all of our meetings with experts from across the globe. She is always keen to pitch in with the lab work too. Outside of iGEM she has grade 8 recorder, but unfortunately serenading our E. coli hasn’t yet helped our transformation efficiency!
 
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    <span id="profile_caption"> Zoe Ford </span>
 
    <div class="subject-icon bioch"></div>
 
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<b>Zoe Ford</b> (Biochemistry)<br/>
 
<i>Wet Lab Co-ordinator &amp; Social Media<br/>
 
'Wee'. cruzi</i><br/>
 
  
Zoe enjoys spending endless hours in the lab pipetting clear liquids from one tube into another. Along with being our Queen of SnapGene, they love taking pictures of everything and everyone to make the prettiest iGEM Instagram account in history. Outside of iGEM they referee quidditch, sing in choirs, and use a lot of their free time in the evenings cross-stitching everything - including our logo!
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    <br/>
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<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>
 +
<br>
  
    </div>
+
<div class="row">
    </div>
+
<div class="col-sm-3">
 +
<a href="#demo" class="btn btn-info" data-toggle="collapse">Bits and Pieces</a>
 +
  <div id="demo" class="collapse">
 +
<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/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/2017/8/8a/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/2017/2/27/T--Oxford--Protocols--bap6.pdf">Making Antibiotics</a> </li>
 +
</ul>
 
</div>
 
</div>
 
 
</div>
 
</div>
 
+
<div class="col-sm-3">
<div class="container-fluid" id="supervisor-container">
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<a href="#demoa" class="btn btn-info" data-toggle="collapse">Various Types of PCR</a>
<div class="container">
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<ul>
<div class="row">
+
<li><a href="https://static.igem.org/mediawiki/2017/5/5b/T--Oxford--Protocols--pcr1.pdf">Normal PCR</a> </li>  
    <div class="col-sm-12" id="supervisor-header">
+
<li><a href="https://static.igem.org/mediawiki/2017/f/ff/T--Oxford--Protocols--pcr2.pdf">Colony PCR</a> </li>
        <center><span>Supervisors</span></center>
+
<li><a href="https://static.igem.org/mediawiki/2017/4/4f/T--Oxford--Protocols--pcr3.pdf">Quick-change PCR</a> </li>
    </div>
+
<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>
 +
</ul>
 
</div>
 
</div>
 
<div class="row supervisor">
 
    <div class="col-sm-3 supervisor-img">
 
        <img class="img-responsive" src="https://static.igem.org/mediawiki/2017/0/01/T--oxford--team--george--circle.jpg">
 
    </div>
 
    <div class="col-sm-9 supervisor-description">
 
    <b>Dr. George Wadhams</b><br />
 
    <i>Oxford Department of Biochemistry</i><br /><br />
 
    George's research interests lie in how bacteria sense and integrate environmental information. His group focuses on understanding in a quantitative manner how multiple, homologous pathways operate in individual cells and how the components of these pathways can be used to create synthetic pathways.<br />
 
    George has been mentoring Oxford iGEM teams since they were founded in 2014.
 
    </div>
 
 
</div>
 
</div>
 
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<div class="col-sm-3">
 
+
<a href="#demob" class="btn btn-info" data-toggle="collapse">Protein Purification</a>
<div class="row supervisor">
+
  <div id="demob" class="collapse">
    <div class="col-sm-3 supervisor-img">
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<ul>
        <img class="img-responsive" src="https://static.igem.org/mediawiki/2017/f/fa/T--oxford--team--nick--circle.jpg">
+
<li><a href="https://static.igem.org/mediawiki/2017/2/2e/T--Oxford--Protocols--purification1.pdf">Making Buffers for Purification</a> </li>  
    </div>
+
<li><a href="https://static.igem.org/mediawiki/2017/4/4a/T--Oxford--Protocols--purification2.pdf">Using the Avanti Centrifuge</a> </li>
    <div class="col-sm-9 supervisor-description">
+
<li><a href="https://static.igem.org/mediawiki/2017/a/aa/T--Oxford--Protocols--purification3.pdf">Using the Berks Cell Disruptor</a> </li>
    <b>Dr. Nicolas Delalez</b><br />
+
<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>
    <i>Oxford Department of Engineering</i><br /><br />
+
</ul>
    Nick's research interests include synthetic biology and its biophysics of molecular machines.
+
</div>
    <br />
+
</div>
    Nick is the main person we go to when we are stuck on something in the lab. He can troubleshoot everything from a unsuccessful PCR to a contaminated plate of cells.
+
<div class="col-sm-2">
    </div>
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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>-->
 +
<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/d/d4/T--Oxford--Protocols--microscopy2.pdf">Using the Fluorescence Microscope</a> </li>  
 +
</ul>
 +
</div>
 +
</div>
 +
<div class="col-sm-1">
 +
<a href="#demod" class="btn btn-info" data-toggle="collapse">OMVs</a>
 +
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<ul>
 +
<li><a href="https://static.igem.org/mediawiki/2017/1/1a/T--Oxford--Protocols--OMV.pdf">OMV Extraction</a> </li>
 +
</ul>
 
</div>
 
</div>
 
<div class="row supervisor">
 
    <div class="col-sm-3 supervisor-img">
 
        <img class="img-responsive" src="https://static.igem.org/mediawiki/2017/5/51/T--oxford--team--antonis--circle.jpg">
 
    </div>
 
    <div class="col-sm-9 supervisor-description">
 
    <b>Prof. Antonis Papachristodoulou</b><br />
 
    <i>Oxford Department of Engineering</i><br /><br />
 
    Antonis' research interests include systems and synthetic biology, network systems, aerospace systems and flow control, and convex optimisation. Furthermore, he works on modern control theory, robust stability analysis and design, as well as nonlinear dynamical systems and Lyapunov stability.
 
    </div>
 
 
</div>
 
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    </div>
 
    <div class="col-sm-9 supervisor-description">
 
    <b>Harrison Steel</b><br />
 
    <i>Oxford Department of Engineering</i><br /><br />
 
    Harry is a PhD student whose research interests include control engineering and its application to Synthetic Biology, as well as mathematical tools for analysis of biological systems. Furthermore, he works on the design and development of new tools and hardware for use in Biological research.
 
    </div>
 
 
</div>
 
</div>
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        <img class="img-responsive" src="https://static.igem.org/mediawiki/2017/8/8b/T--oxford--team--juditharmitage--circle.jpeg" width="500" height="500">
 
    </div>
 
    <div class="col-sm-9 supervisor-description">
 
    <b>Prof. Judy Armitage</b><br />
 
    <i>Oxford Department of Biochemistry</i><br /><br />
 
Judy Armitage is interested in the dynamics of bacterial sensory transduction and the control of bacterial motility. In particular, her research group focuses on the communication between the sensory and adaptation mechanisms of the two pathways as a model for network sensory integration in general.
 
    </div>
 
 
</div>
 
</div>
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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.