Difference between revisions of "Team:ShanghaiTech/InterLab"

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<p>This page is used by the judges to evaluate your team for the <a href="https://2018.igem.org/Judging/Medals">medal criterion</a> or <a href="https://2018.igem.org/Judging/Awards"> award listed below</a>. </p>
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<p> Delete this box in order to be evaluated for this medal criterion and/or award. See more information at <a href="https://2018.igem.org/Judging/Pages_for_Awards"> Instructions for Pages for awards</a>.</p>
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      <img class="img-fluid" src="https://static.igem.org/mediawiki/2018/4/4a/T--ShanghaiTech--InterLab_Title_New.svg" style="z-index:0; margin-top: 10px; width:70%">
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<h1>InterLab</h1>
 
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<h3>Bronze Medal Criterion #4</h3>
 
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<p><b>Standard Tracks:</b> Participate in the Interlab Measurement Study and/or obtain new, high quality experimental characterization data for 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 2018 part number range.
 
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For teams participating in the <a href="https://2018.igem.org/Measurement/InterLab">InterLab study</a>, all work must be shown on this page.
 
  
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        <h3>Introduction</h3>
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        <p>Reliable and reproducible measurement is a key component to all engineering disciplines. The same holds true for synthetic biology. However, it is difficult to repeat the measurement data from different labs. The goal of the iGEM InterLab Study is to identify and correct the sources of systematic variability in synthetic biology measurements, so eventually, measurements that are taken in different labs will be no more variable than measurements taken within the same lab.</p>
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        <p>This year, the objective of the InterLab study is to test if we can reduce lab-to-lab variability in fluorescence measurements by normalizing to absolute cell count or colony-forming units (CFUs) instead of OD reading. Teams from around the world are using standardized biological parts, bacterial strain and measurement procedures provided in a detailed protocol by iGEM.</p>
  
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        <h3>Results and Discussion</h3>
  
  
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        <h4>Calibration</h4>
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        <p><img class="img-fluid mx-auto d-block" style="width: 80%" src='https://static.igem.org/mediawiki/2018/b/b0/T--ShanghaiTech--interlab_1.png' alt='interlab_1'  /></p>
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        <p class="text-center"><small>Fig.1 OD600 reference point</small></p>
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        <p><img class="img-fluid mx-auto d-block" style="width: 90%" src='https://static.igem.org/mediawiki/2018/0/07/T--ShanghaiTech--interlab_2A.png' alt='interlab_2A'  /></p>
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        <p><img class="img-fluid mx-auto d-block" style="width: 90%" src='https://static.igem.org/mediawiki/2018/b/ba/T--ShanghaiTech--interlab_2B.png' alt='interlab_2B'  /></p>
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        <p class="text-center"><small>Fig.2 Particle standard curve</small></p>
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        <p><img class="img-fluid mx-auto d-block" style="width: 90%" src='https://static.igem.org/mediawiki/2018/a/a9/T--ShanghaiTech--interlab_3A.png' alt='interlab_3A'  /></p>
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        <p><img class="img-fluid mx-auto d-block" style="width: 90%" src='https://static.igem.org/mediawiki/2018/a/a1/T--ShanghaiTech--interlab_3B.png' alt='interlab_3B'  /></p>
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        <p class="text-center"><small>Fig.3 Fluorescein standard curve</small></p>
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        <h4>Cell measurement</h4>
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        <p>All the raw data and following tables refer to the well arrangement of iGEM protocal below.</p>
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        <p><img class="img-fluid mx-auto d-block" style="width: 90%" src='https://static.igem.org/mediawiki/2018/c/c5/T--ShanghaiTech--interlab_4.png' alt='interlab_4'  /></p>
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        <p class="text-center"><small>Fig.4  Well arrangement </small></p>
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        <p><img class="img-fluid mx-auto d-block" style="width: 90%" src='https://static.igem.org/mediawiki/2018/1/18/T--ShanghaiTech--interlab_5A.png' alt='interlab_5A'  /></p>
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        <p>&nbsp;</p>
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        <p><img class="img-fluid mx-auto d-block" style="width: 90%" src='https://static.igem.org/mediawiki/2018/c/c8/T--ShanghaiTech--interlab_5B.png' alt='interlab_5B'  /></p>
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        <p class="text-center"><small>Fig.5  Abs600 Raw Readings</small></p>
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        <p>After 18 hours growth at 37°C and 220 rpm orbital rotation speed, cultures were diluted to a target Abs600 of 0.02. After deleting background, 0h time point data has an average Abs600 of 0.0206. The rest of the diluted cultures were incubated at 37°C and 220 rpm for 6 hours, and after 6 hours of growth, significant Abs600 increase could be detected.</p>
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        <p> <img class="img-fluid mx-auto d-block" style="width: 90%" src='https://static.igem.org/mediawiki/2018/f/fa/T--ShanghaiTech--interlab_6A.png' alt='interlab_6A'  /></p>
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        <p><img class="img-fluid mx-auto d-block" style="width: 90%" src='https://static.igem.org/mediawiki/2018/3/3d/T--ShanghaiTech--interlab_6B.png' alt='interlab_6B'  /></p>
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        <p class="text-center"><small>Fig.6 Fluorescence Raw Readings</small></p>
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        <p>At 0h time point no fluorescence or trace fluorescence were detected. At 6h time point, negative control still remain low fluorescence, though the fluorescence in Device 3 and Device 5 behaved unexpected low, yet all other 6 groups appeared apparent increase of fluorescence.</p>
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        <p><img class="img-fluid mx-auto d-block" src='https://static.igem.org/mediawiki/2018/0/09/T--ShanghaiTech--interlab_7.png' alt='interlab_7'  /> </p>
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        <p class="text-center"><small>Fig.7 CFUs per 0.1 OD­600 E. coli cultures</small></p>
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        <p>&nbsp;</p>
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        <h4>Extra Credit</h4>
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        <p><img class="img-fluid mx-auto d-block" src='https://static.igem.org/mediawiki/2018/b/ba/T--ShanghaiTech--interlab_8.png' alt='interlab_8'  /></p>
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        <p class="text-center"><small>Fig.8 Flow Cytometry</small></p>
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        <p>After measuring each plate with the plate reader, we also collected data from all wells by using flow cytometer. At least 10,000 events per well were collected.</p>
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        <p>Instrument information: <strong>CytoFlex S</strong></p>
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        <p>Full data link: <a href='https://styxysmanraschid-my.sharepoint.com/:u:/g/personal/emhj4h29_myod_tech/EeEx2FTAukNPp-mwIH_BrXcBCFIEid_W49IJIymm1X-Y1Q?e=PCywhQ'>link</a></p>
  
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Latest revision as of 12:42, 25 November 2018

ShanghaiTech iGEM

Introduction

Reliable and reproducible measurement is a key component to all engineering disciplines. The same holds true for synthetic biology. However, it is difficult to repeat the measurement data from different labs. The goal of the iGEM InterLab Study is to identify and correct the sources of systematic variability in synthetic biology measurements, so eventually, measurements that are taken in different labs will be no more variable than measurements taken within the same lab.

This year, the objective of the InterLab study is to test if we can reduce lab-to-lab variability in fluorescence measurements by normalizing to absolute cell count or colony-forming units (CFUs) instead of OD reading. Teams from around the world are using standardized biological parts, bacterial strain and measurement procedures provided in a detailed protocol by iGEM.


Results and Discussion

Calibration

interlab_1

Fig.1 OD600 reference point

interlab_2A

interlab_2B

Fig.2 Particle standard curve

interlab_3A

interlab_3B

Fig.3 Fluorescein standard curve

Cell measurement

All the raw data and following tables refer to the well arrangement of iGEM protocal below.

interlab_4

Fig.4 Well arrangement

interlab_5A

 

interlab_5B

Fig.5 Abs600 Raw Readings

After 18 hours growth at 37°C and 220 rpm orbital rotation speed, cultures were diluted to a target Abs600 of 0.02. After deleting background, 0h time point data has an average Abs600 of 0.0206. The rest of the diluted cultures were incubated at 37°C and 220 rpm for 6 hours, and after 6 hours of growth, significant Abs600 increase could be detected.

interlab_6A

interlab_6B

Fig.6 Fluorescence Raw Readings

At 0h time point no fluorescence or trace fluorescence were detected. At 6h time point, negative control still remain low fluorescence, though the fluorescence in Device 3 and Device 5 behaved unexpected low, yet all other 6 groups appeared apparent increase of fluorescence.

interlab_7

Fig.7 CFUs per 0.1 OD­600 E. coli cultures

 

Extra Credit

interlab_8

Fig.8 Flow Cytometry

After measuring each plate with the plate reader, we also collected data from all wells by using flow cytometer. At least 10,000 events per well were collected.

Instrument information: CytoFlex S

Full data link: link


ShanghaiTech iGEM @ 2018