Difference between revisions of "Team:Toronto/InterLab"

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{{Toronto}}
 
 
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<!-- repo for this wiki: https://github.com/igemuoftATG/wiki17 -->
  
<div class="column full_size judges-will-not-evaluate">
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</html>
<h3>★  ALERT! </h3>
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{{Toronto/head}}
<p>This page is used by the judges to evaluate your team for the <a href="https://2017.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2017.igem.org/Judging/Awards"> award listed above</a>. </p>
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<html>
<p> Delete this box in order to be evaluated for this medal criterion and/or award. See more information at <a href="https://2017.igem.org/Judging/Pages_for_Awards"> Instructions for Pages for awards</a>.</p>
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</html>
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<html>
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<div class="section">
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<div class="container header" id="red">
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<h1>Interlab</h1>
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</div>
 
</div>
 
</div>
<div class="clear"></div>
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<div class="section bg-white">
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<div class="container content-page row">
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<div class="block content">
  
<div class="column full_size">
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<!-- subsection 1 -->
<h1>InterLab</h1>
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<div id="subsection-Description" class="subsection">
<h3>Bronze Medal Criterion #4</h3>
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<h2 class="text-red">Description</h2>
<p><b>Standard Tracks:</b> Participate in the Interlab Measurement Study and/or improve the characterization of an existing BioBrick Part or Device and enter this information on that part's Main Page in the Registry. The part that you are characterizing must NOT be from a 2017 part number range.
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<br><br>
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For teams participating in the <a href="https://2017.igem.org/Competition/InterLab_Study">InterLab study</a>, all work must be shown on this page.
+
  
</p>
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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>
 +
</div>
 +
<!-- subsection 1  END-->
 +
 
 +
 
 +
<!-- subsection 2 -->
 +
<div id="subsection-plasmids" class="subsection">
 +
 
 +
<h2 class="text-red">Plasmids</h2>
 +
 
 +
<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>
 +
 
 +
<h3>All the parts:</h3>
 +
<ul class="bullets">
 +
<li>BBa_E0040: a 720 bp GFP gene from the Aequeora victoria jellyfish </li>
 +
<li>Fluorescence is expected within 8 minutes </li>
 +
<li>Excitation max: 501 nm </li>
 +
<li>Emission max: 511 nm </li>
 +
<li>BBa_B0010: an 80 bp transcriptional terminator from E. coli rrnB with 64 bp stem loop </li>
 +
<li>BBa_B0012: a 41 bp transcriptional terminator from coliphageT7 for E. coli RNA Polymerase </li>
 +
<li>Not a good terminator </li>
 +
<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>
 +
</ul>
 +
 
 +
<!-- Figure start -->
 +
<figure>
 +
<div class="figures">
 +
<table>
 +
<thead>
 +
<tr>
 +
<th>Part</th>
 +
<th>Part number</th>
 +
<th>Length (bp)</th>
 +
<th>Promoter</th>
 +
<th>RBS</th>
 +
<th>Reporter Protein</th>
 +
<th>Terminators</th>
 +
</tr>
 +
</thead>
 +
<tbody>
 +
<tr>
 +
<td>Positive control</td>
 +
<td>BBa_I20270</td>
 +
<td>919</td>
 +
<td>BBa_J23151</td>
 +
<td>BBa_B0032</td>
 +
<td>BBa_E0040 (GFP)</td>
 +
<td>BBa_B0010 and BBa_B0012</td>
 +
</tr>
 +
<tr>
 +
<td>Negative control</td>
 +
<td>BBa_R0040</td>
 +
<td>54</td>
 +
<td>N/A</td>
 +
<td>N/A</td>
 +
<td>N/A</td>
 +
<td>N/A</td>
 +
</tr>
 +
<tr>
 +
<td>Test device 1</td>
 +
<td>BBa_J364000</td>
 +
<td>918</td>
 +
<td>BBa_J23101</td>
 +
<td>BBa_B0034</td>
 +
<td>BBa_E0040 (GFP)</td>
 +
<td>BBa_B0010 and BBa_B0012</td>
 +
</tr>
 +
<tr>
 +
<td>Test device 2</td>
 +
<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>
 +
</table>
 +
</div>
 +
<figcaption>Figure 1.1: Wildlife population is wildlife population is wildlife population is wildlife population</figcaption>
 +
</figure>
 +
<!-- figure END -->
 +
 
 +
</div>
 +
<!-- subsection 2 END -->
 +
 
 +
 
 +
<!-- subsection 3 -->
 +
<div id="subsection-Results" class="subsection">
 +
<h2 class="text-red">Results</h2>
 +
<div class="plotly-chart" id="interlab"></div>
 +
</div>
 +
<!-- subsection 3 END -->
 +
 
 +
</div>
 +
 
 +
<div class="block sidebar">
 +
<div id="sidebar-box">
 +
<h3>Contents</h3>
 +
<div class="sidebar-minibox">
 +
<ul></ul>
 +
</div>
 +
<h3>Related Pages</h3>
 +
<div class="sidebar-minibox">
 +
<ul>
 +
<li> <a href="https://2017.igem.org/Competition/InterLab_Study">Interlab Resources</a></li>
 +
<li> <a href="https://2017.igem.org/Team:Toronto/Notebook">Notebook</a></li>
 +
</ul>
 +
</div>
 +
</div>
 +
</div>
 +
</div>
 
</div>
 
</div>
  
 +
<script>
 +
// Interlab graph
 +
var interlab = function() {
 +
var negativeControl = {
 +
x: [0, 2, 4, 6],
 +
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
 +
},
 +
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',
 +
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>
 
</html>
 
</html>
 +
{{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