BME100 f2016:Group14 W8AM L5: Difference between revisions

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<!-- INSTRUCTIONS: In the space below, describe in detail how your team set up your device to capture images from the fluorimeter. -->
<!-- INSTRUCTIONS: In the space below, describe in detail how your team set up your device to capture images from the fluorimeter. -->


To capture images from the flourimeter first the flourimeter was set up by turning it on andplacing a slide in with the smooth side down. We then, set up a phone timer to 3 seconds and turned off the flash. The phone went into a craddle and the flourimeter was lifted with boxes until the slide was in horizontal view of the camera.




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<!-- INSTRUCTIONS: In the space below, in your own words write the steps you performed to place samples onto the fluorimeter -->
<!-- INSTRUCTIONS: In the space below, in your own words write the steps you performed to place samples onto the fluorimeter -->


# ''[Instructions: Step one, in your own words]''
# ''Set micropippete to 80 uL''
# ''[Instructions: Step two, in your own words]''
# ''Place tip on micropipette''
# ''[Instructions: Step three, in your own words]''
# ''Press down on micropipette to first stop''
# ''[Instructions: Step etc., in your own words]''
# ''Place tip to SYBR Green I solution and release to pick up liquid''
# ''Place tip between first 2 circles in the middle of the glass slide''
# ''Press down to second stop on micropipette to release liquid onto slide''
# ''Dispose of tip''
# ''Place new tip on micropipette''
# ''Press down on miropipette to first stop''
# ''Place tip to sample/calibration solution and release to pick up liquid''
# ''Place tip onto drop of SYBR Green I drop''
# ''Press down to second stop to release the sample/calibration drop on top of the SYBR Green I drop''
 


<br>
<br>
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<!-- INSTRUCTIONS: Show ONE image where you drew a circle around the droplet in ImageJ for any image for the (1) 5 μg/mL sample (2) 0.5 μg/mL sample and (3) zero DNA. Please crop your images so that only the drop and a small empty rectangular region around the drop are included. Lots of empty space is a waste of space. -->
<!-- INSTRUCTIONS: Show ONE image where you drew a circle around the droplet in ImageJ for any image for the (1) 5 μg/mL sample (2) 0.5 μg/mL sample and (3) zero DNA. Please crop your images so that only the drop and a small empty rectangular region around the drop are included. Lots of empty space is a waste of space. -->


{| style="wikitable" width="700px"
|- valign="top"
| [[Image:Group14_L5_5_DNA.PNG|thumb|5 μg/mL sample]]


'''Calibrator Mean Values'''  
| [[Image:Group14_L5_0.5_DNA.PNG|thumb|0.5 μg/mL sample]]
 
| [[Image:Group14_L5_Zero_DNA.PNG|thumb|0 μg/mL sample]]
 
|}
 
'''Calibration Mean Values'''  
<!-- INSTRUCTIONS: Show all values from Excel Table 2 from Section 3. '''To save time on typing a new Wiki table from scratch''', use THIS TOOL to auto-generate a Wiki table: http://excel2wiki.net/wikipedia.php. Copy the headers and values from the Excel spreadsheet you made, paste them into the form field, click submit, copy the Wiki code that the tool generated, and replace TABLE GOES HERE (below) with your auto-generated code.  -->
<!-- INSTRUCTIONS: Show all values from Excel Table 2 from Section 3. '''To save time on typing a new Wiki table from scratch''', use THIS TOOL to auto-generate a Wiki table: http://excel2wiki.net/wikipedia.php. Copy the headers and values from the Excel spreadsheet you made, paste them into the form field, click submit, copy the Wiki code that the tool generated, and replace TABLE GOES HERE (below) with your auto-generated code.  -->


 
[[Image:Group14_L5_Calibration_Means.png|thumb|none|700px]]
TABLE GOES HERE




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<!-- INSTRUCTIONS: Place images of your Excel plots (2 total) here. -->
<!-- INSTRUCTIONS: Place images of your Excel plots (2 total) here. -->


 
[[Image:Group14_L5_Calibration_Curves.png|thumb|none|700px]]


'''Images of Our PCR Negative and Positive Controls'''
'''Images of Our PCR Negative and Positive Controls'''
<!-- INSTRUCTIONS: Show ONE image where you drew a circle around the droplet in ImageJ for any image for the (1) Negative control PCR sample AND (2) the Positive control PCR sample.  -->
<!-- INSTRUCTIONS: Show ONE image where you drew a circle around the droplet in ImageJ for any image for the (1) Negative control PCR sample AND (2) the Positive control PCR sample.  -->


{| style="wikitable" width="700px"
|- valign="top"
| [[Image:Group14_L5_Negative.png|thumb|Negative control PCR sample]]
| [[Image:Group14_L5_Positive.png|thumb|Positive Control PCR sample]]
|}




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<!-- INSTRUCTIONS: Show all values from Excel Table 5 from Section 5. '''To save time on typing a new Wiki table from scratch''', use THIS TOOL to auto-generate a Wiki table: http://excel2wiki.net/wikipedia.php. Copy the headers and values from the Excel spreadsheet you made, paste them into the form field, click submit, copy the Wiki code that the tool generated, and replace TABLE GOES HERE (below) with your auto-generated code.  -->
<!-- INSTRUCTIONS: Show all values from Excel Table 5 from Section 5. '''To save time on typing a new Wiki table from scratch''', use THIS TOOL to auto-generate a Wiki table: http://excel2wiki.net/wikipedia.php. Copy the headers and values from the Excel spreadsheet you made, paste them into the form field, click submit, copy the Wiki code that the tool generated, and replace TABLE GOES HERE (below) with your auto-generated code.  -->


TABLE GOES HERE
[[Image:Group14_L5_PCR_Solved.png|thumb|none|700px]]




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'''PCR Results: Summary'''
'''PCR Results: Summary'''
<!-- INSTRUCTIONS: You completed 8 PCR reactions and used the SYBR Green I staining and imaging technique to measure the amount of amplified DNA in each PCR reaction. You used a standard curve (based on known concentrations of calf thymus DNA) to convert INTDEN values into DNA concentration. Your positive control and negative control samples should be used as '''threshold''' values for determining whether an unknown (patient) sample is truly positive or negative. Replace the underscore with your calculated initial concentration values.-->
<!-- INSTRUCTIONS: You completed 8 PCR reactions and used the SYBR Green I staining and imaging technique to measure the amount of amplified DNA in each PCR reaction. You used a standard curve (based on known concentrations of calf thymus DNA) to convert INTDEN values into DNA concentration. Your positive control and negative control samples should be used as '''threshold''' values for determining whether an unknown (patient) sample is truly positive or negative. Replace the underscore with your calculated initial concentration values.-->
* Our positive control PCR result was ____ μg/mL
* Our positive control PCR result was 11.857 μg/mL
* Our negative control PCR result was ____ μg/mL
* Our negative control PCR result was 3.544 μg/mL




<u>Observed results</u>
<u>Observed results</u>
<!-- INSTRUCTIONS: Replace the underscore with each patient ID. After the colon, write both a qualitative (what the images looked like) and a quantitative description (μg/mL) of what you observed -->
<!-- INSTRUCTIONS: Replace the underscore with each patient ID. After the colon, write both a qualitative (what the images looked like) and a quantitative description (μg/mL) of what you observed -->
* Patient _____ :  
* Patient 27929 : When this patient's DNA was exposed to the SYBR green solution, the SYBR green solution made it fluoresce.
* Patient _____ :
* Patient 34835 : When this patient's DNA was exposed to the SYBR green solution, the drop didn't fluoresce at all.




<u>Conclusions</u>
<u>Conclusions</u>
<!-- INSTRUCTIONS: Compare each patient's results to the positive control value and the negative control value. Draw a final conclusion for each patient (positive or negative) and explain why you made that conclusion. -->
<!-- INSTRUCTIONS: Compare each patient's results to the positive control value and the negative control value. Draw a final conclusion for each patient (positive or negative) and explain why you made that conclusion. -->
* Patient _____ :
* Patient 27929 : positive, because the DNA concentration values were greater than that of the positive control.
* Patient _____ :
* Patient 34835 : negative, because the DNA concentration values were less than that of the positive control.
 





Latest revision as of 09:32, 2 November 2016

BME 100 Fall 2016 Home
People
Lab Write-Up 1 | Lab Write-Up 2 | Lab Write-Up 3
Lab Write-Up 4 | Lab Write-Up 5 | Lab Write-Up 6
Course Logistics For Instructors
Photos
Wiki Editing Help

OUR TEAM

Name: Diego Barra
Name: Savanna Bracale
Name: Casin Corallo
Name: Imelda Fragoza
Name: Andrew Samanta


LAB 5 WRITE-UP

PCR Reaction Report

The team's experience went very well with pipetting. Everyone in the team got to pipette and familiarize themselves by the end of the period. Yes, the pre-lab reading helped. The first stop is to pick up the solution and the second stop is to expel it. Yes, the final reactions had the same amount of liquid and there was not any liquid left in the tubes. We kept our labeling scheme the same.

Fluorimeter Procedure

Imaging set-up

To capture images from the flourimeter first the flourimeter was set up by turning it on andplacing a slide in with the smooth side down. We then, set up a phone timer to 3 seconds and turned off the flash. The phone went into a craddle and the flourimeter was lifted with boxes until the slide was in horizontal view of the camera.


Placing Samples onto the Fluorimeter

  1. Set micropippete to 80 uL
  2. Place tip on micropipette
  3. Press down on micropipette to first stop
  4. Place tip to SYBR Green I solution and release to pick up liquid
  5. Place tip between first 2 circles in the middle of the glass slide
  6. Press down to second stop on micropipette to release liquid onto slide
  7. Dispose of tip
  8. Place new tip on micropipette
  9. Press down on miropipette to first stop
  10. Place tip to sample/calibration solution and release to pick up liquid
  11. Place tip onto drop of SYBR Green I drop
  12. Press down to second stop to release the sample/calibration drop on top of the SYBR Green I drop



Data Collection and Analysis

Images of High, Low, and Zero Calf Thymus DNA

5 μg/mL sample
0.5 μg/mL sample
0 μg/mL sample

Calibration Mean Values


Calibration curves

Images of Our PCR Negative and Positive Controls

Negative control PCR sample
Positive Control PCR sample


PCR Results: PCR concentrations solved


PCR Results: Summary

  • Our positive control PCR result was 11.857 μg/mL
  • Our negative control PCR result was 3.544 μg/mL


Observed results

  • Patient 27929 : When this patient's DNA was exposed to the SYBR green solution, the SYBR green solution made it fluoresce.
  • Patient 34835 : When this patient's DNA was exposed to the SYBR green solution, the drop didn't fluoresce at all.


Conclusions

  • Patient 27929 : positive, because the DNA concentration values were greater than that of the positive control.
  • Patient 34835 : negative, because the DNA concentration values were less than that of the positive control.