Difference between revisions of "Team:SCAU-China/Interlab"

 
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                     <span class="caret"></span>
 
                     <span class="caret"></span>
 
                     <ul class='dropdown-menu'>
 
                     <ul class='dropdown-menu'>
                         <li><a href="#">NoteBook</a></li>
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                         <li><a href="https://2018.igem.org/Team:SCAU-China/NoteBook">NoteBook</a></li>
                         <li><a href="#">Gallery</a></li>
+
                         <li><a href="https://2018.igem.org/Team:SCAU-China/Gallery">Gallery</a></li>
                         <li><a href="#">Protocol</a></li>
+
                         <li><a href="https://2018.igem.org/Team:SCAU-China/Protocol">Protocol</a></li>
 
                     </ul>
 
                     </ul>
 
                 </li>
 
                 </li>
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                     <span class="caret"></span>
 
                     <span class="caret"></span>
 
                     <ul class='dropdown-menu'>
 
                     <ul class='dropdown-menu'>
                         <li><a href="#">Integrated</a></li>
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                         <li><a href="https://2018.igem.org/Team:SCAU-China/Integrated">Integrated</a></li>
                         <li><a href="#">Engagement</a></li>
+
                         <li><a href="https://2018.igem.org/Team:SCAU-China/Engagement">Engagement</a></li>
 
                         <li><a href="#">Entrepreneurship</a></li>
 
                         <li><a href="#">Entrepreneurship</a></li>
 
                         <li><a href="#"></a></li>
 
                         <li><a href="#"></a></li>
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                 <h1>Parts</h1>
 
                 <h1>Parts</h1>
 
                 <p>Interlab test devices used, as set by the iGEM measurement committee</p>
 
                 <p>Interlab test devices used, as set by the iGEM measurement committee</p>
                 <table>
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                 <table class="fill">
                     <tr>
+
                     <thead>  
                         <th>Device</th>
+
                         <tr>
                        <th>Part Number</th>
+
                            <th class="hard" style="font-size: 24px;font-weight: bold;">Device</th>
                        <th>Location</th>
+
                            <th class="hard" style="font-size: 24px;font-weight: bold;">Part Number</th>
                    </tr>
+
                            <th class="hard" style="font-size: 24px;font-weight: bold;">Location</th>
                     <tr>
+
                        </tr>
                         <td>Negative control</td>
+
                     </thead>
                        <td>BBa_R0040</td>
+
                    <tbody>
                        <td>Well 2D</td>
+
                         <tr>
                    </tr>
+
                            <td style="text-align: center;">Negative control</td>
                    <tr>
+
                            <td style="text-align: center;">BBa_R0040</td>
                        <td>Positive control</td>
+
                            <td style="text-align: center;">Well 2D</td>
                        <td>BBa_I20270</td>
+
                        </tr>
                        <td>Well 2B</td>
+
                        <tr>
                    </tr>
+
                            <td style="text-align: center;">Positive control</td>
                    <tr>
+
                            <td style="text-align: center;">BBa_I20270</td>
                        <td>Test Device 1</td>
+
                            <td style="text-align: center;">Well 2B</td>
                        <td>BBa_J364000</td>
+
                        </tr>
                        <td>Well 2F</td>
+
                        <tr>
                    </tr>
+
                            <td style="text-align: center;">Test Device 1</td>
                    <tr>
+
                            <td style="text-align: center;">BBa_J364000</td>
                        <td>Test Device 2</td>
+
                            <td style="text-align: center;">Well 2F</td>
                        <td>BBa_J364001</td>
+
                        </tr>
                        <td>Well 2H</td>
+
                        <tr>
                    </tr>
+
                            <td style="text-align: center;">Test Device 2</td>
                    <tr>
+
                            <td style="text-align: center;">BBa_J364001</td>
                        <td>Test Device 3</td>
+
                            <td style="text-align: center;">Well 2H</td>
                        <td>BBa_J364002</td>
+
                        </tr>
                        <td>Well 2J</td>
+
                        <tr>
                    </tr>
+
                            <td style="text-align: center;">Test Device 3</td>
                    <tr>
+
                            <td style="text-align: center;">BBa_J364002</td>
                        <td>Test Device 4</td>
+
                            <td style="text-align: center;">Well 2J</td>
                        <td>BBa_J364007</td>
+
                        </tr>
                        <td>Well 2L</td>
+
                        <tr>
                    </tr>
+
                            <td style="text-align: center;">Test Device 4</td>
                    <tr>
+
                            <td style="text-align: center;">BBa_J364007</td>
                        <td>Test Device 5</td>
+
                            <td style="text-align: center;">Well 2L</td>
                        <td>BBa_J364008</td>
+
                        </tr>
                        <td>Well 2N</td>
+
                        <tr>
                    </tr>
+
                            <td style="text-align: center;">Test Device 5</td>
                    <tr>
+
                            <td style="text-align: center;">BBa_J364008</td>
                        <td>Test Device 6</td>
+
                            <td style="text-align: center;">Well 2N</td>
                        <td>BBa_J364009</td>
+
                        </tr>
                        <td>Well 2P</td>
+
                        <tr>
                    </tr>
+
                            <td style="text-align: center;">Test Device 6</td>
 +
                            <td style="text-align: center;">BBa_J364009</td>
 +
                            <td style="text-align: center;">Well 2P</td>
 +
                        </tr>
 +
                    </tbody>
 
                 </table>
 
                 </table>
 
                 <p>the preparation of competent cells(Escherichia coli strain DH5α) and their transformation according to the cell measurement protocol. Meanwile, we followed the Calibration Protocols supplied by the iGEM HQ to generate OD600 Reference point, Particle Standard Curve and Fluorescence standard curve to calibrate the plate reader(96 well plate) and then measured both the fluorescence and absorbance of our samples in 0-hour and 6-hour. </p>
 
                 <p>the preparation of competent cells(Escherichia coli strain DH5α) and their transformation according to the cell measurement protocol. Meanwile, we followed the Calibration Protocols supplied by the iGEM HQ to generate OD600 Reference point, Particle Standard Curve and Fluorescence standard curve to calibrate the plate reader(96 well plate) and then measured both the fluorescence and absorbance of our samples in 0-hour and 6-hour. </p>
                 <p>We used the set protocol that we were given so as to ensure everyone was doing the same thing. These can be found at <a href="https://2018.igem.org/Team:SCAU-China/Protocol">this</a></p>
+
                 <p>We used the set protocol that we were given so as to ensure everyone was doing the same thing. These can be found at <a href="https://2018.igem.org/Team:SCAU-China/Protocol">this page.</a></p>
 
                 <h1>Results and discussion</h1>
 
                 <h1>Results and discussion</h1>
 
                 <p>We submitted the iGEM’s completed spreadsheet to the measurement committee before the deadline, and received confirmation that the results were accepted on the 2018/7/30</p>
 
                 <p>We submitted the iGEM’s completed spreadsheet to the measurement committee before the deadline, and received confirmation that the results were accepted on the 2018/7/30</p>
 
                 <p>OD600 calibration</p>
 
                 <p>OD600 calibration</p>
                 <table>
+
                 <table style="">
 
                     <tr>
 
                     <tr>
                         <th></th>
+
                         <th class="no-border" style="border: 0;text-align: left; background-color: #ffffff;"></th>
                         <th></th>
+
                         <th colspan="2" class="no-border" style="border: 0;text-align: left; background-color: #ffffff;">LUDOX CL-X  H2O</th>
                        <th></th>
+
 
                     </tr>
 
                     </tr>
 
                     <tr>
 
                     <tr>
                         <td>Replicate 1</td>
+
                         <td class="no-border" style="border: 0;text-align: left;">Replicate 1</td>
                         <td>0.059</td>
+
                         <td class="blue" style=" background-color: #00ccff;text-align: left; border: 1px solid #000000;">0.059</td>
                         <td>0.039</td>
+
                         <td class="blue" style=" background-color: #00ccff;text-align: left; border: 1px solid #000000;">0.039</td>
 
                     </tr>
 
                     </tr>
 
                     <tr>
 
                     <tr>
                         <td>Replicate 2</td>
+
                         <td class="no-border" style="border: 0;text-align: left;">Replicate 2</td>
                         <td>0.060</td>
+
                         <td class="blue" style=" background-color: #00ccff;text-align: left; border: 1px solid #000000;">0.060</td>
                         <td>0.035</td>
+
                         <td class="blue" style=" background-color: #00ccff;text-align: left; border: 1px solid #000000;">0.035</td>
 
                     </tr>
 
                     </tr>
 
                     <tr>
 
                     <tr>
                         <td>Replicate 3</td>
+
                         <td class="no-border" style="border: 0;text-align: left;">Replicate 3</td>
                         <td>0.060</td>
+
                         <td class="blue" style=" background-color: #00ccff;text-align: left; border: 1px solid #000000;">0.060</td>
                         <td>0.035</td>
+
                         <td class="blue" style=" background-color: #00ccff;text-align: left; border: 1px solid #000000;">0.035</td>
 
                     </tr>
 
                     </tr>
 
                     <tr>
 
                     <tr>
                         <td>Replicate 4</td>
+
                         <td class="no-border" style="border: 0;text-align: left;">Replicate 4</td>
                         <td>0.061</td>
+
                         <td class="blue" style=" background-color: #00ccff;text-align: left; border: 1px solid #000000;">0.061</td>
                         <td>0.040</td>
+
                         <td class="blue" style=" background-color: #00ccff;text-align: left; border: 1px solid #000000;">0.040</td>
 
                     </tr>
 
                     </tr>
 
                     <tr>
 
                     <tr>
                         <td>Arith. Mean</td>
+
                         <td class="no-border" style="border: 0;text-align: left;">Arith. Mean</td>
                         <td>0.059</td>
+
                         <td class="yellow" style="background-color: #ffcc00;text-align: left; border: 1px solid #000000;">0.059</td>
                         <td>0.039</td>
+
                         <td class="yellow" style="background-color: #ffcc00;text-align: left; border: 1px solid #000000;">0.039</td>
 
                     </tr>
 
                     </tr>
 
                     <tr>
 
                     <tr>
                         <td>Corrected Abs600</td>
+
                         <td class="no-border" style="border: 0;text-align: left;">Corrected Abs600</td>
                         <td>0.023</td>
+
                         <td class="yellow" style="background-color: #ffcc00;text-align: left; border: 1px solid #000000;">0.023</td>
                         <td></td>
+
                         <td style="border: 0; background-color: transparent;"></td>
 
                     </tr>
 
                     </tr>
 
                     <tr>
 
                     <tr>
                         <td>Reference OD600</td>
+
                         <td class="no-border" style="border: 0;text-align: left;">Reference OD600</td>
                         <td>0.063</td>
+
                         <td class="yellow" style="background-color: #ffcc00;text-align: left; border: 1px solid #000000;">0.063</td>
                         <td></td>
+
                         <td style="border: 0; background-color: transparent;"></td>
 
                     </tr>
 
                     </tr>
 
                     <tr>
 
                     <tr>
                         <td>OD600/Abs600</td>
+
                         <td class="no-border" style="border: 0;text-align: left;">OD600/Abs600</td>
                         <td>2.769</td>
+
                         <td class="yellow" style="background-color: #ffcc00;text-align: left; border: 1px solid #000000;">2.769</td>
                         <td></td>
+
                         <td style="border: 0; background-color: transparent;"></td>
 
                     </tr>
 
                     </tr>
 
                 </table>
 
                 </table>
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                 <img src="https://static.igem.org/mediawiki/2018/8/8d/T--SCAU-China--Particlestandardcurve.jpg">
 
                 <img src="https://static.igem.org/mediawiki/2018/8/8d/T--SCAU-China--Particlestandardcurve.jpg">
 
                 <p>Our goal is to reduce lab-to-lab variability in fluorescence measurements, in order to test the variability of variantion in our sample, we caculate coefficient of variantion for both colony, and compare the CV value under different normalization method(Fluorescence per OD or Fluorescence per particle)</p>
 
                 <p>Our goal is to reduce lab-to-lab variability in fluorescence measurements, in order to test the variability of variantion in our sample, we caculate coefficient of variantion for both colony, and compare the CV value under different normalization method(Fluorescence per OD or Fluorescence per particle)</p>
 
 
                 <p>0th</p>
 
                 <p>0th</p>
 
                 <img src="https://static.igem.org/mediawiki/2018/8/8a/T--SCAU-China--0th1.jpg">
 
                 <img src="https://static.igem.org/mediawiki/2018/8/8a/T--SCAU-China--0th1.jpg">
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                 <img src="https://static.igem.org/mediawiki/2018/9/94/T--SCAU-China--6th1.jpg">
 
                 <img src="https://static.igem.org/mediawiki/2018/9/94/T--SCAU-China--6th1.jpg">
 
                 <img src="https://static.igem.org/mediawiki/2018/a/af/T--SCAU-China--6th2.jpg">
 
                 <img src="https://static.igem.org/mediawiki/2018/a/af/T--SCAU-China--6th2.jpg">
                 <p>After 6h growth, we found that the variation of each type of cells(devices) is decreased, but the CV value of devices 4 and device5 are much more large than others. The variation of fluorescence per OD is much more smaller than fluorescence per particle. what’s more, we also found that colony2’s data is more steady compare with colony1 in most cases.
+
                 <p>After 6h growth, we found that the variation of each type of cells(devices) is decreased, but the CV value of devices 4 and device5 are much more large than others. The variation of fluorescence per OD is much more smaller than fluorescence per particle. what’s more, we also found that colony2’s data is more steady compare with colony1 in most cases. for conveniently compare the normalized value with original value, we removed the data of devices4 and device5, and only compare the colony2 6-hour’s data.
                for conveniently compare the normalized value with original value, we removed the data of devices4 and device5, and only compare the colony2 6-hour’s data.
+
 
                 </p>
 
                 </p>
 
                 <img src="https://static.igem.org/mediawiki/2018/6/65/T--SCAU-China--interlabLast.jpg">
 
                 <img src="https://static.igem.org/mediawiki/2018/6/65/T--SCAU-China--interlabLast.jpg">
                 <p>According to the graph, we found that fluorescence per particle can decrease the variation but it depends on the devices. It seems that use OD value to normalize still better than particle. But one thing need to point out that too steady normalized value will loose sensitivity when test the influence of some factors.  
+
                 <p>According to the graph, we found that fluorescence per particle can decrease the variation but it depends on the devices. It seems that use OD value to normalize still better than particle. But one thing need to point out that too steady normalized value will loose sensitivity when test the influence of some factors. You can see this <a href="https://static.igem.org/mediawiki/2017/e/ef/T--oxford--interlab-data.xlsx">Excel File</a> to check our raw and manipulated data.
                You can see this <a href="https://2017.igem.org/Team:Oxford/InterLab">Excel File</a> to check our raw and manipulated data.
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                 </p>
 
                 </p>
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            </div>
 
                 <p>School's name:SCAU</p>
 
                 <p>School's name:SCAU</p>
 
                 <p>Member's name:SCAU</p>
 
                 <p>Member's name:SCAU</p>
 
                 <p>Designed by:SCAU</p>
 
                 <p>Designed by:SCAU</p>
            </div>
 
           
 
 
         </div>
 
         </div>
 
     </div>
 
     </div>

Latest revision as of 08:45, 1 October 2018

interlab

The goal of the iGEM InterLab Study is reliable and repeatable measurement which is a key component to synthetic biology. We took part in the 5th International InterLab Measurement Study and the big question is

“Can we reduce lab-to-lab variability in fluorescence measurements by normalizing to absolute cell count or colony-forming units (CFUs) instead of OD? ”

Parts

Interlab test devices used, as set by the iGEM measurement committee

Device Part Number Location
Negative control BBa_R0040 Well 2D
Positive control BBa_I20270 Well 2B
Test Device 1 BBa_J364000 Well 2F
Test Device 2 BBa_J364001 Well 2H
Test Device 3 BBa_J364002 Well 2J
Test Device 4 BBa_J364007 Well 2L
Test Device 5 BBa_J364008 Well 2N
Test Device 6 BBa_J364009 Well 2P

the preparation of competent cells(Escherichia coli strain DH5α) and their transformation according to the cell measurement protocol. Meanwile, we followed the Calibration Protocols supplied by the iGEM HQ to generate OD600 Reference point, Particle Standard Curve and Fluorescence standard curve to calibrate the plate reader(96 well plate) and then measured both the fluorescence and absorbance of our samples in 0-hour and 6-hour.

We used the set protocol that we were given so as to ensure everyone was doing the same thing. These can be found at this page.

Results and discussion

We submitted the iGEM’s completed spreadsheet to the measurement committee before the deadline, and received confirmation that the results were accepted on the 2018/7/30

OD600 calibration

LUDOX CL-X H2O
Replicate 1 0.059 0.039
Replicate 2 0.060 0.035
Replicate 3 0.060 0.035
Replicate 4 0.061 0.040
Arith. Mean 0.059 0.039
Corrected Abs600 0.023
Reference OD600 0.063
OD600/Abs600 2.769

Fluorescein standard curves

Particle standard curve

Our goal is to reduce lab-to-lab variability in fluorescence measurements, in order to test the variability of variantion in our sample, we caculate coefficient of variantion for both colony, and compare the CV value under different normalization method(Fluorescence per OD or Fluorescence per particle)

0th

6th

After 6h growth, we found that the variation of each type of cells(devices) is decreased, but the CV value of devices 4 and device5 are much more large than others. The variation of fluorescence per OD is much more smaller than fluorescence per particle. what’s more, we also found that colony2’s data is more steady compare with colony1 in most cases. for conveniently compare the normalized value with original value, we removed the data of devices4 and device5, and only compare the colony2 6-hour’s data.

According to the graph, we found that fluorescence per particle can decrease the variation but it depends on the devices. It seems that use OD value to normalize still better than particle. But one thing need to point out that too steady normalized value will loose sensitivity when test the influence of some factors. You can see this Excel File to check our raw and manipulated data.

School's name:SCAU

Member's name:SCAU

Designed by:SCAU