Difference between revisions of "Team:Groningen/Parts"

 
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<h1>Parts</h1>
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<h1 class="left">Parts</h1>
  
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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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<p class="left">Our months of lab work contributed to the construction of several new parts. Please consult the registry for a more detailed explanation of our parts and the validation work that was performed for it. </p>
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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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<h5 class="left" >Best Basic Part: dCas9 VRER</h5>
  
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<p class="left"> Our favorite part and the Groningen contender for Best New Basic part is dCas9 VRER. This variation on our improved spdCas9s for bacterial use, is adapted in such a way that it recognizes different PAM sites. These different sites ensure that the two Cas-complexes of our system do not compete for the binding sites of their counterpart. The difference in PAM sites ensures that the dCas9 VRER protein only binds to the sites which are specifically located on our pre-programmed reporter plasmid. It also prevent it from binding on the injected phage DNA. This also works the other way around as hCas9 only binds on the infecting phage DNA and not on the reporter plasmid, as it would cleave the plasmid upon binding to one of its sites.
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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 class="left" >Parts list</h5>
  
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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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  <tr class="tableizer-firstrow"><th> </th><th>.gb file</th><th>  </th><th>Part Number</th><th>Type</th><th>Part Name</th><th>Author</th><th>bp</th></tr>
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  <tr><td><img src="https://static.igem.org/mediawiki/2017/0/07/Heart-icon%281%29.png"></td><td><a href="https://static.igem.org/mediawiki/2017/b/b1/PSB1C3_dCas9VRER_bba_k2361001.gb" target="_blank"><img src="https://static.igem.org/mediawiki/2017/f/f2/SnapTube1x.png"></a></td><td>  </td><td><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2361001" target="_blank">BBa_K2361001</td><td>Coding</td><td>dCas9 VRER</td><td>Mart Bartelds</td><td>4108</td></tr>
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  <tr><td>&nbsp;</td><td><a href="https://static.igem.org/mediawiki/2017/a/a2/PSB1C3_dCas9_bba_K2361000.gb" target="_blank"><img src="https://static.igem.org/mediawiki/2017/f/f2/SnapTube1x.png"></a></td><td>  </td><td><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2361000" target="_blank">BBa_K2361000</a></td><td>Coding</td><td>spdCas9</td><td>Mart Bartelds</td><td>4120</td></tr>
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  <tr><td>&nbsp;</td><td><a href="https://static.igem.org/mediawiki/2017/d/da/PSB1C3_pUsp45_tracrRNA_BBa_k2361003.gb" target="_blank"><img src="https://static.igem.org/mediawiki/2017/f/f2/SnapTube1x.png"></a></td><td>  </td><td><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2361003" target="_blank">BBa_K2361003</a></td><td>RNA</td><td>pUSP45 tracrRNA</td><td>Thijs Ettema</td><td>474</td></tr>
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  <tr><td>&nbsp;</td><td><a href="https://static.igem.org/mediawiki/2017/0/07/PSB1C3_CRISPR_array_BsaI_BBa_k2361004.gb" target="_blank"><img src="https://static.igem.org/mediawiki/2017/f/f2/SnapTube1x.png"></a></td><td>  </td><td><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2361004" target="_blank">BBa_K2361004</a></td><td>RNA</td><td>CRISPR array</td><td>Sebald Verkuijl</td><td>639</td></tr>
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  <tr><td>&nbsp;</td><td><a href="https://static.igem.org/mediawiki/2017/b/b5/PSB1C3_CRISPR_array_spacer20_BBa_k2361005.gb" target="_blank"><img src="https://static.igem.org/mediawiki/2017/f/f2/SnapTube1x.png"></a></td><td>  </td><td><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2361005" target="_blank">BBa_K2361005</a></td><td>RNA</td><td>CRISPR array containing a 20 spacer</td><td>Sebald Verkuijl</td><td>691</td></tr>
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  <tr><td>&nbsp;</td><td><a href="https://static.igem.org/mediawiki/2017/4/41/PSB1C3_CRISPR_array_spacer21_BBa_k2361006.gb" target="_blank"><img src="https://static.igem.org/mediawiki/2017/f/f2/SnapTube1x.png"></a></td><td>  </td><td><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2361006" target="_blank">BBa_K2361006</a></td><td>RNA</td><td>CRISPR array containing a 21 spacer</td><td>Sebald Verkuijl</td><td>691</td></tr>
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  <tr><td>&nbsp;</td><td><a href="https://static.igem.org/mediawiki/2017/0/0e/PSB1C3_CRISPR_array_Empty_BBa_k2361007.gb" target="_blank"><img src="https://static.igem.org/mediawiki/2017/f/f2/SnapTube1x.png"></a></td><td>  </td><td><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2361007" target="_blank">BBa_K2361007</a></td><td>RNA</td><td>CRISPR array containing empty spacers</td><td>Sebald Verkuijl</td><td>625</td></tr>
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  <tr><td>&nbsp;</td><td><a href="https://static.igem.org/mediawiki/2017/e/ed/PSB1C3_pNisA_BBa_K2361009.gb" target="_blank"><img src="https://static.igem.org/mediawiki/2017/f/f2/SnapTube1x.png"></a></td><td>  </td><td><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2361009" target="_blank">BBa_K2361009</a></td><td>Regulatory</td><td>Nisin inducable lactococcal promoter</td><td>Thijs Ettema</td><td>198</td></tr>
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  <tr><td><img src="https://static.igem.org/mediawiki/2017/d/df/Webp.net-resizeimage.png"></td><td><a href="https://static.igem.org/mediawiki/2017/b/b0/Psb1c3-hcas9OPERON.gb" target="_blank"><img src="https://static.igem.org/mediawiki/2017/f/f2/SnapTube1x.png"></a></td><td>  </td><td><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2361002" target="_blank">BBa_K2361002</a></td><td>Coding</td><td>hCas9 operon</td><td>Thijs Ettema</td><td>6060</td></tr>
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  <tr><td><img src="https://static.igem.org/mediawiki/2017/d/df/Webp.net-resizeimage.png"></td><td><a href="https://static.igem.org/mediawiki/2017/7/75/PSB1C3-p32-BBa_K2361008.gb" target="_blank"><img src="https://static.igem.org/mediawiki/2017/f/f2/SnapTube1x.png"></a></td><td>  </td><td><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2361008" target="_blank">BBa_K2361008</a></td><td>Regulatory</td><td>p32 lactococcal promoter</td><td>Thijs Ettema</td><td>196</td></tr>
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  <tr><td><img src="https://static.igem.org/mediawiki/2017/d/df/Webp.net-resizeimage.png"></td><td><a href="https://static.igem.org/mediawiki/2017/3/39/PSB1C3-pusp45_BBa_K2361010.gb" target="_blank"><img src="https://static.igem.org/mediawiki/2017/f/f2/SnapTube1x.png"></a></td><td>  </td><td><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2361010" target="_blank">BBa_K2361010</a></td><td>Regulatory</td><td>pUSP45 lactococcal promoter</td><td>Thijs Ettema</td><td>606</td></tr>
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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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<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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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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<a class="button" style="text-decoration: none; color:white; margin-bottom:30px;" href="https://2017.igem.org/Team:Groningen/Collaborations">Next: Collaborations</a>
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<img id="bannerimg" usemap="#imagemap_sponsors" style="width: 100%;" src="https://static.igem.org/mediawiki/2017/b/b5/Banner.jpg" alt="Sponsors">
 
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<h5>Inspiration</h5>
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<p>We have a created  a <a href="http://parts.igem.org/Well_Documented_Parts">collection of well documented parts</a> that can help you get started.</p>
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<p> You can also take a look at how other teams have documented their parts in their wiki:</p>
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<li><a href="https://2014.igem.org/Team:MIT/Parts"> 2014 MIT </a></li>
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<li><a href="https://2014.igem.org/Team:Heidelberg/Parts"> 2014 Heidelberg</a></li>
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<li><a href="https://2014.igem.org/Team:Tokyo_Tech/Parts">2014 Tokyo Tech</a></li>
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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 Groningen</groupparts>
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Latest revision as of 03:59, 2 November 2017


Parts

Our months of lab work contributed to the construction of several new parts. Please consult the registry for a more detailed explanation of our parts and the validation work that was performed for it.

Best Basic Part: dCas9 VRER

Our favorite part and the Groningen contender for Best New Basic part is dCas9 VRER. This variation on our improved spdCas9s for bacterial use, is adapted in such a way that it recognizes different PAM sites. These different sites ensure that the two Cas-complexes of our system do not compete for the binding sites of their counterpart. The difference in PAM sites ensures that the dCas9 VRER protein only binds to the sites which are specifically located on our pre-programmed reporter plasmid. It also prevent it from binding on the injected phage DNA. This also works the other way around as hCas9 only binds on the infecting phage DNA and not on the reporter plasmid, as it would cleave the plasmid upon binding to one of its sites.

Parts list
.gb file Part NumberTypePart NameAuthorbp
BBa_K2361001CodingdCas9 VRERMart Bartelds4108
  BBa_K2361000CodingspdCas9Mart Bartelds4120
  BBa_K2361003RNApUSP45 tracrRNAThijs Ettema474
  BBa_K2361004RNACRISPR arraySebald Verkuijl639
  BBa_K2361005RNACRISPR array containing a 20 spacerSebald Verkuijl691
  BBa_K2361006RNACRISPR array containing a 21 spacerSebald Verkuijl691
  BBa_K2361007RNACRISPR array containing empty spacersSebald Verkuijl625
  BBa_K2361009RegulatoryNisin inducable lactococcal promoterThijs Ettema198
BBa_K2361002CodinghCas9 operonThijs Ettema6060
BBa_K2361008Regulatoryp32 lactococcal promoterThijs Ettema196
BBa_K2361010RegulatorypUSP45 lactococcal promoterThijs Ettema606

Next: Collaborations
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