Difference between revisions of "Team:TUDelft/Project/Results"

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             <img src="https://static.igem.org/mediawiki/2018/a/a8/T--TUDelft--2018_ProjResultshead.png" class="img-fluid img-top" alt="Project Description"></div>
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        <li class="active"><a href="#introprojectresults" class="adpbl">1. Introduction</a></li>
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              <li class="active"><a href="#adope" class="jnnbl">ADOPE</a></li>
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              <li class="dropdown">
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              <a class="dropdown-toggle jnnbl" data-toggle="dropdown" href="#">1. Sample Preparation<span class="caret"></span></a>
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                    <ul class="dropdown-menu">
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                    <li><a href="#sampleprep" class="jnnbl">Sample Preparation</a></li>
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                    <li><a href="#sp2" class="jnnbl">1.1 Kinetics Model</a></li>
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                    <li><a href="#sp3" class="jnnbl">1.2 Extraction Verification</a></li>                       
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                    <li><a href="#sp4" class="jnnbl">1.3 Gene Doping DNA Extraction</a></li> 
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                    </ul>
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              </li>
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              <li class="dropdown">
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              <a class="dropdown-toggle jnnbl" data-toggle="dropdown" href="#">2. Prescreening<span class="caret"></span></a>
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                    <ul class="dropdown-menu">
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                    <li><a href="#prescreening" class="jnnbl">Prescreening</a></li>
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                    <li><a href="#pr2" class="jnnbl">2.1 D-AuNPs: Prescreening <br>with Visible Readout</a></li>
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                    </ul>
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              </li>
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              <li class="dropdown">
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              <a class="dropdown-toggle jnnbl" data-toggle="dropdown" href="#">3. Fusion Protein -<br>dxCas9-Tn5<span class="caret"></span></a>
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                    <ul class="dropdown-menu">
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                    <li><a href="#fusionprotein" class="jnnbl">Fusion Protein - dxCas9-Tn5</a></li>
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                    <li><a href="#fp2" class="jnnbl">3.1 Fusion Protein Plasmid Construction</a></li>
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                    <li><a href="#fp3" class="jnnbl">3.2 Protein Expression and Purification</a></li>
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                    <li><a href="#fp4" class="jnnbl">3.3 <i>In Vivo</i> Functionality of <br>the Fusion Protein</a></li>
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                    <li><a href="#fp5" class="jnnbl">3.4 <i>In Vitro</i> Functionality of <br>the Fusion Protein</a></li>
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                    </ul>
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              </li>
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              <li class="dropdown">
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              <a class="dropdown-toggle jnnbl" data-toggle="dropdown" href="#">4. Targeted Sequencing <br>with dxCas9-Tn5<span class="caret"></span></a>
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                    <ul class="dropdown-menu">
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                    <li><a href="#targetedseq" class="jnnbl">Targeted Sequencing with dxCas9-Tn5</a></li>
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                    <li><a href="#ts2" class="jnnbl">4.1 sgRNA Array Determination <br>for Gene Doping Sequences</a></li>
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                    <li><a href="#ts3" class="jnnbl">4.3 Barcode DNA for Nanopore Sequencing</a></li>
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                    <li><a href="#ts4" class="jnnbl">4.4 Nanopore Targeted Sequencing</a></li>
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                    <li><a href="#ts5" class="jnnbl">4.5 Data Analysis Software</a></li>
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                    </ul>
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  <li><a href="#references" class="jnnbl">References</a></li>
 
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            <h1 class="adpbl">1. Introduction</h1>
 
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<div class="spcmkr" id="adope"></div>
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<h1 class="jnnbl">ADOPE</h1>
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<p>Intoduction </p><br>
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<center><img src="https://static.igem.org/mediawiki/2018/3/37/T--TUDelft--2018_Figure3_DescriptionPage.png" class="img-responsive" style="width: 1000px" alt="Picture of Timeline of the relevance of gene doping"></center>
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<br>
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<center><figcapture class="jnnbl"><b>Figure 1.</b> A flow diagram of our detection method ADOPE. With the four steps sample preparation, prescreening, library preparation and sequencing. </figcapture></center>
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<div class="spcmkr" id="sampleprep"></div>
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<h1 class="jnnbl">1. Sample Preparation</h1>
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<p>Introduction</p><br>
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<center><img src="https://static.igem.org/mediawiki/2018/5/5a/T--TUDelft--Design_2_sample_prep_overview.png" class="img-responsive" style="width: 1000px" alt="sample prep workflow"></center>
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<br>
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<center><figcapture class="jnnbl"><b>Figure 2.</b> Sample preparation workflow. The final process involves a two step PCR to verify the presence of the internal standard albumin gene. </figcapture></center>
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<button class="collapsible cjnnbl"><span class="repositioner" id="sp2"></span>1.1 Kinetics Model</button>
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<div class="content">
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<p><br><b>Design:</b>
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Text <br><br>
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<b>Results and Interpretation:</b>
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Text</p>
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<figure><center> <img src="https://static.igem.org/mediawiki/2018/3/37/T--TUDelft--Human_Model_Figure2_Gif.gif" width="50%" height="auto" alt="Model Figure 2"></center> <br>
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<figcapture class="figjnnbl"> <b>Figure 4.</b> A representation of EPO based gene doping. Viral vectors infect kidney cells, increasing their production of EPO. The increased concentration of EPO in the blood leads to an increased production of red blood cells. The red blood cell count acts as a feedback loop that determines the endogenous production of EPO. </figcapture></figure><br><br>
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<button class="collapsible cjnnbl"><span class="repositioner" id="sp3"></span>1.3 Extraction Verificattion</button>
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<p><br><b>Design:</b>
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Text <br><br>
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<b>Results and Interpretation:</b>
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Text</p>
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<figure><center> <img src="https://static.igem.org/mediawiki/2018/3/37/T--TUDelft--Human_Model_Figure2_Gif.gif" width="50%" height="auto" alt="Model Figure 2"></center> <br>
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<figcapture class="figjnnbl"> <b>Figure 4.</b> A representation of EPO based gene doping. Viral vectors infect kidney cells, increasing their production of EPO. The increased concentration of EPO in the blood leads to an increased production of red blood cells. The red blood cell count acts as a feedback loop that determines the endogenous production of EPO. </figcapture></figure><br><br>
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<div class="spcmkr" id="prescreening"></div>
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<h1 class="jnnbl">2. Prescreening</h1>
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<p>Introduction</p><br>
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<center><img src="https://static.igem.org/mediawiki/2018/5/5a/T--TUDelft--Design_2_sample_prep_overview.png" class="img-responsive" style="width: 1000px" alt="sample prep workflow"></center>
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<br>
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<center><figcapture class="jnnbl"><b>Figure 2.</b> Sample preparation workflow. The final process involves a two step PCR to verify the presence of the internal standard albumin gene. </figcapture></center>
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<button class="collapsible cjnnbl"><span class="repositioner" id="pr2"></span>2.1 D-AuNPs: Generating a prescreening with visible readout</button>
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<p><br><b>Design:</b>
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Text <br><br>
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<b>Results and Interpretation:</b>
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Text</p>
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<figure><center> <img src="https://static.igem.org/mediawiki/2018/3/37/T--TUDelft--Human_Model_Figure2_Gif.gif" width="50%" height="auto" alt="Model Figure 2"></center> <br>
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<figcapture class="figjnnbl"> <b>Figure 4.</b> A representation of EPO based gene doping. Viral vectors infect kidney cells, increasing their production of EPO. The increased concentration of EPO in the blood leads to an increased production of red blood cells. The red blood cell count acts as a feedback loop that determines the endogenous production of EPO. </figcapture></figure><br><br>
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<div class="spcmkr" id="fusionprotein"></div>
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<h1 class="jnnbl">3. Fusion Protein - dxCas9-Tn5</h1>
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<p>Intoduction</p><br>
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<center><img src="https://static.igem.org/mediawiki/2018/8/89/T--TUDelft--Design_8_fusion_protein_overview.png" class="img-responsive" style="width: 1000px" alt="Picture of Timeline of the relevance of gene doping"></center>
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<center><figcapture class="jnnbl"><b>Figure 3.</b> Design, construction, purification and functionality tests of fusion protein dxCas9-Tn5.  </figcapture></center><br>
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<button class="collapsible cjnnbl"><span class="repositioner" id="fp2"></span>3.1 Fusion Protein Plasmid Construction</button>
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<p><br><b>Design:</b>
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Text <br><br>
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<b>Results and Interpretation:</b>
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Text</p>
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<figure><center> <img src="https://static.igem.org/mediawiki/2018/3/37/T--TUDelft--Human_Model_Figure2_Gif.gif" width="50%" height="auto" alt="Model Figure 2"></center> <br>
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<figcapture class="figjnnbl"> <b>Figure 4.</b> A representation of EPO based gene doping. Viral vectors infect kidney cells, increasing their production of EPO. The increased concentration of EPO in the blood leads to an increased production of red blood cells. The red blood cell count acts as a feedback loop that determines the endogenous production of EPO. </figcapture></figure><br><br>
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<button class="collapsible cjnnbl"><span class="repositioner" id="fp3"></span>3.2 Protein Expression and Purification</button>
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<p><br><b>Design:</b>
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Text <br><br>
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<b>Results and Interpretation:</b>
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Text</p>
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<figure><center> <img src="https://static.igem.org/mediawiki/2018/3/37/T--TUDelft--Human_Model_Figure2_Gif.gif" width="50%" height="auto" alt="Model Figure 2"></center> <br>
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<figcapture class="figjnnbl"> <b>Figure 4.</b> A representation of EPO based gene doping. Viral vectors infect kidney cells, increasing their production of EPO. The increased concentration of EPO in the blood leads to an increased production of red blood cells. The red blood cell count acts as a feedback loop that determines the endogenous production of EPO. </figcapture></figure><br><br>
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<button class="collapsible cjnnbl"><span class="repositioner" id="fp4"></span>3.3 <i>In Vivo</i> Functionality of the Fusion Protein</button>
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        <div class="content">
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<p><br><b>Design:</b>
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Text <br><br>
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<b>Results and Interpretation:</b>
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Text</p>
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<figure><center> <img src="https://static.igem.org/mediawiki/2018/3/37/T--TUDelft--Human_Model_Figure2_Gif.gif" width="50%" height="auto" alt="Model Figure 2"></center> <br>
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<figcapture class="figjnnbl"> <b>Figure 4.</b> A representation of EPO based gene doping. Viral vectors infect kidney cells, increasing their production of EPO. The increased concentration of EPO in the blood leads to an increased production of red blood cells. The red blood cell count acts as a feedback loop that determines the endogenous production of EPO. </figcapture></figure><br><br>
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<button class="collapsible cjnnbl"><span class="repositioner" id="fp5"></span>3.4 <i>In Vitro</i> Functionality of the Fusion Protein</button>
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        <div class="content">
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<p><br><b>Design:</b>
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Text <br><br>
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<b>Results and Interpretation:</b>
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Text</p>
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<figure><center> <img src="https://static.igem.org/mediawiki/2018/3/37/T--TUDelft--Human_Model_Figure2_Gif.gif" width="50%" height="auto" alt="Model Figure 2"></center> <br>
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<figcapture class="figjnnbl"> <b>Figure 4.</b> A representation of EPO based gene doping. Viral vectors infect kidney cells, increasing their production of EPO. The increased concentration of EPO in the blood leads to an increased production of red blood cells. The red blood cell count acts as a feedback loop that determines the endogenous production of EPO. </figcapture></figure><br><br>
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<div class="spcmkr" id="targetedseq"></div>
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<h1 class="jnnbl">4. Targeted Sequencing with dxCas9-Tn5</h1>
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<p>Intoduction</p><br>
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<center><img src="https://static.igem.org/mediawiki/2018/8/89/T--TUDelft--Design_8_fusion_protein_overview.png" class="img-responsive" style="width: 1000px" alt="Picture of Timeline of the relevance of gene doping"></center>
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<br>
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<center><figcapture class="jnnbl"><b>Figure 3.</b> Design, construction, purification and functionality tests of fusion protein dxCas9-Tn5.  </figcapture></center><br>
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<button class="collapsible cjnnbl"><span class="repositioner" id="ts2"></span>4.1 sgRNA Array Determination for Gene Doping Sequences</button>
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        <div class="content">
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<p><br><b>Design:</b>
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Text <br><br>
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<b>Results and Interpretation:</b>
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Text</p>
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<figure><center> <img src="https://static.igem.org/mediawiki/2018/3/37/T--TUDelft--Human_Model_Figure2_Gif.gif" width="50%" height="auto" alt="Model Figure 2"></center> <br>
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<figcapture class="figjnnbl"> <b>Figure 4.</b> A representation of EPO based gene doping. Viral vectors infect kidney cells, increasing their production of EPO. The increased concentration of EPO in the blood leads to an increased production of red blood cells. The red blood cell count acts as a feedback loop that determines the endogenous production of EPO. </figcapture></figure><br><br>
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<button class="collapsible cjnnbl"><span class="repositioner" id="ts3"></span>4.2 Barcode DNA for Nanopore Sequencing</button>
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        <div class="content">
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<p><br><b>Design:</b>
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Text <br><br>
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<b>Results and Interpretation:</b>
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Text</p>
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<figure><center> <img src="https://static.igem.org/mediawiki/2018/3/37/T--TUDelft--Human_Model_Figure2_Gif.gif" width="50%" height="auto" alt="Model Figure 2"></center> <br>
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<figcapture class="figjnnbl"> <b>Figure 4.</b> A representation of EPO based gene doping. Viral vectors infect kidney cells, increasing their production of EPO. The increased concentration of EPO in the blood leads to an increased production of red blood cells. The red blood cell count acts as a feedback loop that determines the endogenous production of EPO. </figcapture></figure><br><br>
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<button class="collapsible cjnnbl"><span class="repositioner" id="ts4"></span>4.3 Nanopore Targeted Sequencing</button>
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<p><br><b>Design:</b>
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Text <br><br>
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<b>Results and Interpretation:</b>
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Text</p>
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<figure><center> <img src="https://static.igem.org/mediawiki/2018/3/37/T--TUDelft--Human_Model_Figure2_Gif.gif" width="50%" height="auto" alt="Model Figure 2"></center> <br>
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<figcapture class="figjnnbl"> <b>Figure 4.</b> A representation of EPO based gene doping. Viral vectors infect kidney cells, increasing their production of EPO. The increased concentration of EPO in the blood leads to an increased production of red blood cells. The red blood cell count acts as a feedback loop that determines the endogenous production of EPO. </figcapture></figure><br><br>
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      <button class="collapsible cjnnbl"><span class="repositioner" id="ts4"></span>4.4 Data Analysis Softwar</button>
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<p><br><b>Design:</b>
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Text <br><br>
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<b>Results and Interpretation:</b>
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Text</p>
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<figure><center> <img src="https://static.igem.org/mediawiki/2018/3/37/T--TUDelft--Human_Model_Figure2_Gif.gif" width="50%" height="auto" alt="Model Figure 2"></center> <br>
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<figcapture class="figjnnbl"> <b>Figure 4.</b> A representation of EPO based gene doping. Viral vectors infect kidney cells, increasing their production of EPO. The increased concentration of EPO in the blood leads to an increased production of red blood cells. The red blood cell count acts as a feedback loop that determines the endogenous production of EPO. </figcapture></figure><br><br>
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<div class="spcmkr" id="references"></div>
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<h1 class="jnnbl">5. References</h1>
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Revision as of 09:23, 17 October 2018

Responsive image

ADOPE

Intoduction


Picture of Timeline of the relevance of gene doping

Figure 1. A flow diagram of our detection method ADOPE. With the four steps sample preparation, prescreening, library preparation and sequencing.

1. Sample Preparation

Introduction


sample prep workflow

Figure 2. Sample preparation workflow. The final process involves a two step PCR to verify the presence of the internal standard albumin gene.


Design: Text

Results and Interpretation: Text

Model Figure 2

Figure 4. A representation of EPO based gene doping. Viral vectors infect kidney cells, increasing their production of EPO. The increased concentration of EPO in the blood leads to an increased production of red blood cells. The red blood cell count acts as a feedback loop that determines the endogenous production of EPO.



Design: Text

Results and Interpretation: Text

Model Figure 2

Figure 4. A representation of EPO based gene doping. Viral vectors infect kidney cells, increasing their production of EPO. The increased concentration of EPO in the blood leads to an increased production of red blood cells. The red blood cell count acts as a feedback loop that determines the endogenous production of EPO.


2. Prescreening

Introduction


sample prep workflow

Figure 2. Sample preparation workflow. The final process involves a two step PCR to verify the presence of the internal standard albumin gene.

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Design: Text

Results and Interpretation: Text

Model Figure 2

Figure 4. A representation of EPO based gene doping. Viral vectors infect kidney cells, increasing their production of EPO. The increased concentration of EPO in the blood leads to an increased production of red blood cells. The red blood cell count acts as a feedback loop that determines the endogenous production of EPO.


3. Fusion Protein - dxCas9-Tn5

Intoduction


Picture of Timeline of the relevance of gene doping

Figure 3. Design, construction, purification and functionality tests of fusion protein dxCas9-Tn5.


Design: Text

Results and Interpretation: Text

Model Figure 2

Figure 4. A representation of EPO based gene doping. Viral vectors infect kidney cells, increasing their production of EPO. The increased concentration of EPO in the blood leads to an increased production of red blood cells. The red blood cell count acts as a feedback loop that determines the endogenous production of EPO.



Design: Text

Results and Interpretation: Text

Model Figure 2

Figure 4. A representation of EPO based gene doping. Viral vectors infect kidney cells, increasing their production of EPO. The increased concentration of EPO in the blood leads to an increased production of red blood cells. The red blood cell count acts as a feedback loop that determines the endogenous production of EPO.



Design: Text

Results and Interpretation: Text

Model Figure 2

Figure 4. A representation of EPO based gene doping. Viral vectors infect kidney cells, increasing their production of EPO. The increased concentration of EPO in the blood leads to an increased production of red blood cells. The red blood cell count acts as a feedback loop that determines the endogenous production of EPO.



Design: Text

Results and Interpretation: Text

Model Figure 2

Figure 4. A representation of EPO based gene doping. Viral vectors infect kidney cells, increasing their production of EPO. The increased concentration of EPO in the blood leads to an increased production of red blood cells. The red blood cell count acts as a feedback loop that determines the endogenous production of EPO.


4. Targeted Sequencing with dxCas9-Tn5

Intoduction


Picture of Timeline of the relevance of gene doping

Figure 3. Design, construction, purification and functionality tests of fusion protein dxCas9-Tn5.


Design: Text

Results and Interpretation: Text

Model Figure 2

Figure 4. A representation of EPO based gene doping. Viral vectors infect kidney cells, increasing their production of EPO. The increased concentration of EPO in the blood leads to an increased production of red blood cells. The red blood cell count acts as a feedback loop that determines the endogenous production of EPO.



Design: Text

Results and Interpretation: Text

Model Figure 2

Figure 4. A representation of EPO based gene doping. Viral vectors infect kidney cells, increasing their production of EPO. The increased concentration of EPO in the blood leads to an increased production of red blood cells. The red blood cell count acts as a feedback loop that determines the endogenous production of EPO.



Design: Text

Results and Interpretation: Text

Model Figure 2

Figure 4. A representation of EPO based gene doping. Viral vectors infect kidney cells, increasing their production of EPO. The increased concentration of EPO in the blood leads to an increased production of red blood cells. The red blood cell count acts as a feedback loop that determines the endogenous production of EPO.



Design: Text

Results and Interpretation: Text

Model Figure 2

Figure 4. A representation of EPO based gene doping. Viral vectors infect kidney cells, increasing their production of EPO. The increased concentration of EPO in the blood leads to an increased production of red blood cells. The red blood cell count acts as a feedback loop that determines the endogenous production of EPO.


5. References