Difference between revisions of "Team:RHIT/InterLab"

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<p>We calibrated the plate reader using serial dilutions of fluorescein. The table to the right represents the plate wells, and all values are measured in μM. </p> </div>
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<p>The cells in table 1 to the right represent the plate wells, and all values are measured in μM. </p> </div>
 
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<img src = "https://static.igem.org/mediawiki/2018/f/f0/T--RHIT--PRCallibration.jpg"></div>
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<img src = "https://static.igem.org/mediawiki/2018/f/f0/T--RHIT--PRCallibration.jpg">
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<p> Table 1. Calibration of the plate reader using serial dilutions of fluorescein. </p>
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<img src = "https://static.igem.org/mediawiki/2018/2/28/T--RHIT--MicrosphereCalibration.jpg"></div>
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<img src = "https://static.igem.org/mediawiki/2018/2/28/T--RHIT--MicrosphereCalibration.jpg">
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<center> <p> Table 2. Microsphere calibration to determine a beads to cells conversion. </p></center>
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<p> The table to the left shows our microsphere calibration measured at 630 nm. </p>
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<p> Table 2 to the left shows our microsphere calibration measured at 630 nm. </p>
 
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<p> The table to the right shows our absorbance calibration measured at 630nm. All values are measured in abs. <p></div>
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<p> Table 3 to the right shows our absorbance calibration measured at 630nm. All values are measured in abs. <p></div>
 
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<img src = "https://static.igem.org/mediawiki/2018/3/39/T--RHIT--AbsorbanceCalibration.jpg"></div>
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<img src = "https://static.igem.org/mediawiki/2018/3/39/T--RHIT--AbsorbanceCalibration.jpg">
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<center><p> Table 3. Absorbance calibration </p></center></div>
 
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<h1> Plate Reader Data </h1>
 
<h1> Plate Reader Data </h1>
 
<h2> Absorbance </h2>
 
<h2> Absorbance </h2>
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<p> The following table represents our raw OD600 measurements of our samples at hour 0. </p>
 
 
<img src = "https://static.igem.org/mediawiki/2018/9/94/T--RHIT--AbsHr0.jpg">
 
<img src = "https://static.igem.org/mediawiki/2018/9/94/T--RHIT--AbsHr0.jpg">
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<p> The following table represents our raw OD600 measurements of our samples at hour 6. </p>
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<center><p> Table 4. Our raw OD600 measurements of our samples at hour 0. </p></center>
 
<img src = "https://static.igem.org/mediawiki/2018/6/6d/T--RHIT--AbsHr6.jpg">
 
<img src = "https://static.igem.org/mediawiki/2018/6/6d/T--RHIT--AbsHr6.jpg">
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<center><p> Table 5. Our raw OD600 measurements of our samples at hour 6. </p></center>
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<h2> Fluorescence </h2>
 
<h2> Fluorescence </h2>
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<p> The following table represents our raw fluorescence measurements of our samples at hour 0. </p>
 
 
<img src = "https://static.igem.org/mediawiki/2018/d/dd/T--RHIT--FluorHr0.jpg">
 
<img src = "https://static.igem.org/mediawiki/2018/d/dd/T--RHIT--FluorHr0.jpg">
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<p> The following table represents our raw fluorescence measurements of our samples at hour 6. </p>
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<center><p> Table 6. Our raw fluorescence measurements of our samples at hour 0. </p></center>
 
<img src = "https://static.igem.org/mediawiki/2018/f/f9/T--RHIT--FluorHr6.jpg">  
 
<img src = "https://static.igem.org/mediawiki/2018/f/f9/T--RHIT--FluorHr6.jpg">  
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<br><br> </div>
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<center><p> Table 7. Our raw fluorescence measurements of our samples at hour 6. </p></center>
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<img src = "https://static.igem.org/mediawiki/2018/6/60/T--RHIT--PlateReaderData.jpg">
 
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<p> This shows the normalized fluorescence data for each device. 1-4 are colony 1 and 5-8 are colony 2. </p>
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<center><p> Figure 5. The normalized fluorescence data for each device. 1-4 are from colony 1 and 5-8 are from colony 2. </p></center>
 
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<h1> CFU Data </h1>
 
<h1> CFU Data </h1>
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<p> The following table represents our data from the CFU portion of InterLab. Samples of cells with an OD600 of ~0.1 were diluted and grown on LB + chloramphenicol plates overnight. The next morning, the colonies were counted and used to predict the number of colony forming units in 1 mL of media. </p>
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<p> Table 8 represents our data from the CFU portion of InterLab. Samples of cells with an OD600 of ~0.1 were diluted and grown on LB + chloramphenicol plates overnight. The next morning, the colonies were counted and used to predict the number of colony forming units in 1 mL of media. </p>
 
<img src = "https://static.igem.org/mediawiki/2018/0/0a/T--RHIT--CFUInterLab.jpg">  
 
<img src = "https://static.igem.org/mediawiki/2018/0/0a/T--RHIT--CFUInterLab.jpg">  
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<center><p> Table 8. Our counted colonies per plate as well as calculated CFUs/mL. </p></center>
 
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<img src = "https://static.igem.org/mediawiki/2018/a/ab/T--RHIT--CFUgraph.jpg">
 
<img src = "https://static.igem.org/mediawiki/2018/a/ab/T--RHIT--CFUgraph.jpg">
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<center><p>Figure 6. CFUs/mL vs. OD600 for our positive control cultures (BBa_I20270) and negative control cultures (BBa_R0040) samples. </p></center>
 
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<p> The graph to the left plots the absorbance of each sample in the plate reader against its calculated CFU/mL value after plating the different dilutions. We noticed a general positive correlation between the variables, which makes sense considering a greater number of cells should have a higher absorbance value. We noticed more variability in the positive cultures than the negative cultures. The 3 positive cultures in the bottom left portion of the data are all samples from the first positive culture and the 3 in the top right portion of the data are the three samples from the second positive culture. </p>
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<p> Figure 6 to the left plots the absorbance of each sample in the plate reader against its calculated CFU/mL value after plating the different dilutions. We noticed a general positive correlation between the variables, which makes sense considering a greater number of cells should have a higher absorbance value. We noticed more variability in the positive cultures than the negative cultures. The 3 positive cultures in the bottom left portion of the data are all samples from the first positive culture and the 3 in the top right portion of the data are the three samples from the second positive culture. </p>
 
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<img src = "https://static.igem.org/mediawiki/2018/f/f2/T--RHIT--CFUConversion.jpg">
 
<img src = "https://static.igem.org/mediawiki/2018/f/f2/T--RHIT--CFUConversion.jpg">
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<center><p> Figure 7. The calculated conversion factors for determining CFUs/mL from an absorbance reading. </p></center>
 
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<p> The box and whiskers plot to the left shows the variation in our calculated conversion factor to convert from an OD600 value to a CFU/mL value. It was determined by taking the calculated CFU values for each of the 12 samples and dividing by that sample's OD600 value as determined by the plate reader. The median values between both the positive and negative samples are close, suggesting little variability between a positive and negative sample when determining CFU calculations from an OD600 measurement. </p>
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<p> The box and whiskers plot to the left shows the variation in our calculated conversion factor to convert from an OD600 value to a CFU/mL value. It was determined by taking the calculated CFU values for each of the 12 samples and dividing by that sample's OD600 value as determined by the plate reader. The median values between both the positive control and negative control samples are close, suggesting little variability between a positive and negative sample when determining CFU calculations from an OD600 measurement. </p>
  
  

Revision as of 14:13, 1 August 2018




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Description
Design
Experiments
Notebook
Results
Achievements
InterLab
Attributions

Calibration

Before starting the experiments, our team calibrated the necessary equipment we would need for the InterLab study.

The cells in table 1 to the right represent the plate wells, and all values are measured in μM.

Table 1. Calibration of the plate reader using serial dilutions of fluorescein.

Table 2. Microsphere calibration to determine a beads to cells conversion.

Table 2 to the left shows our microsphere calibration measured at 630 nm.

Table 3 to the right shows our absorbance calibration measured at 630nm. All values are measured in abs.

Table 3. Absorbance calibration

Figure 1 and Figure 2 are calibration curves that show the means at each concentration of fluorescein. Figure 1 is shown with a standard scale, while Figure 2 is shown with a log scale.

Figure 1. Standard scale comparison of the arithmetic mean of the concentration of fluorescein to the fluorescence.
Figure 2. Log scale comparison of the arithmetic mean of the concentration of fluorescein to the fluorescence.

Figure 3 and Figure 4 are calibration curves that show the arithmetic mean of the number of particles compared to the absorbance at OD600. Figure 3 is shown with a standard scale, while Figure 4 is shown with a log scale.

Figure 3. Standard scale comparison of the arithmetic mean of the particle count/100 uL to the absorbance at OD600.
Figure 4. Log scale comparison of the arithmetic mean of the particle count/100 uL to the absorbance at OD600.

Plate Reader Data

Absorbance

Table 4. Our raw OD600 measurements of our samples at hour 0.

Table 5. Our raw OD600 measurements of our samples at hour 6.



Fluorescence

Table 6. Our raw fluorescence measurements of our samples at hour 0.

Table 7. Our raw fluorescence measurements of our samples at hour 6.



Figure 5. The normalized fluorescence data for each device. 1-4 are from colony 1 and 5-8 are from colony 2.

CFU Data

Table 8 represents our data from the CFU portion of InterLab. Samples of cells with an OD600 of ~0.1 were diluted and grown on LB + chloramphenicol plates overnight. The next morning, the colonies were counted and used to predict the number of colony forming units in 1 mL of media.

Table 8. Our counted colonies per plate as well as calculated CFUs/mL.

Figure 6. CFUs/mL vs. OD600 for our positive control cultures (BBa_I20270) and negative control cultures (BBa_R0040) samples.

Figure 6 to the left plots the absorbance of each sample in the plate reader against its calculated CFU/mL value after plating the different dilutions. We noticed a general positive correlation between the variables, which makes sense considering a greater number of cells should have a higher absorbance value. We noticed more variability in the positive cultures than the negative cultures. The 3 positive cultures in the bottom left portion of the data are all samples from the first positive culture and the 3 in the top right portion of the data are the three samples from the second positive culture.

Figure 7. The calculated conversion factors for determining CFUs/mL from an absorbance reading.

The box and whiskers plot to the left shows the variation in our calculated conversion factor to convert from an OD600 value to a CFU/mL value. It was determined by taking the calculated CFU values for each of the 12 samples and dividing by that sample's OD600 value as determined by the plate reader. The median values between both the positive control and negative control samples are close, suggesting little variability between a positive and negative sample when determining CFU calculations from an OD600 measurement.