Team:Brasil-SP/Notebook

From 2014.igem.org

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<h1 align=center>Main Assembly Map</h1>
<h1 align=center>Main Assembly Map</h1>
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<p><div align="justify">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The main assembly map describes all the constructions that would be done in the project, but some of them have not been performed in time of the iGEM deadline. The succesfully constructed assemblies is indicated by a green check point and the unsuccessfull constructions are indicated by a red "X". Click on these assemblies to access the lab form.</div></p>
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   <div class="map_image" style="background-image: url('https://static.igem.org/mediawiki/2014/8/87/Mapa.png');">
<a class="map_link" id="map_link_1" title="" href="https://static.igem.org/mediawiki/2014/b/b7/AI.pdf">AI</a>
<a class="map_link" id="map_link_1" title="" href="https://static.igem.org/mediawiki/2014/b/b7/AI.pdf">AI</a>
<a class="map_link" id="map_link_2" title="" href="https://static.igem.org/mediawiki/2014/3/38/AII.pdf">AII</a>
<a class="map_link" id="map_link_2" title="" href="https://static.igem.org/mediawiki/2014/3/38/AII.pdf">AII</a>
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<a class="map_link" id="map_link_9" title="" href="https://static.igem.org/mediawiki/2014/d/d6/AVI.pdf">AVI</a>
<a class="map_link" id="map_link_9" title="" href="https://static.igem.org/mediawiki/2014/d/d6/AVI.pdf">AVI</a>
<a class="map_link" id="map_link_10" title="" href="https://static.igem.org/mediawiki/2014/f/fe/AV.pdf">AV</a>
<a class="map_link" id="map_link_10" title="" href="https://static.igem.org/mediawiki/2014/f/fe/AV.pdf">AV</a>
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        <a class="map_link" id="map_link_11" title="" href="https://static.igem.org/mediawiki/2014/5/5b/BIV.pdf">BIV</a>
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<h1 align=center>Assemblies forms</h1>
<h1 align=center>Assemblies forms</h1>
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     <td>08/09
     <td>08/09
     <ul>
     <ul>
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       <li><a href="https://static.igem.org/mediawiki/2014/6/63/QuickChange_PCR.pdf" style="color:#f05151">QuickChange PCR</a> to mutate the cleavage site of the <a href="http://parts.igem.org/Part:BBa_K316037" style="color:#3ab473">BBa_K316037<a/> to a Cathepsin S recognition site</li>
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       <li><a href="https://static.igem.org/mediawiki/2014/6/63/QuickChange_PCR.pdf" style="color:#f05151">QuickChange PCR</a> to mutate the cleavage site of the <a href="http://parts.igem.org/Part:BBa_K316037" style="color:#3ab473">BBa_K316037</a> to a Cathepsin S recognition site</li>
       <li><a href="https://static.igem.org/mediawiki/2014/a/a5/Transformation_in_Escherichia_coli_DH5.pdf" style="color:#f05151"> Transformation</a> of the QuickCHange PCR product</li>
       <li><a href="https://static.igem.org/mediawiki/2014/a/a5/Transformation_in_Escherichia_coli_DH5.pdf" style="color:#f05151"> Transformation</a> of the QuickCHange PCR product</li>
     </ul>
     </ul>
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     <ul>
     <ul>
       <li>The QuickChange protocol didn't work well. So try again with more attention!</li>
       <li>The QuickChange protocol didn't work well. So try again with more attention!</li>
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       <li><a href="https://static.igem.org/mediawiki/2014/6/63/QuickChange_PCR.pdf" style="color:#f05151">QuickChange PCR</a> to mutate the cleavage site of the <a href="http://parts.igem.org/Part:BBa_K316037" style="color:#3ab473">BBa_K316037<a/> to a Cathepsin S recognition site</li>
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       <li><a href="https://static.igem.org/mediawiki/2014/6/63/QuickChange_PCR.pdf" style="color:#f05151">QuickChange PCR</a> to mutate the cleavage site of the <a href="http://parts.igem.org/Part:BBa_K316037" style="color:#3ab473">BBa_K316037</a> to a Cathepsin S recognition site</li>
       <li><a href="https://static.igem.org/mediawiki/2014/a/a5/Transformation_in_Escherichia_coli_DH5.pdf" style="color:#f05151"> Transformation</a> of the QuickCHange PCR product</li>
       <li><a href="https://static.igem.org/mediawiki/2014/a/a5/Transformation_in_Escherichia_coli_DH5.pdf" style="color:#f05151"> Transformation</a> of the QuickCHange PCR product</li>
       <li>Assemblies <a href="https://static.igem.org/mediawiki/2014/7/72/DI.pdf">DI</a>,  
       <li>Assemblies <a href="https://static.igem.org/mediawiki/2014/7/72/DI.pdf">DI</a>,  
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         <li><a href="https://static.igem.org/mediawiki/2014/4/42/Restriction_Anaysis_and_Digestion_in_large_scale.pdf" style="color:#f05151">Restriction analysis</a></li>
         <li><a href="https://static.igem.org/mediawiki/2014/4/42/Restriction_Anaysis_and_Digestion_in_large_scale.pdf" style="color:#f05151">Restriction analysis</a></li>
       </ul>
       </ul>
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       <li>Assemblies KIX, CIII and KXVI</li>
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       <li>Assemblies <a href="https://static.igem.org/mediawiki/2014/d/da/KIX.pdf">KIX</a>,
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          <a href="https://static.igem.org/mediawiki/2014/5/5b/BIV.pdf">BIV</a> and
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          <ahref="https://static.igem.org/mediawiki/2014/6/64/KXVI.pdf">KXVI</a></li>
       <ul>
       <ul>
         <li><a href="https://static.igem.org/mediawiki/2014/4/42/Restriction_Anaysis_and_Digestion_in_large_scale.pdf" style="color:#f05151">Digestion EXSP</a></li>
         <li><a href="https://static.igem.org/mediawiki/2014/4/42/Restriction_Anaysis_and_Digestion_in_large_scale.pdf" style="color:#f05151">Digestion EXSP</a></li>
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     </ul>
     </ul>
     </td>
     </td>
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     <td>07/10</td>
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     <td>07/10  
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     <td>08/10</td>
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    <ul>
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     <td>09/10</td>
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      <li>Assemblies <a href="https://static.igem.org/mediawiki/2014/d/da/KIX.pdf">KIX</a>,
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     <td>10/10</td>
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          <a href="https://static.igem.org/mediawiki/2014/5/5b/BIV.pdf">BIV</a> and
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          <a href="https://static.igem.org/mediawiki/2014/6/64/KXVI.pdf">KXVI</a></li>
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      <ul>
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        <li><a href="https://static.igem.org/mediawiki/2014/a/af/Agarose_Gel_Electrophoresis_and_DNA_Gel_Purification.pdf"  style="color:#f05151">Gel Purification</a></li>
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        <li><a href="https://static.igem.org/mediawiki/2014/7/7a/Cohesive-end_assembly_cloning.pdf" style="color:#f05151">Ligation</a></li>
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      </ul>
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    </ul>
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    </td>
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     <td>08/10
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    <ul>
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      <li>Assemblies <a href="https://static.igem.org/mediawiki/2014/d/da/KIX.pdf">KIX</a>,
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          <a href="https://static.igem.org/mediawiki/2014/5/5b/BIV.pdf">BIV</a> and
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          <a href="https://static.igem.org/mediawiki/2014/6/64/KXVI.pdf">KXVI</a></li>
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      <ul>
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        <li><a href="https://static.igem.org/mediawiki/2014/a/a5/Transformation_in_Escherichia_coli_DH5.pdf" style="color:#f05151"> Transformation</a></li>
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      </ul>
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    <ul>
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    </td>
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     <td>09/10
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      <li>Assemblies <a href="https://static.igem.org/mediawiki/2014/d/da/KIX.pdf">KIX</a>,
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          <a href="https://static.igem.org/mediawiki/2014/5/5b/BIV.pdf">BIV</a> and
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          <a href="https://static.igem.org/mediawiki/2014/6/64/KXVI.pdf">KXVI</a></li>
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      <ul>
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        <li>Inoculum</li>
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      </ul>
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    </td>
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     <td>10/10
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    <ul>
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      <li>Assemblies <a href="https://static.igem.org/mediawiki/2014/d/da/KIX.pdf">KIX</a>,
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          <a href="https://static.igem.org/mediawiki/2014/5/5b/BIV.pdf">BIV</a> and
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          <a href="https://static.igem.org/mediawiki/2014/6/64/KXVI.pdf">KXVI</a></li>
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      <ul>
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        <li><a href="https://static.igem.org/mediawiki/2014/4/42/Restriction_Anaysis_and_Digestion_in_large_scale.pdf" style="color:#f05151">Restriction analysis</a></li>
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      </ul>
 +
    </ul>
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    </td>
     <td>11/10</td>
     <td>11/10</td>
     <td>12/10</td>
     <td>12/10</td>

Latest revision as of 20:32, 17 October 2014

HeaderNotebookBRASILAP.png

Main Assembly Map

     The main assembly map describes all the constructions that would be done in the project, but some of them have not been performed in time of the iGEM deadline. The succesfully constructed assemblies is indicated by a green check point and the unsuccessfull constructions are indicated by a red "X". Click on these assemblies to access the lab form.

AI AII AIII BIII AIV BII CII DI AVI AV BIV

Assemblies forms

Assembly form template

This is the template designed to help with the laboratory organization during the assemble of biological parts. If you want to use the assembly method we used you can print the form and complete it for each construction. Hope it helps :)

Life Inside the LAB

July

Monday Tuesday Wednesday Thursday Friday Saturday Sunday
30/06
  • PCR lasR (BBa_C0079). The purpose of this PCR was to add the RBS (BBa_K143021), through addition of the sequence in the primer foward, and also to remove the LVA tag. In our primers we only added the restriction sites X and S, so we still need to put it in the pSB1C3 for the Biobrick standard completion. When standardized this part will be called BBa_K1521001.
 01/07 02/07 03/07 04/07 05/07 06/07
07/07 08/07 09/07 10/07
  • Miniprep, Quantification and Restriction Analysis:
    • BBa_B0015 (restriction analysis fail, repeat)
  • PCR the qteE gene for amplification. We also added the RBS (BBa_K143021,) using the foward primer. In our primers we only added the restriction sites X and S, so we still need to put it in the pSB1C3 for the Biobrick standard completion. When standardized this biobrick will be called BBa_K1521000.
  • Ligation of RBS+lasR in PTZ57R/T vector (instaclone kit)
 11/07 12/07 13/07
14/07 15/07 16/07 17/07 18/07 19/07 20/07
21/07 22/07 23/07 24/07 25/07 26/07 27/07
28/07
  • Assembly AIII:
    • Restriction analysis (+NdeI enzyme)
    • OBS: This analysis was reapeted because we had problems confirming the assembly. The issue was that both the construction and the pSB1C3 vector had similar size.
  • Assembly AII, AV and AVI:
 29/07 30/07 31/07
  • Assembly AII, AV and AVI:
    • Inoculum
  • PCR BBa_K143055 for RBS removal
  • OBS: This was one of the parts sent by the Imperial College Team. Because of a comunication failure we assumed that this part was comming without the RBS, so we included a RBS in the parts we were going to use with this Lac promotor :)
  • PCR of Plac BBa_K143055 was followed by a Gel Purification and Ligation in the PUC19 vector



August

Monday Tuesday Wednesday Thursday Friday Saturday Sunday
01/08 02/08 03/08
04/08 05//08 06/08 07/08 08/08 09/08 10/08
11/08
  • Prepare Plac BBa_K143055 for sequencing
  • Analyse the RBS+qteE and RBS+lasR sequencing file
 12/08
  • Digestion:
    • RBS+qteE
    • RBS+lasR
    • OBS: this digestion was performed so we clone this parts in the pSB1C3 vector to put them in Biobrick standard
 13/08 14/08
  • Gel Purification and Ligation in pSB1C3 for BBiobrick standard:
    • RBS+qteE
    • RBS+lasR
  • Assemblies BII and BIII:
    • Gel Purification
    • OBS: we had some problems here with the purification and we lost all our digestions, so we're repeating the digestion
 15/08 16/08 17/08
18/08 19/08 20/08
  • RBS+qteE, RBS+lasR and Assemblies BII and BIII:
    • Inoculum
 21/08 22/08 23/08 24/08
25/08 26/08 27/08 28/08 29/08 30/08 31/08



September

Monday Tuesday Wednesday Thursday Friday Saturday Sunday
01/09 02/09 03/09 04/09 05/09 06/09 07/09
08/09 09/09 10/09 11/09 12/09 13/09
  • Assembly KX
    • Inoculum
  • Assemblies DI, KVIII and KXI:
  • Prepare LB medium (solid and liquid)
 14/09
15/09 16/09 17/09
  • Measurement Interlab Study - Samples growth biobrick devices 1, 2 and 3
 18/09
  • Measurement Interlab Study - Sample preparation and characterization by Flow Cytometry and Fluorometry
 19/09 20/09 21/09
22/09 23/09 24/09 25/09
  • Assembly KXIV:
    • Inoculum
 26/09 27/09 28/09
29/09 30/09



October

Monday Tuesday Wednesday Thursday Friday Saturday Sunday
01/10 02/10 03/10 04/10 05/10
06/10 07/10 08/10 09/10
  • Assemblies KIX, BIV and KXVI
    • Inoculum
    		 10/10 11/10 12/10
    13/10 14/10 15/10 16/10 17/10 18/10 19/10
    20/10 21/10 22/10 23/10 24/10 25/10 26/10
    27/10 28/10 29/10 30/10 31/10

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