Difference between revisions of "Team:UCopenhagen/InterLab"

 
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<h3></h3>
 
<h3></h3>
 
                         <h1>I N T E R  L A B</h1>   
 
                         <h1>I N T E R  L A B</h1>   
−
<h3></h3>
 
 
                     </div>
 
                     </div>
 
                 </div>
 
                 </div>
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                 <div class="clearfix"></div>
 
                 <div class="clearfix"></div>
 
                     <h2 class="section-heading">Calibrations</h2>
 
                     <h2 class="section-heading">Calibrations</h2>
−
                     <p class="lead"> Before our measurements began, we performed some calibrations: First an OD600 reference point for our plate reader, performed with LUDOX according to the protocol. Here we found a correction factor which can be used to calculate OD from measured absorbance. Our correction fator is 3.11. <br><br>
+
                     <p class="lead"> Before our measurements began, we performed some calibrations: First an OD<sub>600</sub> reference point for our plate reader, performed with LUDOX according to the protocol. Here we found a correction factor which can be used to calculate OD from measured absorbance. Our correction fator is 3.11. <br><br>
  
 
Secondly we made a fluorescence standard curve with a serial dilution of fluorescein (figure 1). We used the lower 5 data points to calculate a mean µM fluorescein pr a.u. We chose to use the lower concentration range due to two factors: 1) Linearity is better for the lower fluorescein concentrations, and 2) our measured data has a maximum fluorescence of 500, which makes it more important to have a good fit in the lower range.  
 
Secondly we made a fluorescence standard curve with a serial dilution of fluorescein (figure 1). We used the lower 5 data points to calculate a mean µM fluorescein pr a.u. We chose to use the lower concentration range due to two factors: 1) Linearity is better for the lower fluorescein concentrations, and 2) our measured data has a maximum fluorescence of 500, which makes it more important to have a good fit in the lower range.  
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                     <img class="img-responsive" src="https://static.igem.org/mediawiki/2017/b/b9/InterLab-figure_UCopenhagen.png" alt="" width="250" height="200">
 
                     <img class="img-responsive" src="https://static.igem.org/mediawiki/2017/b/b9/InterLab-figure_UCopenhagen.png" alt="" width="250" height="200">
  
−
  <figcaption>Figure 1. - Standard curve of fluorescein fluorescence.
+
  <figcaption><b>Figure 1 </b>Standard curve of fluorescein fluorescence.
 
Fluorescence in arbitraty units (a.u.), fluorescein concentration in µM.</figcaption>
 
Fluorescence in arbitraty units (a.u.), fluorescein concentration in µM.</figcaption>
 
</figure>
 
</figure>
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                     <h2 class="section-heading">Cell measurements </h2>
 
                     <h2 class="section-heading">Cell measurements </h2>
 
                     <p class="lead">Two colonies from each transformation were picked, and grown in foil-covered 50 ml falcon tubes over night (18 hours). </p>
 
                     <p class="lead">Two colonies from each transformation were picked, and grown in foil-covered 50 ml falcon tubes over night (18 hours). </p>
−
<p class="lead"><strong>Preparation</strong> OD was measured, and a dilution was calculated to achieve an OD of 0.02. Dilution calculations can be found in the table next to this. Here we used the calculated correction factor from our initial abs/OD calibration. From the absorption measurements taken at 0 hours, we see indications of pipetting errors, as the OD600 (average) ranges from 0.015 to 0.6 (table 1). </p>
+
<p class="lead"><strong>Preparation</strong> OD was measured, and a dilution was calculated to achieve an OD of 0.02. Dilution calculations can be found in the table next to this. Here we used the calculated correction factor from our initial abs/OD calibration. From the absorption measurements taken at 0 hours, we see indications of pipetting errors, as the OD<sub>600</sub> (average) ranges from 0.015 to 0.6 (table 1). </p>
 +
 
 +
<button onclick="javascript:showhide('InterLab-table')">Show table 1</button>
 +
<div id="InterLab-table" style="display:none;">
 
<div class="container">
 
<div class="container">
 
   <table class="responsive-table">
 
   <table class="responsive-table">
−
     <caption>Title</caption>
+
     <caption><b>Table 1</b> Starting OD.</caption>
 
     <thead>
 
     <thead>
 
       <tr>
 
       <tr>
−
         <th scope="col">Abs600</th>
+
<th scope="col"></th>
−
         <th scope="col">OD600 before</th>
+
         <th scope="col">Abs<sub>600</sub></th>
 +
         <th scope="col">OD<sub>600</sub> before</th>
 
         <th scope="col">Volume (ml) added to 12 ml media</th>
 
         <th scope="col">Volume (ml) added to 12 ml media</th>
−
         <th scope="col">OD600 after dilution (0 hours)</th>
+
         <th scope="col">OD<sub>600</sub> after dilution (0 hours)</th>
 
       </tr>
 
       </tr>
 
     </thead>
 
     </thead>
 
     <tfoot>
 
     <tfoot>
−
      <tr>
 
−
        <td colspan="7">Sources: <a href="http://en.wikipedia.org/wiki/List_of_highest-grossing_animated_films" rel="external">Wikipedia</a> &amp; <a href="http://www.boxofficemojo.com/genres/chart/?id=animation.htm" rel="external">Box Office Mojo</a>. Data is current as of August 25, 2016.</td>
 
−
      </tr>
 
 
     </tfoot>
 
     </tfoot>
 
     <tbody>
 
     <tbody>
 
       <tr>
 
       <tr>
−
         <th scope="row">Frozen</th>
+
         <th scope="row">Negative Control (Colony 1)</th>
−
         <td data-title="Released">2013</td>
+
         <td data-title="Abs600">0,461</td>
−
         <td data-title="Studio">Disney</td>
+
         <td data-title="OD600 before">1,435</td>
−
        <td data-title="Worldwide Gross" data-type="currency">$1,287,000,000</td>
+
         <td data-title="Volume (ml) added to 12 ml media" data-type="currency">0,167</td>
−
         <td data-title="Domestic Gross" data-type="currency">$400,738,009  </td>
+
         <td data-title="OD600 after dilution (0 hours)" data-type="currency">0,06483974</td>
−
         <td data-title="Foreign Gross" data-type="currency">$875,742,326</td>
+
−
        <td data-title="Budget" data-type="currency">$150,000,000</td>
+
 
       </tr>
 
       </tr>
 
       <tr>
 
       <tr>
−
         <th scope="row">Minions</th>
+
         <th scope="row">Negative Control (Colony 2)</th>
−
         <td data-title="Released">2015</td>
+
         <td data-title="Abs600">0,463</td>
−
         <td data-title="Studio">Universal</td>
+
         <td data-title="OD600 before">1,439</td>
−
        <td data-title="Worldwide Gross" data-type="currency">$1,159,398,397</td>
+
         <td data-title="Volume (ml) added to 12 ml media" data-type="currency">0,167</td>
−
         <td data-title="Domestic Gross" data-type="currency">$336,045,770</td>
+
         <td data-title="OD600 after dilution (0 hours)" data-type="currency">0,02584249</td>
−
         <td data-title="Foreign Gross" data-type="currency">$823,352,627</td>
+
−
        <td data-title="Budget" data-type="currency">$74,000,000</td>
+
 
       </tr>
 
       </tr>
−
      <tr>
+
        <tr>
−
         <th scope="row">Toy Story 3</th>
+
         <th scope="row">Positive Control (Colony 1)</th>
−
         <td data-title="Released">2010</td>
+
         <td data-title="Abs<sub>600</sub>">0,450</td>
−
         <td data-title="Studio">Disney Pixar</td>
+
         <td data-title="OD<sub>600</sub> before">1,400</td>
−
        <td data-title="Worldwide Gross" data-type="currency">$1,066,969,703</td>
+
         <td data-title="Volume (ml) added to 12 ml media" data-type="currency">0,171</td>
−
         <td data-title="Domestic Gross" data-type="currency">$415,004,880</td>
+
         <td data-title="OD<sub>600</sub> after dilution (0 hours)" data-type="currency">0,04467949</td>
−
         <td data-title="Foreign Gross" data-type="currency">$651,964,823</td>
+
−
        <td data-title="Budget" data-type="currency">$200,000,000</td>
+
 
       </tr>
 
       </tr>
−
      <tr>
+
    <tr>
−
         <th scope="row">Zootopia</th>
+
         <th scope="row">Positive Control (Colony 2)</th>
−
         <td data-title="Released">2016</td>
+
         <td data-title="Abs<sub>600</sub>">0,474</td>
−
         <td data-title="Studio">Disney</td>
+
         <td data-title="OD<sub>600</sub> before">1,475</td>
−
        <td data-title="Worldwide Gross" data-type="currency">$1,023,227,498</td>
+
         <td data-title="Volume (ml) added to 12 ml media" data-type="currency">0,163</td>
−
         <td data-title="Domestic Gross" data-type="currency">$341,268,248</td>
+
         <td data-title="OD<sub>600</sub> after dilution (0 hours)" data-type="currency">0,01689103</td>
−
         <td data-title="Foreign Gross" data-type="currency">$681,959,250</td>
+
−
        <td data-title="Budget" data-type="currency">$150,000,000</td>
+
 
       </tr>
 
       </tr>
−
      <tr>
+
          <tr>
−
         <th scope="row">Despicable Me 2</th>
+
         <th scope="row">Test Device 1: J23101+I13504 (Colony 1)</th>
−
         <td data-title="Released">2013</td>
+
         <td data-title="Abs<sub>600</sub>">0,462</td>
−
         <td data-title="Studio">Universal</td>
+
         <td data-title="OD<sub>600</sub> before">1,437</td>
−
        <td data-title="Worldwide Gross" data-type="currency">$970,761,885</td>
+
         <td data-title="Volume (ml) added to 12 ml media" data-type="currency">0,167</td>
−
         <td data-title="Domestic Gross" data-type="currency">$368,061,265</td>
+
         <td data-title="OD<sub>600</sub> after dilution (0 hours)" data-type="currency">0,03043498</td>
−
         <td data-title="Foreign Gross" data-type="currency">$602,700,620</td>
+
−
        <td data-title="Budget" data-type="currency">$76,000,000</td>
+
 
       </tr>
 
       </tr>
−
      <tr>
+
        <tr>
−
         <th scope="row">The Lion King</th>
+
         <th scope="row">Test Device 1: J23101+I13504 (Colony 2)</th>
−
         <td data-title="Released">1994</td>
+
         <td data-title="Abs<sub>600</sub>">0,472</td>
−
         <td data-title="Studio">Disney</td>
+
         <td data-title="OD<sub>600</sub> before">1,469</td>
−
         <td data-title="Worldwide Gross" data-type="currency">$987,483,777</td>
+
         <td data-title="Volume (ml) added to 12 ml media" data-type="currency">0,163</td>
−
         <td data-title="Domestic Gross" data-type="currency">$422,783,777</td>
+
        <td data-title="OD<sub>600</sub> after dilution (0 hours)" data-type="currency">0,01977106</td>
−
         <td data-title="Foreign Gross" data-type="currency">$564,700,000</td>
+
      </tr>
−
         <td data-title="Budget" data-type="currency">$45,000,000</td>
+
        <tr>
 +
        <th scope="row">Test Device 2: J23106+I13504 (Colony 1)</th>
 +
        <td data-title="Abs<sub>600</sub>">0,477</td>
 +
        <td data-title="OD<sub>600</sub> before">1,483</td>
 +
        <td data-title="Volume (ml) added to 12 ml media" data-type="currency">0,162</td>
 +
         <td data-title="OD<sub>600</sub> after dilution (0 hours)" data-type="currency">0,03175824</td>
 +
      </tr>
 +
        <tr>
 +
        <th scope="row">Test Device 2: J23106+I13504 (Colony 2)</th>
 +
        <td data-title="Abs<sub>600</sub>">0,454</td>
 +
         <td data-title="OD<sub>600</sub> before">1,410</td>
 +
        <td data-title="Volume (ml) added to 12 ml media" data-type="currency">0,170</td>
 +
        <td data-title="OD<sub>600</sub> after dilution (0 hours)" data-type="currency">0,018837</td>
 +
      </tr>
 +
          <tr>
 +
        <th scope="row">Test Device 3: J23117+I13504 (Colony 1)</th>
 +
         <td data-title="Abs<sub>600</sub>">0,507</td>
 +
        <td data-title="OD<sub>600</sub> before">1,577</td>
 +
        <td data-title="Volume (ml) added to 12 ml media" data-type="currency">0,152</td>
 +
        <td data-title="OD<sub>600</sub> after dilution (0 hours)" data-type="currency">0,03261447</td>
 +
      </tr>
 +
          <tr>
 +
        <th scope="row">Test Device 3: J23117+I13504 (Colony 2)</th>
 +
        <td data-title="Abs<sub>600</sub>">0,492</td>
 +
        <td data-title="OD<sub>600</sub> before">1,529</td>
 +
        <td data-title="Volume (ml) added to 12 ml media" data-type="currency">0,157</td>
 +
        <td data-title="OD<sub>600</sub> after dilution (0 hours)" data-type="currency">0,01471154</td>
 +
      </tr>
 +
          <tr>
 +
        <th scope="row">Test Device 4: J23101.BCD2.E0040.B0015 (Colony 1)</th>
 +
        <td data-title="Abs<sub>600</sub>">0,420</td>
 +
        <td data-title="OD<sub>600</sub> before">1,307</td>
 +
        <td data-title="Volume (ml) added to 12 ml media" data-type="currency">0,184</td>
 +
        <td data-title="OD<sub>600</sub> after dilution (0 hours)" data-type="currency">0,03759615</td>
 +
      </tr>
 +
          <tr>
 +
        <th scope="row">Test Device 4: J23101.BCD2.E0040.B0015 (Colony 2)</th>
 +
        <td data-title="Abs600">0,472</td>
 +
        <td data-title="OD600 before">1,468</td>
 +
        <td data-title="Volume (ml) added to 12 ml media" data-type="currency">0,163</td>
 +
        <td data-title="OD600 after dilution (0 hours)" data-type="currency">0,01860348</td>
 
       </tr>
 
       </tr>
 
       <tr>
 
       <tr>
−
         <th scope="row">Finding Nemo</th>
+
         <th scope="row">Test Device 5: J23106.BCD2.E0040.B0015 (Colony 1)</th>
−
         <td data-title="Released">2003</td>
+
         <td data-title="Abs600">0,513</td>
−
        <td data-title="Studio">Pixar</td>
+
         <td data-title="OD600 before">1,595</td>
−
        <td data-title="Worldwide Gross" data-type="currency">$936,743,261</td>
+
         <td data-title="Volume (ml) added to 12 ml media" data-type="currency">0,150</td>
−
         <td data-title="Domestic Gross" data-type="currency">$380,843,261</td>
+
         <td data-title="OD600 after dilution (0 hours)" data-type="currency">0,04234432</td>
−
         <td data-title="Foreign Gross" data-type="currency">$555,900,000</td>
+
−
         <td data-title="Budget" data-type="currency">$94,000,000</td>
+
 
       </tr>
 
       </tr>
 
       <tr>
 
       <tr>
−
         <th scope="row">Shrek 2</th>
+
         <th scope="row">Test Device 5: J23106.BCD2.E0040.B0015 (Colony 2)</th>
−
         <td data-title="Released">2004</td>
+
         <td data-title="Abs600">0,467</td>
−
        <td data-title="Studio">Dreamworks</td>
+
         <td data-title="OD600 before">1,451</td>
−
        <td data-title="Worldwide Gross" data-type="currency">$919,838,758</td>
+
         <td data-title="Volume (ml) added to 12 ml media" data-type="currency">0,165</td>
−
         <td data-title="Domestic Gross" data-type="currency">$441,226,247</td>
+
         <td data-title="OD600 after dilution (0 hours)" data-type="currency">0,01494505</td>
−
         <td data-title="Foreign Gross" data-type="currency">$478,612,511</td>
+
−
         <td data-title="Budget" data-type="currency">$150,000,000</td>
+
 
       </tr>
 
       </tr>
 
       <tr>
 
       <tr>
−
         <th scope="row">Finding Dory</th>
+
         <th scope="row">Test Device 6: J23117.BCD2.E0040.B0015 (Colony 1)</th>
−
         <td data-title="Released">2016</td>
+
         <td data-title="Abs600">0,482</td>
−
        <td data-title="Studio">Disney Pixar</td>
+
         <td data-title="OD600 before">1,498</td>
−
        <td data-title="Worldwide Gross" data-type="currency">$916,221,557</td>
+
         <td data-title="Volume (ml) added to 12 ml media" data-type="currency">0,160</td>
−
         <td data-title="Domestic Gross" data-type="currency">$478,714,390</td>
+
         <td data-title="OD600 after dilution (0 hours)" data-type="currency">0,04452381</td>
−
         <td data-title="Foreign Gross" data-type="currency">$437,507,167    </td>
+
−
         <td data-title="Budget" data-type="currency">$250,000,000</td>  
+
 
       </tr>
 
       </tr>
 
       <tr>
 
       <tr>
−
         <th scope="row">Ice Age: Dawn of the Dinosaurs</th>
+
         <th scope="row">Test Device 6: J23117.BCD2.E0040.B0015 (Colony 2)</th>
−
         <td data-title="Released">2009</td>
+
         <td data-title="Abs600">0,455</td>
−
        <td data-title="Studio">Fox</td>
+
         <td data-title="OD600 before">1,416</td>
−
        <td data-title="Worldwide Gross" data-type="currency">$886,686,817</td>
+
         <td data-title="Volume (ml) added to 12 ml media" data-type="currency">0,170</td>
−
         <td data-title="Domestic Gross" data-type="currency">$196,573,705</td>
+
         <td data-title="OD600 after dilution (0 hours)" data-type="currency">0,02008242</td>
−
         <td data-title="Foreign Gross" data-type="currency">$690,113,112    </td>
+
−
         <td data-title="Budget" data-type="currency">$90,000,000</td>
+
 
       </tr>
 
       </tr>
 
     </tbody>
 
     </tbody>
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   </div>
 
   </div>
 +
</div>
 
</div>
 
</div>
 
</div>
 
</div>
  
 +
<div class="content-section-b">
 +
<div class="container">
 +
            <div>
 +
                    <hr class="section-heading-spacer">
 +
                    <div class="clearfix"></div>
 +
                    <h2 class="section-heading">OD<sub>600</sub></h2>
 +
                    <p class="lead">
 +
 +
Cell growth stagnated between 4 and 6 hours. Cells transformed with Test Device 1 and 4 grew slower than the 6 other transformations, and even decreased in OD between 4 and 6 hours.
 +
<figure>
 +
                    <img class="img-responsive3" src="https://static.igem.org/mediawiki/2017/3/37/Interlab_OD_positive.png" alt="" width="250" height="200">
 +
<br>
 +
<figcaption><b>Figure 2 </b>Fluorescence measurement in high-fluorescing samples (positive control and test devices 1, 2 and 4) over 6 hours.
 +
</figcaption>
 +
</figure>
 +
<br>
 +
 +
<figure>
 +
                    <img class="img-responsive3" src="https://static.igem.org/mediawiki/2017/d/d8/Interlab_OD_negative.png" alt="" width="250" height="200">
 +
<br>
 +
<figcaption><b>Figure 3 </b>OD measurements in low-fluorescing samples (negative control and test devides 3, 5 and 6) over 6 hours.
 +
</figcaption>
 +
</figure>
 +
</p>
 +
 +
</div>
 +
    </div>
 +
</div>
 +
 +
<div class="content-section-a">
 +
<div class="container">
 +
            <div>
 +
                    <hr class="section-heading-spacer">
 +
                    <div class="clearfix"></div>
 +
                    <h2 class="section-heading">Fluorescence</h2>
 +
                    <p class="lead">
 +
 +
Some transformed cells continue to increase fluorescence despite a decrease in OD in the same samples. Devices 3 and 6 are very close to the negative control in fluorescence.
 +
<figure>
 +
                    <img class="img-responsive3" src="https://static.igem.org/mediawiki/2017/d/df/Interlab_fluorescence_positive.png" alt="" width="250" height="200">
 +
<br>
 +
<figcaption><b>Figure 4 </b>Fluorescence measurement in high-fluorescing samples (positive control and test devices 1, 2 and 4) over 6 hours.
 +
</figcaption>
 +
</figure>
 +
<br>
 +
 +
<figure>
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<figcaption><b>Figure 5 </b>Fluorescence measurements in low-fluorescing samples (negative control and test devides 3, 5 and 6) over 6 hours.
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                    <h2 class="section-heading">Conclusion </h2>
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                    <p class="lead">Our data indicate which plasmid elements induce the highest production of GFP.
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Plasmids containing J23117 (Test devices 3 and 6) does not express fluorescence to a higher degree than the negative control. Plasmids with J23101 (Device 1 and 4) induced the highest fluorescence, and plasmids containing J23106 (Test devices 2 and 5) were somewhere in between. Combining the J23101 or J23106 with I13504 (Test devices 1-3) gave a higher fluorescence than adding BCD2.E0040.B0015 (Test devices 4-6).
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These results are not reliable on their own, but will be more robust and reliable when combined with data from the other teams participating in the interlab study.
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Latest revision as of 20:10, 1 November 2017

I N T E R L A B

Introduction

We participated in InterLitab, as we want to be contribute to the scientific progress made through this globe spanning project. In InterLab, 6 test devices are inserted in E.coli D5 α, and the growth and fluorescence is measured.

We used the following plasmids provided by iGEM HQ to transform E.coli:

  • Positive control
  • Negative control
  • Test Device 1: J23101+I13504
  • Test Device 2: J23106+I13504
  • Test Device 3: J23117+I13504
  • Test Device 4: J23101.BCD2.E0040.B0015
  • Test Device 5: J23106.BCD2.E0040.B0015
  • Test Device 6: J23117.BCD2.E0040.B0015

Calibrations

Before our measurements began, we performed some calibrations: First an OD600 reference point for our plate reader, performed with LUDOX according to the protocol. Here we found a correction factor which can be used to calculate OD from measured absorbance. Our correction fator is 3.11.

Secondly we made a fluorescence standard curve with a serial dilution of fluorescein (figure 1). We used the lower 5 data points to calculate a mean µM fluorescein pr a.u. We chose to use the lower concentration range due to two factors: 1) Linearity is better for the lower fluorescein concentrations, and 2) our measured data has a maximum fluorescence of 500, which makes it more important to have a good fit in the lower range.



Figure 1 Standard curve of fluorescein fluorescence. Fluorescence in arbitraty units (a.u.), fluorescein concentration in µM.

Cell measurements

Two colonies from each transformation were picked, and grown in foil-covered 50 ml falcon tubes over night (18 hours).

Preparation OD was measured, and a dilution was calculated to achieve an OD of 0.02. Dilution calculations can be found in the table next to this. Here we used the calculated correction factor from our initial abs/OD calibration. From the absorption measurements taken at 0 hours, we see indications of pipetting errors, as the OD600 (average) ranges from 0.015 to 0.6 (table 1).

OD600

Cell growth stagnated between 4 and 6 hours. Cells transformed with Test Device 1 and 4 grew slower than the 6 other transformations, and even decreased in OD between 4 and 6 hours.


Figure 2 Fluorescence measurement in high-fluorescing samples (positive control and test devices 1, 2 and 4) over 6 hours.


Figure 3 OD measurements in low-fluorescing samples (negative control and test devides 3, 5 and 6) over 6 hours.

Fluorescence

Some transformed cells continue to increase fluorescence despite a decrease in OD in the same samples. Devices 3 and 6 are very close to the negative control in fluorescence.


Figure 4 Fluorescence measurement in high-fluorescing samples (positive control and test devices 1, 2 and 4) over 6 hours.


Figure 5 Fluorescence measurements in low-fluorescing samples (negative control and test devides 3, 5 and 6) over 6 hours.

Conclusion

Our data indicate which plasmid elements induce the highest production of GFP. Plasmids containing J23117 (Test devices 3 and 6) does not express fluorescence to a higher degree than the negative control. Plasmids with J23101 (Device 1 and 4) induced the highest fluorescence, and plasmids containing J23106 (Test devices 2 and 5) were somewhere in between. Combining the J23101 or J23106 with I13504 (Test devices 1-3) gave a higher fluorescence than adding BCD2.E0040.B0015 (Test devices 4-6).

These results are not reliable on their own, but will be more robust and reliable when combined with data from the other teams participating in the interlab study.

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