Difference between revisions of "Team:Toronto/InterLab"

 
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<div class="section">
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<h1>Dry Lab</h1>
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<h1>Interlab</h1>
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<div class="block content">
  
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<h2 class="text-yellow">content-yellow</h2>
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<div id="subsection-Description" class="subsection">
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<h2 class="text-red">Description</h2>
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<div id="myDiv">
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<figure>
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<p>iGEM Toronto was excited to participate in the 2017 Interlab Study to help establish a GFP fluorescence measurement protocol and characterize important promoters and RBS devices. In science and engineering, standardization is an important key to generating reliable data and comparing results from different labs. By comparing our data with labs from around the world, iGEM will be able to establish common standards of measurement for GFP fluoresecence with different plate readers.</p>
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<div class="figures">
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</div>
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<div class="image"><img src="http://www.excel-easy.com/data-analysis/images/charts/column-chart.png" alt="data"></div>
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<!-- subsection 1  END-->
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</div>
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<figcaption>Figure 1.1: Wildlife population is wildlife population is wildlife population is wildlife population</figcaption>
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</figure>
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<!-- subsection 2 -->
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<figure>
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<div id="subsection-plasmids" class="subsection">
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<div class="figures">
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<div class="image"><img src="http://www.excel-easy.com/data-analysis/images/charts/column-chart.png" alt="data"></div>
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<h2 class="text-red">Plasmids</h2>
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</div>
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<figcaption>Figure 1.1: Wildlife population is wildlife population is wildlife population is wildlife population</figcaption>
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<p>iGEM HQ provided 8 Interlab parts in total, all in the  pSB1C3 backbone. They included a positive control, a negative control, and 6 test devices which contained various combinations of three promoters and two RBS devices. The positive control contained BBa_J23151, a 35 bp constitutive promoter, and BBa_B0032, a 13 bp weak RBS, while the negative control consisted only of BBa_R0040, a 54 bp TetR repressible promoter.</p>
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</figure>
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<p>Lorem is haha ipsum dolor sit amet consectetur adipisicing elit. Inventore maiores quibusdam, adipisci ipsum quisquam, aspernatur aperiam optio odit deleniti eaque illum nobis, non neque reprehenderit consequatur ipsam ullam perferendis magni.</p>
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<h3>All the parts:</h3>
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<figure>
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<ul class="bullets">
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<div class="figures">
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<li>BBa_E0040: a 720 bp GFP gene from the Aequeora victoria jellyfish </li>
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<div class="image"><img src="https://zippy.gfycat.com/MedicalAdventurousCanine.gif" alt="data" width="200px"></div>
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<li>Fluorescence is expected within 8 minutes </li>
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<div class="image"><img src="https://media.giphy.com/media/R6vXyeo7NA0gg/giphy.gif" alt="data" width="200px"></div>
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<li>Excitation max: 501 nm </li>
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</div>
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<li>Emission max: 511 nm </li>
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<figcaption>Figure 1.1: Wildlife population is wildlife population is wildlife population is wildlife population</figcaption>
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<li>BBa_B0010: an 80 bp transcriptional terminator from E. coli rrnB with 64 bp stem loop </li>
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</figure>
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<li>BBa_B0012: a 41 bp transcriptional terminator from coliphageT7 for E. coli RNA Polymerase </li>
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<p>Lorem is haha ipsum dolor sit amet consectetur adipisicing elit. Inventore maiores quibusdam, adipisci ipsum quisquam, aspernatur aperiam optio odit deleniti eaque illum nobis, non neque reprehenderit consequatur ipsam ullam perferendis magni. </p>
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<li>Not a good terminator </li>
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<li>promoter in reverse direction </li>
 +
</ul>
 +
 
 +
<h3>The test devices were all 918 bp plasmids which constitutively express GFP. All consist of:</h3>
 +
<ul class="bullets">
 +
<li>A 35 bp constitutive promoter in the BBa_J23100-J23119 family </li>
 +
<li>1 and 4 have BBa_J23101 </li>
 +
<li>2 and 5 have BBa_J23106 - medium strength; more characterization info from Sheffield 2016 </li>
 +
<li>3 and 6 have BBa_J23117 </li>
 +
<li>A 12 bp RBS, </li>
 +
<li>1-3 have BBa_B0034, a 12 bp RBS </li>
 +
<li>4-6 have BBa_J364100, an 84 bp bicistronic design element (BCD2) </li>
 +
<li>BBa_E0040 </li>
 +
<li>BBa_B0010 </li>
 +
<li>BBa_B0012</li>
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</ul>
 +
 
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<!-- Figure start -->
 
<figure>
 
<figure>
 
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<div class="figures">
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<thead>
 
<thead>
 
<tr>
 
<tr>
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<th>Time</th>
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<th>Part</th>
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<th>Quantity</th>
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<th>Part number</th>
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<th>iunno</th>
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<th>Length (bp)</th>
 +
<th>Promoter</th>
 +
<th>RBS</th>
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<th>Reporter Protein</th>
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<th>Terminators</th>
 
</tr>
 
</tr>
 
</thead>
 
</thead>
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<tbody class="table-hover">
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<tbody>
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<tr>
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<tr>
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<td>Hello</td>
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<td>Positive control</td>
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<td>9adsf asd</td>
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<td>BBa_I20270</td>
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<td>2 ads fads fdsa s </td>
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<td>919</td>
−
</tr>
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<td>BBa_J23151</td>
−
<tr>
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<td>BBa_B0032</td>
−
<td>1</td>
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<td>BBa_E0040 (GFP)</td>
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<td>2 ads fads fdsa s </td>
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<td>BBa_B0010 and BBa_B0012</td>
−
<td>2 ads fads fdsa s </td>
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</tr>
−
</tr>
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<tr>
−
<tr>
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<td>Negative control</td>
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<td>1</td>
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<td>BBa_R0040</td>
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<td>2</td>
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<td>54</td>
−
<td>2 ads fads fdsa s </td>
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<td>N/A</td>
−
</tr>
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<td>N/A</td>
−
<tr>
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<td>N/A</td>
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<td>1</td>
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<td>N/A</td>
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<td>2</td>
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</tr>
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<td>2 ads fads fdsa s </td>
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<tr>
−
</tr>
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<td>Test device 1</td>
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<tr>
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<td>BBa_J364000</td>
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<td>Hello</td>
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<td>918</td>
−
<td>911 asd afd </td>
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<td>BBa_J23101</td>
−
<td>2 ads fads fdsa s </td>
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<td>BBa_B0034</td>
−
</tr>
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<td>BBa_E0040 (GFP)</td>
−
<tr>
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<td>BBa_B0010 and BBa_B0012</td>
−
<td>1</td>
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</tr>
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<td>2</td>
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<tr>
−
<td>2 ads fads fdsa s </td>
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<td>Test device 2</td>
−
</tr>
+
<td>BBa_J364001</td>
 +
<td>918</td>
 +
<td>BBa_J23106</td>
 +
<td>BBa_B0034</td>
 +
<td>BBa_E0040 (GFP)</td>
 +
<td>BBa_B0010 and BBa_B0012</td>
 +
</tr>
 +
<tr>
 +
<td>Test device 3</td>
 +
<td>BBa_J364002</td>
 +
<td>918</td>
 +
<td>BBa_J23117</td>
 +
<td>BBa_B0034</td>
 +
<td>BBa_E0040 (GFP)</td>
 +
<td>BBa_B0010 and BBa_B0012</td>
 +
</tr>
 +
<tr>
 +
<td>Test device 4</td>
 +
<td>BBa_J364003</td>
 +
<td>918</td>
 +
<td>BBa_J23101</td>
 +
<td>BBa_J364100</td>
 +
<td>BBa_E0040 (GFP)</td>
 +
<td>BBa_B0010 and BBa_B0012</td>
 +
</tr>
 +
<tr>
 +
<td>Test device 5</td>
 +
<td>BBa_J364004</td>
 +
<td>918</td>
 +
<td>BBa_J23106</td>
 +
<td>BBa_J364100</td>
 +
<td>BBa_E0040 (GFP)</td>
 +
<td>BBa_B0010 and BBa_B0012</td>
 +
</tr>
 +
<tr>
 +
<td>Test device 6</td>
 +
<td>BBa_J364005</td>
 +
<td>918</td>
 +
<td>BBa_J23117</td>
 +
<td>BBa_J364100</td>
 +
<td>BBa_E0040 (GFP)</td>
 +
<td>BBa_B0010 and BBa_B0012</td>
 +
</tr>
 
</tbody>
 
</tbody>
 
</table>
 
</table>
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<figcaption>Figure 1.1: Wildlife population is wildlife population is wildlife population is wildlife population</figcaption>
 
<figcaption>Figure 1.1: Wildlife population is wildlife population is wildlife population is wildlife population</figcaption>
 
</figure>
 
</figure>
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<p>Lorem is haha ipsum dolor sit amet consectetur adipisicing elit. Inventore maiores quibusdam, adipisci ipsum quisquam, aspernatur aperiam optio odit deleniti eaque illum nobis, non neque reprehenderit consequatur ipsam ullam perferendis magni.</p><a>
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<!-- figure END -->
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<button class="btn-primary red">More Info</button></a>
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</div>
 
</div>
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<hr>
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<!-- subsection 2 END -->
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<div id="content-yellow" class="subsection">
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<h2 class="text-cyan">References</h2>
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<ol>
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<!-- subsection 3 -->
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<li id="ref1">Lorem is haha ipsum dolor sit amet consectetur adipisicing elit. Inventore maiores quibusdam, adipisci ipsum quisquam</li>
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<div id="subsection-Results" class="subsection">
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</ol>
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<h2 class="text-red">Results</h2>
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<div class="plotly-chart" id="interlab"></div>
 
</div>
 
</div>
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<!-- subsection 3 END -->
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<div class="sidebar-minibox">
 
<ul>
 
<ul>
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<li> <a href="#">Content 1</a></li>
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<li> <a href="https://2017.igem.org/Competition/InterLab_Study">Interlab Resources</a></li>
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<li> <a href="#">Content 2</a></li>
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<li> <a href="https://2017.igem.org/Team:Toronto/Notebook">Notebook</a></li>
 
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<script>
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// Interlab graph
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var interlab = function() {
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var negativeControl = {
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x: [0, 2, 4, 6],
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y: [-0.27, -0.04, -0.01, 0.00],
 +
error_y: {
 +
type: 'data',
 +
array: [0.26, 0.01, 0.00, 0.00],
 +
visible: true
 +
},
 +
mode: 'lines+markers',
 +
name: 'Negative Control',
 +
line: {shape: 'spline'},
 +
type: 'scatter'
 +
};
 +
 +
var positiveControl = {
 +
x: [0, 2, 4, 6],
 +
y: [0.06, 0.49, 0.30, 0.27],
 +
error_y: {
 +
type: 'data',
 +
array: [0.08, 0.05, 0.01, 0.01],
 +
visible: true
 +
},
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mode: 'lines+markers',
 +
name: 'Positive Control',
 +
line: {shape: 'spline'},
 +
type: 'scatter'
 +
};
 +
 +
var testDevice1 = {
 +
x: [0, 2, 4, 6],
 +
y: [0.23, 0.67, 0.40, 0.41],
 +
error_y: {
 +
type: 'data',
 +
array: [0.18, 0.16, 0.02, 0.01],
 +
visible: true
 +
},
 +
mode: 'lines+markers',
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name: 'Test Device 1',
 +
line: {shape: 'spline'},
 +
type: 'scatter'
 +
};
 +
 +
var testDevice2 = {
 +
x: [0, 2, 4, 6],
 +
y: [0.37, 0.78, 0.49, 0.47],
 +
error_y: {
 +
type: 'data',
 +
array: [0.16, 0.09, 0.03, 0.01],
 +
visible: true
 +
},
 +
mode: 'lines+markers',
 +
name: 'Test Device 2',
 +
line: {shape: 'spline'},
 +
type: 'scatter'
 +
};
 +
 +
var testDevice3 = {
 +
x: [0, 2, 4, 6],
 +
y: [-0.13, -0.01, 0.00, 0.01],
 +
error_y: {
 +
type: 'data',
 +
array: [0.08, 0.01, 0.00, 0.00],
 +
visible: true
 +
},
 +
mode: 'lines+markers',
 +
name: 'Test Device 3',
 +
line: {shape: 'spline'},
 +
type: 'scatter'
 +
};
 +
 +
var testDevice4 = {
 +
x: [0, 2, 4, 6],
 +
y: [-0.04, 0.45, 0.38, 0.36],
 +
error_y: {
 +
type: 'data',
 +
array: [0.18, 0.06, 0.02, 0.02],
 +
visible: true
 +
},
 +
mode: 'lines+markers',
 +
name: 'Test Device 4',
 +
line: {shape: 'spline'},
 +
type: 'scatter'
 +
};
 +
 +
var testDevice5 = {
 +
x: [0, 2, 4, 6],
 +
y: [-0.10, 0.23, 0.13, 0.12],
 +
error_y: {
 +
type: 'data',
 +
array: [0.09, 0.02, 0.01, 0.00],
 +
visible: true
 +
},
 +
mode: 'lines+markers',
 +
name: 'Test Device 5',
 +
line: {shape: 'spline'},
 +
type: 'scatter'
 +
};
 +
 +
var testDevice6 = {
 +
x: [0, 2, 4, 6],
 +
y: [-0.12, -0.02, 0.00, 0.00],
 +
error_y: {
 +
type: 'data',
 +
array: [0.05, 0.01, 0.00, 0.00],
 +
visible: true
 +
},
 +
mode: 'lines+markers',
 +
name: 'Test Device 6',
 +
line: {shape: 'spline'},
 +
type: 'scatter'
 +
};
 +
 +
var data = [negativeControl, positiveControl, testDevice1, testDevice2, testDevice3, testDevice4, testDevice5, testDevice6];
 +
 +
var layout = {
 +
title: 'iGEM Interlab Data 2017',
 +
xaxis: {
 +
title: 'Hour'
 +
},
 +
yaxis: {
 +
title: 'uM Fluorescein / OD600'
 +
}
 +
};
 +
 +
Plotly.newPlot('interlab', data, layout);
 +
}
  
 +
interlab();
 +
</script>
 
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{{Toronto/footer}}
 
{{Toronto/footer}}

Latest revision as of 20:04, 14 December 2017

Interlab

Description

iGEM Toronto was excited to participate in the 2017 Interlab Study to help establish a GFP fluorescence measurement protocol and characterize important promoters and RBS devices. In science and engineering, standardization is an important key to generating reliable data and comparing results from different labs. By comparing our data with labs from around the world, iGEM will be able to establish common standards of measurement for GFP fluoresecence with different plate readers.

Plasmids

iGEM HQ provided 8 Interlab parts in total, all in the pSB1C3 backbone. They included a positive control, a negative control, and 6 test devices which contained various combinations of three promoters and two RBS devices. The positive control contained BBa_J23151, a 35 bp constitutive promoter, and BBa_B0032, a 13 bp weak RBS, while the negative control consisted only of BBa_R0040, a 54 bp TetR repressible promoter.

All the parts:

  • BBa_E0040: a 720 bp GFP gene from the Aequeora victoria jellyfish
  • Fluorescence is expected within 8 minutes
  • Excitation max: 501 nm
  • Emission max: 511 nm
  • BBa_B0010: an 80 bp transcriptional terminator from E. coli rrnB with 64 bp stem loop
  • BBa_B0012: a 41 bp transcriptional terminator from coliphageT7 for E. coli RNA Polymerase
  • Not a good terminator
  • promoter in reverse direction

The test devices were all 918 bp plasmids which constitutively express GFP. All consist of:

  • A 35 bp constitutive promoter in the BBa_J23100-J23119 family
  • 1 and 4 have BBa_J23101
  • 2 and 5 have BBa_J23106 - medium strength; more characterization info from Sheffield 2016
  • 3 and 6 have BBa_J23117
  • A 12 bp RBS,
  • 1-3 have BBa_B0034, a 12 bp RBS
  • 4-6 have BBa_J364100, an 84 bp bicistronic design element (BCD2)
  • BBa_E0040
  • BBa_B0010
  • BBa_B0012
Part Part number Length (bp) Promoter RBS Reporter Protein Terminators
Positive control BBa_I20270 919 BBa_J23151 BBa_B0032 BBa_E0040 (GFP) BBa_B0010 and BBa_B0012
Negative control BBa_R0040 54 N/A N/A N/A N/A
Test device 1 BBa_J364000 918 BBa_J23101 BBa_B0034 BBa_E0040 (GFP) BBa_B0010 and BBa_B0012
Test device 2 BBa_J364001 918 BBa_J23106 BBa_B0034 BBa_E0040 (GFP) BBa_B0010 and BBa_B0012
Test device 3 BBa_J364002 918 BBa_J23117 BBa_B0034 BBa_E0040 (GFP) BBa_B0010 and BBa_B0012
Test device 4 BBa_J364003 918 BBa_J23101 BBa_J364100 BBa_E0040 (GFP) BBa_B0010 and BBa_B0012
Test device 5 BBa_J364004 918 BBa_J23106 BBa_J364100 BBa_E0040 (GFP) BBa_B0010 and BBa_B0012
Test device 6 BBa_J364005 918 BBa_J23117 BBa_J364100 BBa_E0040 (GFP) BBa_B0010 and BBa_B0012
Figure 1.1: Wildlife population is wildlife population is wildlife population is wildlife population

Results

General Pages

Wet Lab

Dry Lab

Human Practices

iGEM Toronto