Difference between revisions of "Team:Edinburgh/InterLab"

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                     <h2 class="section-heading">Protocol Section</h2>                     
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                     <h2 class="section-heading">Protocols</h2>                     
 
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                     <h2 class="section-heading">mRFP</h2>                     
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                     <h2 class="section-heading">Results</h2>                     
 
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                     <a data-toggle="collapse" data-parent="#accordion" href="#collapseOne">1. What is HTML?</a>
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                     <a data-toggle="collapse" data-parent="#accordion" href="#collapseOne">How was the raw data processed?</a>
  
 
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                     <p>HTML stands for HyperText Markup Language. HTML is the main markup language for describing the structure of Web pages. <a href="http://www.tutorialrepublic.com/html-tutorial/" target="_blank">Learn more.</a></p>
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                     <p>The background absorbance of 6 wells containing 200µl of LB was measured. The average of these readings was then subtracted from the fluorescence values obtained for the devices.</p>
  
 
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                     <a data-toggle="collapse" data-parent="#accordion" href="#collapseTwo">2. What is Bootstrap?</a>
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                     <a data-toggle="collapse" data-parent="#accordion" href="#collapseTwo">What were the units of the results?</a>
  
 
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                     <p>Bootstrap is a powerful front-end framework for faster and easier web development. It is a collection of CSS and HTML conventions. <a href="http://www.tutorialrepublic.com/twitter-bootstrap-tutorial/" target="_blank">Learn more.</a></p>
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                     <p>The data is in relative fluorescent units.</p>
 
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                     <a data-toggle="collapse" data-parent="#accordion" href="#collapseThree">3. What is CSS?</a>
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                     <a data-toggle="collapse" data-parent="#accordion" href="#collapseThree">Fluorescence of 3 biological replicates of positive control</a>
  
 
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                     <p>CSS stands for Cascading Style Sheet. CSS allows you to specify various style properties for a given HTML element such as colors, backgrounds, fonts etc. <a href="http://www.tutorialrepublic.com/css-tutorial/" target="_blank">Learn more.</a></p>
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                     <p>1.) 1278.712 2.) 1216.887 3.) 1110.834</p>
  
 
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                    <a data-toggle="collapse" data-parent="#accordion" href="#collapseFour">Fluorescence of 3 biological replicates of negative control</a>
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                    <p>1.) -36.863 2.) -33.066 3.) -44.696</p>
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                    <a data-toggle="collapse" data-parent="#accordion" href="#collapseFive">Fluorescence of 3 biological replicates of J23101 + I13504, mean and st.dev (device 1)</a>
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                    <p>1.)5082.078 2.) 5879.239 3.) 5973.973
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                        Mean = 5645.097
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                        <br>
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                        Standard Deviation = 489.884
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                    <a data-toggle="collapse" data-parent="#accordion" href="#collapseSix">Fluorescence of 3 biological replicates of J23106 + I13504, mean and st.dev (device 2)</a>
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                      1.) 3185.188 2.) 3119.913 3.) 2396.115
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                      <br>
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                      Mean = 2900.405
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                      <br>
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                      Standard Deviation = 437.946
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                    <a data-toggle="collapse" data-parent="#accordion" href="#collapseSeven">Fluorescence of 3 biological replicates of J23117 + I13504, mean and st.dev (device3)</a>
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                      1.) -14.003 2.) -27.149 3.) -16.631
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                      Mean = -19.261
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                      <br>
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                      Standard Deviation = 6.956
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Revision as of 11:39, 8 September 2015

InterLab Study

Protocols

The protocol supplied in the iGEM 2015 InterLab Protocol form was followed with a few minor changes.
Each device and the two controls were streaked out onto LB agar plates supplemented with chloramphenicol and incubated at 37°C for 22 hours. 3 colonies from each plate were inoculated into 50ml Falcon tubes containing 10ml of LB media and chloramphenicol. The tubes were incubated upright on a platform shaker in a room kept at 37°C for 16 hours.

The positive control used was the recommended BBa_I20270, a chloramphenicol resistant GFP expression device in pSB1C3.
The negative control used consisted of cells transformed with BioBrick number BBa_R0040. This part consists of the promoter pTetR and should therefore have very low fluorescence

The cells were grown on LB agar supplemented with 1000x chloramphenicol.

A colony of cells was inoculated into 10ml of liquid LB with 10µl of 1000x chloramphenicol. The cultures were grown in a 50ml falcon tube, upright on shaking platform at 275rpm in 37°C room overnight.
For each device three colonies were inoculated to act as the three biological replicates.

After the overnight incubation period of 16 hours the liquid cultures were removed from the 37°C room. 200µl from each culture was added to a 96-well plate. The initial optical density of each sample was measured at 600nm using a plate reader. All samples were then diluted appropriately so as to have an OD600 value within 5% of 0.5. Two additional technical replicates for each of the biological replicates were set up at this point. The OD600 was measured again to ensure all samples had an optical density within 5% of 0.5 before the fluorescence measurements were taken.
To measure fluorescence, the cells were excited at a wavelength of 485nm and emitted light at 538nm as measured.
The values obtained for fluorescence were in relative fluorescence units.

A SpectaMax M5 plate reader was used to obtain the values of fluorescence.

Results

The background absorbance of 6 wells containing 200µl of LB was measured. The average of these readings was then subtracted from the fluorescence values obtained for the devices.

The data is in relative fluorescent units.

1.) 1278.712 2.) 1216.887 3.) 1110.834

1.)5082.078 2.) 5879.239 3.) 5973.973
Mean = 5645.097
Standard Deviation = 489.884

1.) 3185.188 2.) 3119.913 3.) 2396.115
Mean = 2900.405
Standard Deviation = 437.946

1.) -14.003 2.) -27.149 3.) -16.631
Mean = -19.261
Standard Deviation = 6.956