BME100 s2016:Group7 W1030AM L5

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Contents

OUR TEAM

Name: Milan Patel
Name: Milan Patel
Name: Ryan Masayesva
Name: Ryan Masayesva
Name: student
Name: student
Name: student
Name: student
Name: student
Name: student
Name: student
Name: student


LAB 5 WRITE-UP

PCR Reaction Report

The pre-lab helped us to correctly pippete our samples. Without it we could've possibly mishandled and cross contaminated our samples. The final reactions didn't have the same amount of liquid. There was trace amounts of liquid left in the tubes, but not a significant amount. We didn't have to change our labeling scheme.

Fluorimeter Procedure

Web camera set-up

Take the camera stand and place it next to fluorometer. Put phone on stand and set it up to take pictures of sample so that the picture is clear and close up.


Placing Samples onto the Fluorimeter

  1. Step 1: Place necessary amount of SYBR green onto middle of first two dot rows.
  2. Step 2: Place neccesary amount of DNA sample into the SYBR green dot
  3. Step 3: Align the slide so the fluorescent light shines into the optic piece on other side
  4. Step 4: Put cover box over system.
  5. Step 5: Set camera timer to 3 seconds and take picture, making sure to use the cover box to block out light
  6. Step 6: Take 3 pictures for each sample.


Data Collection and Analysis

Images of High, Low, and Zero Calf Thymus DNA
High
Image:5calib.png
Low
Image:point5calib.png
Zero
Image:0calib.png

Calibrator Mean Values


Calibrator Mean Values
Initial Concentration of 2X Calf Thymus DNA solution (micrograms/mL) Final DNA concentration in SYBR Green I solution (µg/mL) Sample Number RAWINTDEN DRO-BACKGROUND Mean Standard Deviation
5 2.5 C-1 2186129 2188483 2191151 2188587.667 2512.635535
2 1 C-2 2056335 2042466 2040840 2046547 8515.555002
1 .5 C-3 2087348 2088135 2102797 209276 8701.199285
.5 .25 C-4 1643382 1627741 1625240 1632121 9832.158512
.25 .125 C-5 1420245 1441205 1449159 1436869.667 14936.57207
0 0 C-6 767545 808998 716664 764402.3333 46247.15293


Calibration curves
Image:Calibration_Curve.png Image:Calibration_2.png


Images of Our PCR Negative and Positive Controls
Positive
Image:G7+_3.JPG_(green)-1.jpg‎
Negative
Image:G7-_1.JPG_(green)-1.jpg‎


PCR Results: PCR concentrations solved

PCR concentrations solved
PCR Product Tube Label MEAN (of RAWINTDEN DROP - BACKGROUND) "PCR Product Concentration (µg /mL)

(Step 5 calculation)"

Total Dilution "Initial PCR Product Concentration

(µg /mL) (Step 6 calculation)"

G7+ 8154383.333 12.94575944 0.08335 1.079029049
G7- 5398040.667 7.958194833 0.08335 0.6633155393
G7 1-1 5527930.333 8.193228419 0.08335 0.6829055887
G7 1-2 3753018.667 4.981549874 0.08335 0.415212182
G7 1-3 5557640.333 8.246988261 0.08335 0.6873864715
G7 2-1 7128031.667 11.08859004 0.08335 0.92423398
G7 2-2 8313322 13.2333568 0.08335 1.103000289
G7 2-3 7451784.333 11.67441609 0.08335 0.9730625814


PCR Results: Summary

  • Our positive control PCR result was 12.946 μg/mL
  • Our negative control PCR result was 7.958 μg/mL


Observed results

  • Patient 56256 : The images from patient 56256 looked like the negative control, and had a PCR concentration of ~ 8 microliters.
  • Patient 98031 : The images from patient 98031 looked like the positive control, and had a PCR concentration of ~ 12 microliters.


Conclusions

  • Patient 56256 : Patient 56256 appeared to test negative, from analysis of data.
  • Patient 98031 : Patient 98031 appeared to test positive, from analysis of data.



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