Difference between revisions of "Team:TUDelft/Parts/Main"

 
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<div class="col-lg-10 col-md-10 col-sm-10 col-xs-10 nowbg">  
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                      <li class="active"><a href="#jnr" class="adpbl">Parts Overview</a></li>
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                      <li><a href="#basicpart"  class="adpbl">Basic Parts </a></li>
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                      <li><a href="#compositepart"  class="adpbl">Composite Parts    </a></li> 
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                      <li><a href="#partcollection"    class="adpbl">Part Collection    </a></li>
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            <div id="partsoverview"></div>
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             <p>stuff to write here</p>
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             <h1 class="grnbl">Parts Overview</h1>
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            <br>
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<p>
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            <div class="spcmkr" id="partsoverview"></div>
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When constructing our BioBricks, we made use of the IDT synthesis offer. This way we were able to generate our required parts in a fast and efficient way. Additionally, we made use of PCR amplification with our constructed expression plasmids as template to construct several BioBricks. All of the parts contain a coding sequence, some of which extended with promoters or introns. Since our fusion protein <a href="http://parts.igem.org/Part:BBa_K2643000" class="grnbl" target="_blank">BBa_K2643000</a> consists of the dxCas9, linker and Tn5 coding sequences this part is registered as <a href="https://2018.igem.org/Team:TUDelft/Composite_Parts" class="grnbl">composite part</a>. The basic parts comprising the fusion protein composite part are documented separately and also exist as separate BioBricks. This is advantageous for those wishing to combine one of our <a href="https://2018.igem.org/Team:TUDelft/Basic_Part" class="grnbl">basic parts</a> with a different expression level or compose a different composite part altogether. We created a <a href="https://2018.igem.org/Team:TUDelft/Part_Collection" class="grnbl">part collection</a> comprised of 6 basic parts encoding for different EPO coding sequences, 2 basic parts encoding for the required components for targeted sequencing and 1 composite part: our fusion protein. All BioBricks are submitted with elaborate characterisation so the user may choose the best part for their project accordingly. Our favourite basic part is dxCas9 <a href="http://parts.igem.org/Part:BBa_K2643001" class="grnbl" target="_blank">BBa_K2643001</a> and our favourite composite part is dxCas9-Lin-Tn5 <a href="http://parts.igem.org/Part:BBa_K2643000" class="grnbl" target="_blank">BBa_K2643000</a>.
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            <h1 class="adpbl">1. Parts Overview</h1>
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</p>
  
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<!-- TABEL WITH PART OVERVIEW -->
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<figcapture class="grnbl"><b>Table 1.</b> BioBrick Parts submitted by TU Delft iGEM 2018 team. All BioBricks were constructed by the team members involved in wetlab: Susan Bouwmeester, Kavish Kohabir, Venda Mangkusaputra, Timmy Paez, Lisbeth Schmidtchen and Nicole Bennis</figcapture>
 
<table>
 
<table>
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   <tr>
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   <tr class="tableheadergrnbl">
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     <th>Favorite Part</th>
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     <th class="tableheadergrnbl">&hearts;</th>
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     <th>BioBrick Name</th>
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     <th class="tableheadergrnbl">Name</th>
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     <th>Type</th>
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     <th class="tableheadergrnbl">Type</th>
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     <th>Description</th>
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     <th class="tableheadergrnbl">Description</th>
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     <th>Designer</th>
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     <th class="tableheadergrnbl">Designer</th>
 
   </tr>
 
   </tr>
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   <tr>
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   <tr class="tableunevengrnbl">
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     <td>Fav</td>
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     <td>&hearts;</td>
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     <td>BioBrick#1</td>
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     <td><a href="http://parts.igem.org/Part:BBa_K2643000" target="_blank" class="jnnbl">BBa_K2643000</a></td>
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     <td>Basic Part</td>
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     <td>Composite</td>
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     <td>Hay this part is not yet created</td>
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     <td>dxCas9-linker-Tn5 fusion protein (HIS Tag)</td>
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     <td>Me myself and I</td>
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     <td>TU Delft 2018</td>
 
   </tr>
 
   </tr>
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   <tr>
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   <tr class="tableevengrnbl">
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     <td>Fav</td>
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     <td>&hearts;</td>
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     <td>BioBrick#2</td>
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     <td><a href="http://parts.igem.org/Part:BBa_K2643001" target="_blank" class="jnnbl">BBa_K2643001</a></td>
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    <td>Basic Part</td>
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     <td>Basic</td>
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    <td>Hay this part is not yet created</td>
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     <td>dxCas9 (HIS Tag)</td>
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    <td>Me myself and I</td> </tr>
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     <td>TU Delft 2018</td>
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  <tr>
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    <td>Fav</td>
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    <td>BioBrick#3</td>
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     <td>Basic Part</td>
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−
     <td>Hay this part is not yet created</td>
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−
     <td>Me myself and I</td>
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   </tr>
 
   </tr>
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   <tr>
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   <tr class="tableunevengrnbl">
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    <td>Fav</td>
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    <td>&hearts;</td>
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     <td>BioBrick#4</td>
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     <td><a href="http://parts.igem.org/Part:BBa_K2643002" target="_blank" class="jnnbl">BBa_K2643002</a></td>
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     <td>Basic Part</td>
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     <td>Basic</td>
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     <td>Hay this part is not yet created</td>
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     <td>Tn5 Transposase (HIS Tag)</td>
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     <td>Me myself and I</td>
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     <td>TU Delft 2018</td>
 
   </tr>
 
   </tr>
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   <tr>
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   <tr class="tableevengrnbl">
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     <td>Fav</td>
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     <td></td>
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     <td>BioBrick#5</td>
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     <td><a href="http://parts.igem.org/Part:BBa_K2643003" target="_blank" class="jnnbl">BBa_K2643003</a></td>
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     <td>Basic Part</td>
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     <td>Basic</td>
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     <td>Hay this part is not yet created</td>
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     <td>Glycine Helical peptide Linker (GHL)</td>
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     <td>Me myself and I</td>
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     <td>TU Delft 2018</td>
 
   </tr>
 
   </tr>
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   <tr>
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   <tr class="tableunevengrnbl">
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     <td>Fav</td>
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     <td>&hearts;</td>
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     <td>BioBrick#6</td>
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     <td><a href="http://parts.igem.org/Part:BBa_K2643004" target="_blank" class="jnnbl">BBa_K2643004</a></td>
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     <td>Basic Part</td>
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     <td>Basic</td>
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     <td>Hay this part is not yet created</td>
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     <td>Coding region (CDS) of human erythropoietin (EPO) hormone</td>
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     <td>Me myself and I</td>
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     <td>TU Delft 2018</td>
 
   </tr>
 
   </tr>
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</table>
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  <tr class="tableevengrnbl">
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    <td></td>
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      <div class="spcmkr" id="basicparts"></div>
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     <td><a href="http://parts.igem.org/Part:BBa_K2643005" target="_blank" class="jnnbl">BBa_K2643005</a></td>
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            <h1 class="adpbl">2. Basic Parts</h1>
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     <td>Basic</td>
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     <td>Human EPO gene with artificial intron (615 bp)</td>
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<!-- TABEL WITH BASIC PART -->
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     <td>TU Delft 2018</td>
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<table>
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  <tr>
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−
     <th>Favorite Part</th>
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    <th>BioBrick Name</th>
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     <th>Type</th>
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     <th>Description</th>
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     <th>Designer</th>
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   </tr>
 
   </tr>
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   <tr class="tableunevengrnbl">
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     <td>Fav</td>
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     <td></td>
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     <td>BioBrick#1</td>
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     <td><a href="http://parts.igem.org/Part:BBa_K2643006" target="_blank" class="jnnbl">BBa_K2643006</a></td>
−
     <td>Basic Part</td>
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     <td>Basic</td>
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     <td>Hay this part is not yet created</td>
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     <td>Human EPO gene with artificial intron (135 bp)</td>
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     <td>Me myself and I</td>
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     <td>TU Delft 2018</td>
 
   </tr>
 
   </tr>
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   <tr class="tableevengrnbl">
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     <td>Fav</td>
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     <td></td>
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     <td>BioBrick#2</td>
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     <td><a href="http://parts.igem.org/Part:BBa_K2643007" target="_blank" class="jnnbl">BBa_K2643007</a></td>
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    <td>Basic Part</td>
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     <td>Basic</td>
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    <td>Hay this part is not yet created</td>
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     <td>Human EPO gene with 2 artificial introns (615 + 135 bp)</td>
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    <td>Me myself and I</td> </tr>
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     <td>TU Delft 2018</td>
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  <tr>
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−
    <td>Fav</td>
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−
    <td>BioBrick#3</td>
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−
     <td>Basic Part</td>
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−
     <td>Hay this part is not yet created</td>
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−
     <td>Me myself and I</td>
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   </tr>
 
   </tr>
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   <tr>
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   <tr class="tableunevengrnbl">
−
     <td>Fav</td>
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     <td></td>
−
     <td>BioBrick#4</td>
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     <td><a href="http://parts.igem.org/Part:BBa_K2643008" target="_blank" class="jnnbl">BBa_K2643008</a></td>
−
     <td>Basic Part</td>
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     <td>Basic</td>
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     <td>Hay this part is not yet created</td>
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     <td>Human EPO gene with mutation 1 (5 bp)</td>
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     <td>Me myself and I</td>
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     <td>TU Delft 2018</td>
 
   </tr>
 
   </tr>
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   <tr>
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   <tr class="tableevengrnbl">
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     <td>Fav</td>
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     <td></td>
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     <td>BioBrick#5</td>
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     <td><a href="http://parts.igem.org/Part:BBa_K2643009" target="_blank" class="jnnbl">BBa_K2643009</a></td>
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     <td>Basic Part</td>
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     <td>Basic</td>
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     <td>Hay this part is not yet created</td>
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     <td>Human EPO gene with mutation 2 (12 bp)</td>
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     <td>Me myself and I</td>
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     <td>TU Delft 2018</td>
 
   </tr>
 
   </tr>
−
   <tr>
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   <tr class="tableunevengrnbl">
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     <td>Fav</td>
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     <td></td>
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     <td>BioBrick#6</td>
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     <td><a href="http://parts.igem.org/Part:BBa_K2643010" target="_blank" class="jnnbl">BBa_K2643010</a></td>
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     <td>Basic Part</td>
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     <td>Basic</td>
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     <td>Hay this part is not yet created</td>
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     <td>gRNA expression cassette for CRISPR-targeting <i>lacZ</i></td>
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     <td>Me myself and I</td>
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     <td>TU Delft 2018</td>
 
   </tr>
 
   </tr>
−
</table>
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  <tr class="tableevengrnbl">
−
 
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     <td></td>
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            <div class="spcmkr" id="compositeparts"></div>
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     <td><a href="http://parts.igem.org/Part:BBa_K2643011" target="_blank" class="jnnbl">BBa_K2643011</a></td>
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            <h1 class="adpbl">3. Composite Parts</h1>
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     <td>Basic</td>
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     <td>Mosaic Ends-flanked Kanamycin cassette and RFP</td>
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<!-- TABEL WITH COMPOSITE PART -->
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     <td>TU Delft 2018</td>
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<table>
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−
  <tr>
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−
    <th>Favorite Part</th>
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−
    <th>BioBrick Name</th>
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    <th>Type</th>
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    <th>Description</th>
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−
    <th>Designer</th>
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−
  </tr>
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−
  <tr>
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−
     <td>Fav</td>
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−
     <td>BioBrick#1</td>
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−
    <td>Basic Part</td>
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−
    <td>Hay this part is not yet created</td>
+
−
    <td>Me myself and I</td>
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−
  </tr>
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−
  <tr>
+
−
    <td>Fav</td>
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−
    <td>BioBrick#2</td>
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−
    <td>Basic Part</td>
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−
    <td>Hay this part is not yet created</td>
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−
    <td>Me myself and I</td>  </tr>
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−
  <tr>
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−
    <td>Fav</td>
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−
    <td>BioBrick#3</td>
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−
     <td>Basic Part</td>
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−
     <td>Hay this part is not yet created</td>
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−
    <td>Me myself and I</td>
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−
  </tr>
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−
  <tr>
+
−
     <td>Fav</td>
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−
    <td>BioBrick#4</td>
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−
    <td>Basic Part</td>
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−
    <td>Hay this part is not yet created</td>
+
−
    <td>Me myself and I</td>
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−
  </tr>
+
−
  <tr>
+
−
    <td>Fav</td>
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−
    <td>BioBrick#5</td>
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−
    <td>Basic Part</td>
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−
    <td>Hay this part is not yet created</td>
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−
    <td>Me myself and I</td>
+
 
   </tr>
 
   </tr>
−
   <tr>
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   <tr class="tableunevengrnbl">
−
     <td>Fav</td>
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     <td></td>
−
     <td>BioBrick#6</td>
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     <td><a href="http://parts.igem.org/Part:BBa_K2643012" target="_blank" class="jnnbl">BBa_K2643012</a></td>
−
     <td>Basic Part</td>
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     <td>Basic</td>
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     <td>Hay this part is not yet created</td>
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     <td>T7p expressing sgRNA targeting the EPO coding sequence</td>
−
     <td>Me myself and I</td>
+
     <td>TU Delft 2018</td>
 
   </tr>
 
   </tr>
 
</table>
 
</table>
  
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            <div class="spcmkr" id="partcollection"></div>
 
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            <h1 class="adpbl">4. Part Collection</h1>
 
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<!-- TABEL WITH PART COLLECTION -->
 
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<table>
 
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  <tr>
 
−
    <th>Favorite Part</th>
 
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    <th>BioBrick Name</th>
 
−
    <th>Type</th>
 
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    <th>Description</th>
 
−
    <th>Designer</th>
 
−
  </tr>
 
−
  <tr>
 
−
    <td>Fav</td>
 
−
    <td>BioBrick#1</td>
 
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    <td>Basic Part</td>
 
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    <td>Hay this part is not yet created</td>
 
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    <td>Me myself and I</td>
 
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  </tr>
 
−
  <tr>
 
−
    <td>Fav</td>
 
−
    <td>BioBrick#2</td>
 
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    <td>Basic Part</td>
 
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    <td>Hay this part is not yet created</td>
 
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    <td>Me myself and I</td>  </tr>
 
−
  <tr>
 
−
    <td>Fav</td>
 
−
    <td>BioBrick#3</td>
 
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    <td>Basic Part</td>
 
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    <td>Hay this part is not yet created</td>
 
−
    <td>Me myself and I</td>
 
−
  </tr>
 
−
  <tr>
 
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    <td>Fav</td>
 
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    <td>BioBrick#4</td>
 
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    <td>Basic Part</td>
 
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    <td>Hay this part is not yet created</td>
 
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    <td>Me myself and I</td>
 
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  </tr>
 
−
  <tr>
 
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    <td>Fav</td>
 
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    <td>BioBrick#5</td>
 
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    <td>Basic Part</td>
 
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    <td>Hay this part is not yet created</td>
 
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    <td>Me myself and I</td>
 
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  </tr>
 
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  <tr>
 
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    <td>Fav</td>
 
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    <td>BioBrick#6</td>
 
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    <td>Basic Part</td>
 
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    <td>Hay this part is not yet created</td>
 
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    <td>Me myself and I</td>
 
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  </tr>
 
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Latest revision as of 13:10, 14 October 2018

partsoverview

Parts Overview

When constructing our BioBricks, we made use of the IDT synthesis offer. This way we were able to generate our required parts in a fast and efficient way. Additionally, we made use of PCR amplification with our constructed expression plasmids as template to construct several BioBricks. All of the parts contain a coding sequence, some of which extended with promoters or introns. Since our fusion protein BBa_K2643000 consists of the dxCas9, linker and Tn5 coding sequences this part is registered as composite part. The basic parts comprising the fusion protein composite part are documented separately and also exist as separate BioBricks. This is advantageous for those wishing to combine one of our basic parts with a different expression level or compose a different composite part altogether. We created a part collection comprised of 6 basic parts encoding for different EPO coding sequences, 2 basic parts encoding for the required components for targeted sequencing and 1 composite part: our fusion protein. All BioBricks are submitted with elaborate characterisation so the user may choose the best part for their project accordingly. Our favourite basic part is dxCas9 BBa_K2643001 and our favourite composite part is dxCas9-Lin-Tn5 BBa_K2643000.

Table 1. BioBrick Parts submitted by TU Delft iGEM 2018 team. All BioBricks were constructed by the team members involved in wetlab: Susan Bouwmeester, Kavish Kohabir, Venda Mangkusaputra, Timmy Paez, Lisbeth Schmidtchen and Nicole Bennis
♥ Name Type Description Designer
♥ BBa_K2643000 Composite dxCas9-linker-Tn5 fusion protein (HIS Tag) TU Delft 2018
♥ BBa_K2643001 Basic dxCas9 (HIS Tag) TU Delft 2018
♥ BBa_K2643002 Basic Tn5 Transposase (HIS Tag) TU Delft 2018
BBa_K2643003 Basic Glycine Helical peptide Linker (GHL) TU Delft 2018
♥ BBa_K2643004 Basic Coding region (CDS) of human erythropoietin (EPO) hormone TU Delft 2018
BBa_K2643005 Basic Human EPO gene with artificial intron (615 bp) TU Delft 2018
BBa_K2643006 Basic Human EPO gene with artificial intron (135 bp) TU Delft 2018
BBa_K2643007 Basic Human EPO gene with 2 artificial introns (615 + 135 bp) TU Delft 2018
BBa_K2643008 Basic Human EPO gene with mutation 1 (5 bp) TU Delft 2018
BBa_K2643009 Basic Human EPO gene with mutation 2 (12 bp) TU Delft 2018
BBa_K2643010 Basic gRNA expression cassette for CRISPR-targeting lacZ TU Delft 2018
BBa_K2643011 Basic Mosaic Ends-flanked Kanamycin cassette and RFP TU Delft 2018
BBa_K2643012 Basic T7p expressing sgRNA targeting the EPO coding sequence TU Delft 2018