Difference between revisions of "Team:Stanford-Brown/SB16 Collaborations Interlab"

 
(14 intermediate revisions by the same user not shown)
Line 42: Line 42:
 
<!--index-->
 
<!--index-->
 
            <li><a href="https://2016.igem.org/Team:Stanford-Brown">Home</a></li>
 
            <li><a href="https://2016.igem.org/Team:Stanford-Brown">Home</a></li>
−
<!--vision-->
+
<!--attributions-->
−
                <li><a href="https://2016.igem.org/Team:Stanford-Brown/SB16_Vision">Vision</a></li>
+
                <li><a href="https://2016.igem.org/Team:Stanford-Brown/Attributions">Attributions</a></li>
 
<!--biomembrane-->
 
<!--biomembrane-->
 
                <li class="dropdown">
 
                <li class="dropdown">
Line 81: Line 81:
 
<li><a href="https://2016.igem.org/Team:Stanford-Brown/Integrated_Practices">Integrated Human Practices</a></li>
 
<li><a href="https://2016.igem.org/Team:Stanford-Brown/Integrated_Practices">Integrated Human Practices</a></li>
 
<li><a href="https://2016.igem.org/Team:Stanford-Brown/Engagement">Outreach</a></li>
 
<li><a href="https://2016.igem.org/Team:Stanford-Brown/Engagement">Outreach</a></li>
−
<li><a href="https://2016.igem.org/Team:Stanford-Brown/SB16_Practices_Interviews">Interviews</a></li>
+
−
<li><a href="https://2016.igem.org/Team:Stanford-Brown/SB16_Practices_Exploration">Exploration</a></li>
+
<li><a href="https://2016.igem.org/Team:Stanford-Brown/SB16_Practices_Exploration">Life Beyond the Lab</a></li>
 
</ul>
 
</ul>
 
</li>
 
</li>
Line 96: Line 96:
 
<!--biobricks-->
 
<!--biobricks-->
 
                <li><a href="https://2016.igem.org/Team:Stanford-Brown/Parts">BioBricks</a></li>
 
                <li><a href="https://2016.igem.org/Team:Stanford-Brown/Parts">BioBricks</a></li>
−
<!--attributions-->
+
<!--protocols-->
 
<li class="dropdown">
 
<li class="dropdown">
−
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Attributions<span class="caret"></span></a>
+
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Protocols<span class="caret"></span></a>
 
<ul class="dropdown-menu">
 
<ul class="dropdown-menu">
−
<li><a href="https://2016.igem.org/Team:Stanford-Brown/Attributions">General Attributions</a>
+
<li><a href="https://2016.igem.org/Team:Stanford-Brown/SB16_Protocols">Protocols</a>
 +
</li>
 +
<li><a href="https://2016.igem.org/Team:Stanford-Brown/SB16_Software">Software Design</a>
 +
</li>
 +
<li><a href="https://2016.igem.org/Team:Stanford-Brown/SB16_Modeling">Modeling</a>
 
</li>
 
</li>
 
<li role="separator" class="divider"></li>
 
<li role="separator" class="divider"></li>
Line 158: Line 162:
 
<!--TEXT BEGIN-->
 
<!--TEXT BEGIN-->
  
 +
<h2 class="subHead">Background</h2>
 
<div class="row">
 
<div class="row">
−
<div class="col-sm-12 pagetext"><i>Background</i><br>For the past two years, iGEM has hosted the <b><a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0150182">InterLab Measurement Study</a></b>, utilizing iGEM's resources and spirit of collaboration to create the two biggest interlaboratory studies ever done in synthetic biology. These studies seek to standardize the tools available to the synthetic biology community and focus on establishing a baseline for replicability of fluorescence measurements. This year, iGEM teams from around the world tested two protocols that used plate readers and flow cytometry to quantify the expression of five different reporter constructs. The measured fluorescence of Green Fluorescent Protein (GFP) was used as a proxy for promoter activity.<br><br>For this study, we used the following constructs:
+
<div class="col-sm-12 pagetext">
−
<br>• <b><a href="http://parts.igem.org/Part:BBa_J23101">J23101</a></b> + <b><a href="http://parts.igem.org/Part:BBa_I13504">I13504</a></b> as Test Device 1
+
            For the past two years, iGEM has hosted the <b><a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0150182">InterLab Measurement Study</a></b>, utilizing iGEM's resources and spirit of collaboration to create the two biggest interlaboratory studies ever done in synthetic biology. These studies seek to standardize the tools available to the synthetic biology community and focus on establishing a baseline for replicability of fluorescence measurements. This year, iGEM teams from around the world tested two protocols that used plate readers and flow cytometry to quantify the expression of five different reporter constructs. The measured fluorescence of Green Fluorescent Protein (GFP) was used as a proxy for promoter activity.<br><br>For this study, we used the following constructs:
−
<br>• <b><a href="http://parts.igem.org/Part:BBa_J23117">J23106</a></b> + <b><a href="http://parts.igem.org/Part:BBa_I13504">I13504</a></b> as Test Device 2
+
            <br>• <b><a href="http://parts.igem.org/Part:BBa_J23101">J23101</a></b> + <b><a href="http://parts.igem.org/Part:BBa_I13504">I13504</a></b> as Test Device 1
−
<br>• <b><a href="http://parts.igem.org/Part:BBa_J23117">J23117</a></b> + <b><a href="http://parts.igem.org/Part:BBa_I13504">13504</a></b> as Test Device 3
+
            <br>• <b><a href="http://parts.igem.org/Part:BBa_J23117">J23106</a></b> + <b><a href="http://parts.igem.org/Part:BBa_I13504">I13504</a></b> as Test Device 2
−
<br>• <b><a href="http://parts.igem.org/Part:BBa_I20270">I20270</a></b> as our Positive Control Device
+
            <br>• <b><a href="http://parts.igem.org/Part:BBa_J23117">J23117</a></b> + <b><a href="http://parts.igem.org/Part:BBa_I13504">13504</a></b> as Test Device 3
−
<br>• <b><a href="http://parts.igem.org/Part:BBa_R0040">R0040</a></b> as our Negative Control Device<br><br>All devices and parts were obtained from the iGEM 2016 InterLab Distribution Kit. Devices were made with a <b><a href="http://parts.igem.org/Part:pSB1C3">pSB1C3</b></a> plasmid backbone and transformed in the E. coli strain NEB5-alpha.
+
            <br>• <b><a href="http://parts.igem.org/Part:BBa_I20270">I20270</a></b> as our Positive Control Device
 +
            <br>• <b><a href="http://parts.igem.org/Part:BBa_R0040">R0040</a></b> as our Negative Control Device<br><br>All devices and parts were obtained from the iGEM 2016 InterLab Distribution Kit. Devices were made with a <b><a href="http://parts.igem.org/Part:pSB1C3">pSB1C3</b></a> plasmid backbone and transformed in the E. coli strain NEB5-alpha.
 
</div> <!--END col-sm-12-->
 
</div> <!--END col-sm-12-->
−
</div>
+
</div> <!--END row-->
 
<!--TEXT END-->
 
<!--TEXT END-->
  
Line 178: Line 184:
  
 
<!--TEXT BEGIN-->
 
<!--TEXT BEGIN-->
 +
 +
<h2 class="subHead">Calibration</h2>
 
<div class="row">
 
<div class="row">
 
<div class="col-sm-5 imgcol-L">
 
<div class="col-sm-5 imgcol-L">
−
<figure><img src="https://static.igem.org/mediawiki/2016/1/13/T--Stanford-Brown--interlabfitcstandard.jpg" class="img-L"><figcaption>Figure 1: Our team's FITC standard curve, as calculated by iGEM's official InterLab spreadsheet.</figcaption></figure>
+
<figure class="fig"><img src="https://static.igem.org/mediawiki/2016/1/13/T--Stanford-Brown--interlabfitcstandard.jpg" class="img-L"><figcaption>Figure 1: Our team's FITC standard curve, as calculated by iGEM's official InterLab spreadsheet.</figcaption></figure>
 
</div> <!--END col-sm-5-->
 
</div> <!--END col-sm-5-->
−
<div class="col-sm-7 pagetext-R"><div class="text"><i>Calibration</i><br>LUDOX-S30 was used as a single point reference to obtain a conversion factor that transforms Abs<sub>600</sub> absorbance data into a standard OD<sub>600</sub> measurement. A 96-well plate was prepared with a column of 4 wells containing 100 µl 100% LUDOX and 4 wells containing 100 µl H<sub>2</sub>O. The absorbance 600 nm of all samples in all standard measurement modes of our plate reader was measured, and our Reference OD<sub>600</sub> data was divided by our Abs<sub>600</sub> data to get our correction factor. Data was converted to OD<sub>600</sub> measurements through multiplication by our correction factor.</div>
+
       
 +
<div class="col-sm-7 pagetext-R"><div class="text">
 +
            LUDOX-S30 was used as a single point reference to obtain a conversion factor that transforms Abs<sub>600</sub> absorbance data into a standard OD<sub>600</sub> measurement. A 96-well plate was prepared with a column of 4 wells containing 100 µl 100% LUDOX and 4 wells containing 100 µl H<sub>2</sub>O. The absorbance 600 nm of all samples in all standard measurement modes of our plate reader was measured, and our Reference OD<sub>600</sub> data was divided by our Abs<sub>600</sub> data to get our correction factor. Data was converted to OD<sub>600</sub> measurements through multiplication by our correction factor.</div>
 
</div> <!--END col-sm-7-->
 
</div> <!--END col-sm-7-->
 
</div> <!--END row-->
 
</div> <!--END row-->
 +
   
 
<div class="row">
 
<div class="row">
−
<div class="col-sm-12 pagetext last">We created 200 µl of 2.5 µM fluorescein stock solution and serially diluted it 1:2 with 1x PBS across plate columns 1-11. We then mixed 100 µl of fluorescein 5x stock solution with 100 µl of PBS in each well. Column 12 contained only 100 µl PBS buffer. This calibration plate was then measured in our plate reader under standard GFP settings and no path length correction to give us a standard measurement curve.<br><br>
+
<div class="col-sm-12 pagetext">
 +
            We created 200 µl of 2.5 µM fluorescein stock solution and serially diluted it 1:2 with 1x PBS across plate columns 1-11. We then mixed 100 µl of fluorescein 5x stock solution with 100 µl of PBS in each well. Column 12 contained only 100 µl PBS buffer. This calibration plate was then measured in our plate reader under standard GFP settings and no path length correction to give us a standard measurement curve.
 
</div> <!--END col-sm-12-->
 
</div> <!--END col-sm-12-->
 +
    </div><!--END row-->
 +
  
 +
<h2 class="subHead">Cell Measurement Protocol</h2>
 
<div class="row">
 
<div class="row">
−
<div class="col-sm-7 pagetext-L"><div class="text"><i>Cell Measurement Protocol</i><br>
+
<div class="col-sm-6 pagetext-L"><div class="text">
−
1. Inoculate 2 colonies per DNA sample on 5-10 ml LB + Chloramphenicol. Grow 16-18 hours at 37˚C and 220 rpm<br>
+
<ol>
−
2. Measure OD<sub>600</sub> of overnight cultures<br>
+
<li>Inoculate 2 colonies per DNA sample on 5-10 ml LB + Chloramphenicol. Grow 16-18 hours at 37˚C and 220 rpm</li>
−
3. Dilute cultures to a target OD<sub>600</sub> of 0.02 in 10 ml 0.5x LB medium + Chloramphenicol and incubate at 37˚C and 220 rpm<br>
+
<li>Measure OD<sub>600</sub> of overnight cultures</li>
−
4. Take 1% of total volume (100 µl) samples at 0, 1, 2, 3, 4, 5, and 6 hours of incubation<br>
+
<li>Dilute cultures to a target OD<sub>600</sub> of 0.02 in 10 ml 0.5x LB medium + Chloramphenicol and incubate at 37˚C and 220 rpm</li>
−
5. Place samples on ice and measure OD and Fl at the end of sampling point</div>
+
<li>Take 1% of total volume (100 µl) samples at 0, 1, 2, 3, 4, 5, and 6 hours of incubation</li>
−
</div> <!--END col-sm-7-->
+
<li>Place samples on ice and measure OD and Fl at the end of sampling point</li>
−
<div class="col-sm-5 imgcol-R">
+
</ol>
−
<figure><img src="https://static.igem.org/mediawiki/2016/9/96/T--Stanford-Brown--interlabprot.jpg" class="img-R"><figcaption>Figure 2: An illustration of the InterLab Study's protocol, done by team member Taylor Pullinger.</figcaption></figure>
+
</div>
−
</div> <!--END col-sm-5-->
+
</div> <!--END col-sm-6-->
 +
       
 +
 
 +
<div class="col-sm-6 imgcol-R">
 +
<figure class="fig"><img src="https://static.igem.org/mediawiki/2016/9/96/T--Stanford-Brown--interlabprot.jpg" class="img-R"><figcaption>Figure 2: An illustration of the InterLab Study's protocol, done by team member Taylor Pullinger.</figcaption></figure>
 +
</div> <!--END col-sm-6-->
 
</div> <!--END row-->
 
</div> <!--END row-->
−
 
−
</div>
 
−
<!--TEXT END-->
 
−
</div>
 
  
 
<!--SECTION TITLE BEGIN-->
 
<!--SECTION TITLE BEGIN-->
Line 215: Line 231:
  
 
<!--TEXT BEGIN-->
 
<!--TEXT BEGIN-->
−
<div class="row">
+
    <div class="row">
−
<div class="col-sm-5 imgcol-L">
+
<div class="col-sm-6 imgcol-L">
−
<figure><img src="https://static.igem.org/mediawiki/2016/9/9c/T--Stanford-Brown--interlababs600.jpg" class="img-L"><figcaption>Figure 3: Our team's Abs<sub>600</sub> curve, as calculated by iGEM's official InterLab spreadsheet.</figcaption></figure>
+
<figure class="fig"><img src="https://static.igem.org/mediawiki/2016/9/9c/T--Stanford-Brown--interlababs600.jpg" class="img-L"><figcaption>Figure 3: Our team's Abs<sub>600</sub> curve, as calculated by iGEM's official InterLab spreadsheet.</figcaption></figure>
−
</div> <!--END col-sm-5-->
+
</div> <!--END col-sm-6-->
−
<div class="col-sm-7 pagetext-R"><div class="text">For our Abs<sub>600</sub> and OD<sub>600</sub> data, we used a Synergy HT plate reader and a 96-well plate. We used the following settings:<br>Wavelengths: 600<br>Pathlength correction: 977/900<br>Absorbance at 1 cm: 0.18</div>
+
       
−
</div> <!--END col-sm-7-->
+
<div class="col-sm-6 pagetext-R"><div class="text"><br>For our Abs<sub>600</sub> and OD<sub>600</sub> data, we used a Synergy HT plate reader and a 96-well plate. We used the following settings:<br>Wavelengths: 600<br>Pathlength correction: 977/900<br>Absorbance at 1 cm: 0.18</div>
 +
</div> <!--END col-sm-6-->
 
</div> <!--END row-->
 
</div> <!--END row-->
−
<br><br>
+
 
 
<div class="row">
 
<div class="row">
−
<div class="col-sm-7 pagetext-L"><div class="text">For our fluorescence data, we used a Synergy HT plate reader and a 96-well plate. We used the following settings:<br>Excitation: 485/20<br>Emission: 528/20<br>Optics: Top<br>Gain: 35<br>Read height: 1mm
+
<div class="col-sm-6 pagetext-L"><div class="text"><br>For our fluorescence data, we used a Synergy HT plate reader and a 96-well plate. We used the following settings:<br>Excitation: 485/20<br>Emission: 528/20<br>Optics: Top<br>Gain: 35<br>Read height: 1mm</div>
−
</div> <!--END col-sm-7-->
+
</div> <!--END col-sm-6-->
−
<div class="col-sm-5 imgcol-R">
+
       
−
<figure><img src="https://static.igem.org/mediawiki/2016/e/e0/T--Stanford-Brown--interlabfluorescence.jpg" class="img-R"><figcaption>Figure 4: Our team's fluorescence graph, made from our raw fluorescence data and calculated by iGEM's official InterLab spreadsheet.</figcaption></figure>
+
<div class="col-sm-6 imgcol-R">
−
</div> <!--END col-sm-5-->
+
<figure class="fig"><img src="https://static.igem.org/mediawiki/2016/e/e0/T--Stanford-Brown--interlabfluorescence.jpg" class="img-R"><figcaption>Figure 4: Our team's fluorescence graph, made from our raw fluorescence data and calculated by iGEM's official InterLab spreadsheet.</figcaption></figure>
 +
</div> <!--END col-sm-6-->
 
</div> <!--END row-->
 
</div> <!--END row-->
−
<br><br>
+
 
−
<div class="row">
+
    <div class="row">
−
<div class="col-sm-5 imgcol-L">
+
<div class="col-sm-6 imgcol-L">
−
<figure><img src="https://static.igem.org/mediawiki/2016/7/71/T--Stanford-Brown--interlabaveragesd.jpg" class="img-L"><figcaption>Figure 5: Our team's Abs<sub>600</sub> data divided by our fluorescence data, calculated as an average with a standard deviation on a curve by iGEM's official InterLab spreadsheet.</figcaption></figure>
+
<figure class="fig"><img src="https://static.igem.org/mediawiki/2016/7/71/T--Stanford-Brown--interlabaveragesd.jpg" class="img-L"><figcaption>Figure 5: Our team's Abs<sub>600</sub> data divided by our fluorescence data, calculated as an average with a standard deviation on a curve by iGEM's official InterLab spreadsheet.</figcaption></figure>
−
</div> <!--END col-sm-5-->
+
</div> <!--END col-sm-6-->
−
<div class="col-sm-7 pagetext-R"><div class="text">Upon collecting our data, we uploaded our raw numbers into the provided spreadsheet "Stanford-Brown_iGEM2016_Interlab_Sheet_1" and allowed for iGEM's number crunching algorithms to generate standard curves for our experiments. The filled out spreadsheet was then emailed to iGEM headquarters to be submitted as a data point in the 2016 InterLab Measurement Study!</div>
+
       
−
</div> <!--END col-sm-7-->
+
<div class="col-sm-6 pagetext-R"><div class="text"><br>Upon collecting our data, we uploaded our raw numbers into the provided spreadsheet <br> "Stanford-Brown_iGEM2016_Interlab_Sheet_1" and allowed for iGEM's number crunching algorithms to generate standard curves for our experiments. The filled out spreadsheet was then emailed to iGEM headquarters to be submitted as a data point in the 2016 InterLab Measurement Study!</div>
 +
</div> <!--END col-sm-6-->
 
</div> <!--END row-->
 
</div> <!--END row-->
  

Latest revision as of 01:31, 20 October 2016


Stanford-Brown 2016

2016 InterLab Measurement Study

Background

For the past two years, iGEM has hosted the InterLab Measurement Study, utilizing iGEM's resources and spirit of collaboration to create the two biggest interlaboratory studies ever done in synthetic biology. These studies seek to standardize the tools available to the synthetic biology community and focus on establishing a baseline for replicability of fluorescence measurements. This year, iGEM teams from around the world tested two protocols that used plate readers and flow cytometry to quantify the expression of five different reporter constructs. The measured fluorescence of Green Fluorescent Protein (GFP) was used as a proxy for promoter activity.

For this study, we used the following constructs:
• J23101 + I13504 as Test Device 1
• J23106 + I13504 as Test Device 2
• J23117 + 13504 as Test Device 3
• I20270 as our Positive Control Device
• R0040 as our Negative Control Device

All devices and parts were obtained from the iGEM 2016 InterLab Distribution Kit. Devices were made with a pSB1C3 plasmid backbone and transformed in the E. coli strain NEB5-alpha.

Plate Reader Protocol

Calibration

Figure 1: Our team's FITC standard curve, as calculated by iGEM's official InterLab spreadsheet.
LUDOX-S30 was used as a single point reference to obtain a conversion factor that transforms Abs600 absorbance data into a standard OD600 measurement. A 96-well plate was prepared with a column of 4 wells containing 100 µl 100% LUDOX and 4 wells containing 100 µl H2O. The absorbance 600 nm of all samples in all standard measurement modes of our plate reader was measured, and our Reference OD600 data was divided by our Abs600 data to get our correction factor. Data was converted to OD600 measurements through multiplication by our correction factor.
We created 200 µl of 2.5 µM fluorescein stock solution and serially diluted it 1:2 with 1x PBS across plate columns 1-11. We then mixed 100 µl of fluorescein 5x stock solution with 100 µl of PBS in each well. Column 12 contained only 100 µl PBS buffer. This calibration plate was then measured in our plate reader under standard GFP settings and no path length correction to give us a standard measurement curve.

Cell Measurement Protocol

  1. Inoculate 2 colonies per DNA sample on 5-10 ml LB + Chloramphenicol. Grow 16-18 hours at 37˚C and 220 rpm
  2. Measure OD600 of overnight cultures
  3. Dilute cultures to a target OD600 of 0.02 in 10 ml 0.5x LB medium + Chloramphenicol and incubate at 37˚C and 220 rpm
  4. Take 1% of total volume (100 µl) samples at 0, 1, 2, 3, 4, 5, and 6 hours of incubation
  5. Place samples on ice and measure OD and Fl at the end of sampling point
Figure 2: An illustration of the InterLab Study's protocol, done by team member Taylor Pullinger.

Data & Results

Figure 3: Our team's Abs600 curve, as calculated by iGEM's official InterLab spreadsheet.

For our Abs600 and OD600 data, we used a Synergy HT plate reader and a 96-well plate. We used the following settings:
Wavelengths: 600
Pathlength correction: 977/900
Absorbance at 1 cm: 0.18

For our fluorescence data, we used a Synergy HT plate reader and a 96-well plate. We used the following settings:
Excitation: 485/20
Emission: 528/20
Optics: Top
Gain: 35
Read height: 1mm
Figure 4: Our team's fluorescence graph, made from our raw fluorescence data and calculated by iGEM's official InterLab spreadsheet.
Figure 5: Our team's Abs600 data divided by our fluorescence data, calculated as an average with a standard deviation on a curve by iGEM's official InterLab spreadsheet.

Upon collecting our data, we uploaded our raw numbers into the provided spreadsheet
"Stanford-Brown_iGEM2016_Interlab_Sheet_1" and allowed for iGEM's number crunching algorithms to generate standard curves for our experiments. The filled out spreadsheet was then emailed to iGEM headquarters to be submitted as a data point in the 2016 InterLab Measurement Study!