Talk:BE.109:Systems engineering/RT-PCR data analysis

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(Team Blue!)
(Team Blue!)
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We varied cell density and culture volume by increasing cell density and lowering volume - the two factors worked against each other, which we did not plan well.  This condition lowered beta-gal activity and lowered copies of lac Z in the cells, so the net effect of our varied conditions was to reduce the total number of cells in the sample.  The curve from the standard DNA had an r squared value of 1 and an equation of y = -0.33x+13.03.  This curve was made with two values, the undiluted sample and 1:10 dilution, which corresponded to 10,000 and 1,000 copies of lac z gene, respectively.  
We varied cell density and culture volume by increasing cell density and lowering volume - the two factors worked against each other, which we did not plan well.  This condition lowered beta-gal activity and lowered copies of lac Z in the cells, so the net effect of our varied conditions was to reduce the total number of cells in the sample.  The curve from the standard DNA had an r squared value of 1 and an equation of y = -0.33x+13.03.  This curve was made with two values, the undiluted sample and 1:10 dilution, which corresponded to 10,000 and 1,000 copies of lac z gene, respectively.  
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One standard was done with DNA from lys-n-go reactions. One curve from standard conditions, and one curve from our variable condition. The condition we varied was the amount of air-flow allowed the cells. The standard culture was given air-flow, but the variable condition was completely sealed off in order to stress the cells.
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The curve from the standard air-flow condition had an r squared value of 0.8219, and equation of y = -0.35x + 12.44
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The curve from the standard no air-flow condition had an r squared value of 1.000, and equation of y = -.37x + 13.22
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Each curve was made with three values (the 1000, 100, 10 copies of LacZ)
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===Team Purple===
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We compared cells growing in LB medium vs. SOC medium.  The raw qPCR results had 2869 copies in the sample (average) for the LB triplicates and 6211 copies (average) for the SOC triplicates, while the LB no RT failed to reach the threshold (ie had <100 copies) and SOC no RT had 875 copies.  The primers only and blank wells also had <100 copies.  The melting temperature data was narrow and consistent, showing that contamination with other DNA was probably minimal.
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The best fit line yielded y = -0.24x + 9.82 with r^2 = 0.92.
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Since we added the same amount of RNA (in terms of mass), the results indicate that a greater proportion of the mRNA in the SOC cells was devoted to producing LacZ.  However, the better measure is copies of mRNA/cell.  After calculations, we found that, assuming 100% RT efficiency, that the LB samples had 4.2 million cells' worth of mRNA while the SOC samples had 14.4 million cells' worth.  Therefore, there were 0.68 copies of the LacZ mRNA per 1000 LB cells and 0.43 copies of the LacZ mRNA per 1000 SOC cells.  Overall, the SOC cells produced less LacZ mRNA, but they also produced less mRNA overall.  This makes sense given that SOC medium has nutrients that the E. coli no longer have to produce mRNA in order to produce those nutrients.
==Wed/Fri section==
==Wed/Fri section==

Revision as of 15:44, 25 April 2006

Contents

Tues/Thurs section

Team Blue!

Our situation is special because we did two standard curves instead of one standard and data. One standard was done with DNA from lys-n-go reactions. One curve from standard conditions, and one curve from our variable condition. The condition we varied was the amount of air-flow allowed the cells. The standard culture was given air-flow, but the variable condition was completely sealed off in order to stress the cells. The curve from the standard air-flow condition had an r squared value of 0.8219, and equation of y = -0.35x + 12.44 The curve from the standard no air-flow condition had an r squared value of 1.000, and equation of y = -.37x + 13.22 Each curve was made with three values (the 1000, 100, 10 copies of LacZ)

Team Green

Because of outside factors, our group tested light and dark cells versus each other. Our standard was done with DNA from the lys-n-go reaction. The curve had an equation of y = -0.63x + 21.29, with an R^2 value of 0.633. The poor corelation can be attributed to the first measurement of the undiluted DNA.

Team Pink!

We varied cell density and culture volume by increasing cell density and lowering volume - the two factors worked against each other, which we did not plan well. This condition lowered beta-gal activity and lowered copies of lac Z in the cells, so the net effect of our varied conditions was to reduce the total number of cells in the sample. The curve from the standard DNA had an r squared value of 1 and an equation of y = -0.33x+13.03. This curve was made with two values, the undiluted sample and 1:10 dilution, which corresponded to 10,000 and 1,000 copies of lac z gene, respectively.

One standard was done with DNA from lys-n-go reactions. One curve from standard conditions, and one curve from our variable condition. The condition we varied was the amount of air-flow allowed the cells. The standard culture was given air-flow, but the variable condition was completely sealed off in order to stress the cells. The curve from the standard air-flow condition had an r squared value of 0.8219, and equation of y = -0.35x + 12.44 The curve from the standard no air-flow condition had an r squared value of 1.000, and equation of y = -.37x + 13.22 Each curve was made with three values (the 1000, 100, 10 copies of LacZ)

Team Purple

We compared cells growing in LB medium vs. SOC medium. The raw qPCR results had 2869 copies in the sample (average) for the LB triplicates and 6211 copies (average) for the SOC triplicates, while the LB no RT failed to reach the threshold (ie had <100 copies) and SOC no RT had 875 copies. The primers only and blank wells also had <100 copies. The melting temperature data was narrow and consistent, showing that contamination with other DNA was probably minimal.

The best fit line yielded y = -0.24x + 9.82 with r^2 = 0.92.

Since we added the same amount of RNA (in terms of mass), the results indicate that a greater proportion of the mRNA in the SOC cells was devoted to producing LacZ. However, the better measure is copies of mRNA/cell. After calculations, we found that, assuming 100% RT efficiency, that the LB samples had 4.2 million cells' worth of mRNA while the SOC samples had 14.4 million cells' worth. Therefore, there were 0.68 copies of the LacZ mRNA per 1000 LB cells and 0.43 copies of the LacZ mRNA per 1000 SOC cells. Overall, the SOC cells produced less LacZ mRNA, but they also produced less mRNA overall. This makes sense given that SOC medium has nutrients that the E. coli no longer have to produce mRNA in order to produce those nutrients.

Wed/Fri section

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