BME100 f2015:Group4 1030amL5: Difference between revisions

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'''Smart Phone Camera Settings'''<br>
'''Smart Phone Camera Settings'''<br>
<!-- The type of smart phone you used and how you adjusted the camera settings, if applicable. If you used more than one phone, make an additional list. -->
<!-- The type of smart phone you used and how you adjusted the camera settings, if applicable. If you used more than one phone, make an additional list. -->
* Type of Smartphone: Samsung Galaxy S5
* Type of Smartphone:
** Flash: off
** Flash:
** ISO setting:800
** ISO setting:
** White Balance: auto
** White Balance:  
** Exposure:  
** Exposure:
** Saturation:  
** Saturation:
** Contrast:  
** Contrast:


* Type of Smartphone: HTC 1
** Flash:off
** ISO setting:1600
** White Balance: auto
** Exposure:
** Saturation: +2
** Contrast: -2


'''Calibration'''<br>
'''Camera set-up'''<br>
<!-- INSTRUCTIONS: In the space below, briefly describe how to set up your camera in front of the fluorimeter. Add a PHOTO of this set-up for bonus points. -->
<!-- INSTRUCTIONS: In the space below, briefly describe how to set up your camera in front of the fluorimeter. -->


<!-- INSTRUCTIONS: Type the distance between your phone cradle and the drop after the equal sign. -->
<!-- INSTRUCTIONS: Type the distance between your phone cradle and the drop after the equal sign. -->
Line 57: Line 50:




'''Solutions Used for Calibration'''
'''Placing Samples onto the Fluorimeter'''
{| {{table}} width=700
# ''[Instructions: Step one, in your OWN words]''
|-
# ''[Instructions: Step two, in your own words]''
| Initial Concentration of 2X Calf Thymus DNA solution (micrograms/mL) || Volume of the 2X DNA solution (μL) || Volume of the SYBR GREEN I Dye solution (μL) || Final DNA Concentration in SYBR Green I solution (μL/mL)
# ''[Instructions: Step three, in your own words]''
|-
# ''[Instructions: Step etc., in your own words]''
| 5 || 80* || 80* || 2.5
 
|-
<br>
| 2 || 80* || 80* || 1
<!-- Note: Be sure to delete the instruction text in brackets: ''[ ]'' -->
|-
 
| 1 || 80* || 80* || 0.5
==Data Collection and Analysis==
|-
 
| 0.5 || 80* || 80* || 0.25
'''Images of High, Low, and Zero Calf Thymus DNA'''
|-
<!-- 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. -->
| 0.25 || 80* || 80* || 0.125
|-
| 0 || 80* || 80* || 0
|}


<!-- Add more rows and cells as needed. -->


'''Calibrator 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.  -->




'''Placing Samples onto the Fluorimeter'''
TABLE GOES HERE
# ''On the slide, add a drop of SYBR Green with the amount of eighty microliters at the midpoint of the first two rows.  Use a pipettor to ensure the symmetry and adhesion of this drop.''
# ''Add eightly microliters of one of the chosen water blank (or calf thymus).''
# ''Adjust the slide so that the sample aligns with blue LED light, allowing this light to be focused by the sample drop onto the midpoint of the black fiber-optic fitting.''
# ''[Instructions: Step etc., in your own words]''


<br>
<!-- Note: Be sure to delete the instruction text in brackets: ''[ ]'' -->


==Data Analysis==
'''Calibration curves'''<br>
<!-- INSTRUCTIONS: Place images of your Excel plots (2 total) here. -->


'''Representative Images of Negative and Positive Samples'''
<!-- INSTRUCTIONS: (1) Show ONE image where you drew a circle around the droplet with the freehand tool for any sample with *no* DNA. (2) Show ONE image where you drew a circle around the droplet with the freehand tool for a sample *with* DNA (positive signal). -If you include more than two images, you will not receive any additional credit. -->


[[Image:AnonymousShrew.png‎]]


[[Image:AnonymousGopher.png‎]]
'''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. -->




'''Image J Values for All Calibrator Samples'''
<!-- INSTRUCTIONS: Show a table for the ImageJ calf thymus DNA data. '''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.  -->


'''PCR Results: PCR concentrations solved'''
<!-- 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
TABLE GOES HERE




'''Calibration curve'''<br>
<!-- INSTRUCTIONS: Place an image of your Excel plot with a line of best fit here. -->


 
'''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 claculated initial concentration values.-->
* Our positive control PCR result was ____ μg/mL
* Our positive control PCR result was ____ μg/mL
* Our negative control PCR result was ____ μg/mL
* Our negative control PCR result was ____ 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 12188 :  
* Patient _____ :  
* Patient 54737 :
* Patient _____ :
 


<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 12188 :
* Patient _____ :
* Patient 54737 :
* Patient _____ :





Revision as of 10:15, 28 October 2015

BME 100 Fall 2015 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: Gabrielle Mills
Role(s)
Name: Christa Deckman
Role(s)
Name: Neil Rastogi
Role(s)
Name: Ngan Nguyen
Role(s)
Name: Evan Higgs
Role(s)
Name: Dylan Bunch
Role(s)


LAB 5 WRITE-UP

PCR Reaction Report

Our pipetting of the samples was successful for the setup of this laboratory procedure. The appropriate amounts of DNA sample liquids and PCR reaction mix were added to the tubes with no observable error. The tubes were labeled as we planned and we successfully transferred the liquids between the tubes without contamination.The pre-lab provided appropriate information over how to complete a PCR lab. Through the interactive activities, we were able to familiarize ourselves with the important and significant procedure. In addition, the reading provided informative background descriptions and definitions that helped in the progression and completion of the laboratory procedure. The first and second stops on the pipettor were easy to distinguish after the first few pipetting steps. When you hit the first stop, it is quite hard to go past it accidentally. Therefore, when you purposefully expel the sample into the PCR tube, you can perceive when it is fully expelled at the second stop.The final reactions had the same amount of liquid as the original components combined. Precision was used in transferring the components into the reaction, and therefore, there was the exact same amount of liquid.There was no component liquids left in the tubes of DNA and the PCR reaction mix. Since precision was used in removing these liquids, there was no liquid left in these tubes and all was added into the PCR tubes.We used our original labeling scheme from Part A for the procedure in Part C. We saw no need to change it, given that it was unique to our group seeing as we labeled our PCR tubes with “G4.”

Fluorimeter Procedure

Smart Phone Camera Settings

  • Type of Smartphone:
    • Flash:
    • ISO setting:
    • White Balance:
    • Exposure:
    • Saturation:
    • Contrast:


Camera set-up

  • Distance between the smart phone cradle and drop =


Placing Samples onto the Fluorimeter

  1. [Instructions: Step one, in your OWN words]
  2. [Instructions: Step two, in your own words]
  3. [Instructions: Step three, in your own words]
  4. [Instructions: Step etc., in your own words]


Data Collection and Analysis

Images of High, Low, and Zero Calf Thymus DNA


Calibrator Mean Values


TABLE GOES HERE


Calibration curves


Images of Our PCR Negative and Positive Controls


PCR Results: PCR concentrations solved

TABLE GOES HERE


PCR Results: Summary

  • Our positive control PCR result was ____ μg/mL
  • Our negative control PCR result was ____ μg/mL


Observed results

  • Patient _____ :
  • Patient _____ :


Conclusions

  • Patient _____ :
  • Patient _____ :