Difference between revisions of "Team:Oxford/Parts"

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{{Oxford}}
 
{{Oxford}}
 
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<h1>Parts</h1>
 
<h1>Parts</h1>
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<h2>Parts for the Cell-Free System</h2>
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<p>Each team will make new parts during iGEM and will submit them to the Registry of Standard Biological Parts. The iGEM software provides an easy way to present the parts your team has created. The <code>&lt;groupparts&gt;</code> tag (see below) will generate a table with all of the parts that your team adds to your team sandbox.</p>
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<div id="cell-free-parts-table">
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<p>Remember that the goal of proper part documentation is to describe and define a part, so that it can be used without needing to refer to the primary literature. Registry users in future years should be able to read your documentation and be able to use the part successfully. Also, you should provide proper references to acknowledge previous authors and to provide for users who wish to know more.</p>
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<table class="table table-hover">
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    <thead>
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      <tr>
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        <th>Registry Number</th>
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        <th>Code used in Lab</th>
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        <th>Brief Description</th>
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        <th>Key Details</th>
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        <th>Biobricks used</th>
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        <th>Other sequence sources</th>
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      </tr>
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    </thead>
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    <tbody>
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      <tr>
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        <td>BBa_K2450101</td>
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        <td>C100</td>
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        <td>mCherry - TEV protease (non-cleaving)</td>
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        <td>Doesn’t self-cleave</td>
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        <td>?</td>
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        <td>?</td>
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      </tr>
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      <tr>
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    <td>BBa_K2450201</td>
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    <td>C200</td>
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    <td>Modified TetR with TEV cleavage site - CFP</td>
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    <td>TEV cleavage site in linker between DNA binding and dimerisation domains</td>
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    <td>BBa_K106669; BBa_K???????</td>
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    <td>TEV cleavage site from Merck; CFP from AddGene</td>
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      </tr>
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      <tr>
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      <td>BBa_K2450251</td>
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      <td>C250</td>
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      <td>TetR - CFP</td>
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      <td>Normal TetR Class B</td>
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      <td>BBa_K106669; BBa_K???????</td>
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      <td>CFP from AddGene</td>
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  </tr>
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  <tr>
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      <td>BBa_K2450301</td>
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      <td>C300</td>
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      <td>Tet promoter - RBS - YFP</td>
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      <td>DNA part, contains promoter and RBS to give signal of YFP</td>
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      <td>BBa_R0040</td>
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      <td>?</td>
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  </tr>
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    </tbody>
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  </table>
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  </div>
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  <h2>Parts for the OMV System</h2>
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  <div id="omv-parts-table">
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  <table class="table table-hover">
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    <thead>
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      <tr>
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        <th>Registry Number</th>
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        <th>Code used in Lab</th>
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        <th>Brief Description</th>
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        <th>Key Details</th>
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        <th>Biobricks used</th>
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        <th>Other sequence sources</th>
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      </tr>
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    </thead>
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    <tbody>
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      <tr>
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        <td>BBa_K2450401</td>
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        <td>V100</td>
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        <td>N-SpyCatcher - OmpA - sfGFP</td>
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        <td>SpyCatcher is between leader sequence and OmpA. Used sfGFP to help it fold out of cytoplasm</td>
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        <td>?</td>
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        <td>Alves et al, 2016 AddGene</td>
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      </tr>
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      <tr>
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    <td>BBa_K2450451</td>
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    <td>v150</td>
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    <td>OmpA - C-SpyCatcher - sfGFP</td>
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    <td>SpyCatcher is after OmpA - will be compared to BBa_K2450401. Used sfGFP to help it fold out of cytoplasm</td>
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    <td>?</td>
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    <td>Alves et al, 2016</td>
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      </tr>
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      <tr>
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      <td>BBa_K2450501</td>
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      <td>v200</td>
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      <td>SpyTag - sfGFP - Quencher</td>
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      <td>TEV cleavage site between sfGFP and the quenching peptide</td>
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      <td>BBa_K1319014</td>
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      <td>Alves et al, 2016</td>
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  </tr>
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  <tr>
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      <td>BBa_K2450502</td>
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      <td>V200noQ</td>
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      <td>SpyTag - sfGFP</td>
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      <td>Control to check localisation to OMVs</td>
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      <td>?</td>
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      <td>Alves et al, 2016</td>
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  </tr>
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    <tr>
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      <td>BBa_K2450701</td>
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      <td>V500</td>
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      <td>sfGFP - N-terminal split TEV Protease - Inhibited Coiled Coil</td>
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      <td>Inhibited coiled coil contains a TEV cleavage site between the two helicies, leaving the acid coiled coil attached to the N-terminal split protease</td>
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      <td>?</td>
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      <td>Alves et al, 2016 Split TEV paper</td>
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  </tr>
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    <tr>
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      <td>BBa_K2450702</td>
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      <td>V600</td>
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      <td>mCherry - Inhibited Coiled Coil - C-terminal Split TEV Protease</td>
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      <td>Inhibited coiled coil contains a TEV protease cleavage site. This will result in the cleavage of the mCherry - Acid Coil being cleaved from the Base Coil - C Terminal Split TEV Protease.</td>
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      <td>?</td>
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      <td>Alves et al, 2016 Split TEV paper</td>
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  </tr>
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    </tbody>
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  </table>
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  </div>
 
</div>
 
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<h5>Note</h5>
 
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<p>Note that parts must be documented on the <a href="http://parts.igem.org/Main_Page"> Registry</a>. This page serves to <i>showcase</i> the parts you have made. Future teams and other users and are much more likely to find parts by looking in the Registry than by looking at your team wiki.</p>
 
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<h5>Adding parts to the registry</h5>
 
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<p>You can add parts to the Registry at our <a href="http://parts.igem.org/Add_a_Part_to_the_Registry">Add a Part to the Registry</a> link.</p>
 
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<p>We encourage teams to start completing documentation for their parts on the Registry as soon as you have it available. The sooner you put up your parts, the better you will remember all the details about your parts. Remember, you don't need to send us the DNA sample before you create an entry for a part on the Registry. (However, you <b>do</b> need to send us the DNA sample before the Jamboree. If you don't send us a DNA sample of a part, that part will not be eligible for awards and medal criteria.)</p>
 
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<h5>What information do I need to start putting my parts on the Registry?</h5>
 
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<p>The information needed to initially create a part on the Registry is:</p>
 
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<ul>
 
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<li>Part Name</li>
 
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<li>Part type</li>
 
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<li>Creator</li>
 
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<li>Sequence</li>
 
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<li>Short Description (60 characters on what the DNA does)</li>
 
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<li>Long Description (Longer description of what the DNA does)</li>
 
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<li>Design considerations</li>
 
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</ul>
 
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<p>
 
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We encourage you to put up <em>much more</em> information as you gather it over the summer. If you have images, plots, characterization data and other information, please also put it up on the part page. </p>
 
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<h5>Part Table </h5>
 
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<p>Please include a table of all the parts your team has made during your project on this page. Remember part characterization and measurement data must go on your team part pages on the Registry. </p>
 
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<groupparts>iGEM17 Oxford</groupparts>
 
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Revision as of 14:53, 29 October 2017

Parts

Parts for the Cell-Free System

Registry Number Code used in Lab Brief Description Key Details Biobricks used Other sequence sources
BBa_K2450101 C100 mCherry - TEV protease (non-cleaving) Doesn’t self-cleave ? ?
BBa_K2450201 C200 Modified TetR with TEV cleavage site - CFP TEV cleavage site in linker between DNA binding and dimerisation domains BBa_K106669; BBa_K??????? TEV cleavage site from Merck; CFP from AddGene
BBa_K2450251 C250 TetR - CFP Normal TetR Class B BBa_K106669; BBa_K??????? CFP from AddGene
BBa_K2450301 C300 Tet promoter - RBS - YFP DNA part, contains promoter and RBS to give signal of YFP BBa_R0040 ?

Parts for the OMV System

Registry Number Code used in Lab Brief Description Key Details Biobricks used Other sequence sources
BBa_K2450401 V100 N-SpyCatcher - OmpA - sfGFP SpyCatcher is between leader sequence and OmpA. Used sfGFP to help it fold out of cytoplasm ? Alves et al, 2016 AddGene
BBa_K2450451 v150 OmpA - C-SpyCatcher - sfGFP SpyCatcher is after OmpA - will be compared to BBa_K2450401. Used sfGFP to help it fold out of cytoplasm ? Alves et al, 2016
BBa_K2450501 v200 SpyTag - sfGFP - Quencher TEV cleavage site between sfGFP and the quenching peptide BBa_K1319014 Alves et al, 2016
BBa_K2450502 V200noQ SpyTag - sfGFP Control to check localisation to OMVs ? Alves et al, 2016
BBa_K2450701 V500 sfGFP - N-terminal split TEV Protease - Inhibited Coiled Coil Inhibited coiled coil contains a TEV cleavage site between the two helicies, leaving the acid coiled coil attached to the N-terminal split protease ? Alves et al, 2016 Split TEV paper
BBa_K2450702 V600 mCherry - Inhibited Coiled Coil - C-terminal Split TEV Protease Inhibited coiled coil contains a TEV protease cleavage site. This will result in the cleavage of the mCherry - Acid Coil being cleaved from the Base Coil - C Terminal Split TEV Protease. ? Alves et al, 2016 Split TEV paper
Inspiration

We have a created a collection of well documented parts that can help you get started.

You can also take a look at how other teams have documented their parts in their wiki: