BME103 s2013:TEMPwu2

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=LAB 1 WRITE-UP=
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<!-- Note: Delete any image placeholders that you do not need. -->
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==Initial Machine Testing==
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=LAB 2 WRITE-UP=
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==Background Information==
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'''The Original Design'''<br>
 
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(Add image of the full OpenPCR machine here, from the Week 9 exercise. Write a paragraph description for visitors who have no idea what this is)<br>
 
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'''SYBR Green Dye'''<br>
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''[A short summary describing SYBR green dye]''<br>
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'''Experimenting With the Connections'''<br>
 
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When we unplugged (part 3) from (part 6), the machine ... (did what? fill in your answer)
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'''Single-Drop Fluorimeter'''<br>
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''[A description of the single-drop fluorimeter device. Add a PHOTO for bonus points]''<br>
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When we unplugged the white wire that connects (part 6) to (part 2), the machine ... (did what? fill in your answer)
 
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'''How the Fluorescence Technique Works'''<br>
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''[In your own words, a summary of the information from page 9 of the worksheet]''
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'''Test Run'''
 
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(Write the date you first tested Open PCR and your experience(s) with the machine)<br>
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<br>
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<!-- Note: Be sure to delete the text in brackets: ''[ ]'' -->
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==Procedure==
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'''Smart Phone Camera Settings'''<br>
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* ''[The type of smart phone you used and how you adjusted the camera settings, if applicable (see worksheet page 4).]''
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** Flash:
 +
** ISO setting:
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** White Balance:
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** Exposure:
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** Saturation:
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** Contrast:
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<br><br>
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* ''[If you used an additional phone, describe the other type of smart phone you used and how you adjusted the camera settings, if applicable (see worksheet page 4).]''
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** Flash:
 +
** ISO setting:
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** White Balance:
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** Exposure:
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** Saturation:
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** Contrast:
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==Protocols==
 
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'''Thermal Cycler Program'''<br>
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'''Calibration'''<br>
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''[Describe how to set up your camera in front of the fluorimeter. Add a PHOTO of this set-up for bonus points.]''
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'''DNA Sample Set-up'''<br>
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* Distance between the smart phone cradle and drop =
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''[See worksheet page 5]''
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{| {{table}}
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'''Solutions Used for Calibration''' ''[See worksheet page 5]''
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{| {{table}} width=700
|-
|-
| row 1 cell 1 || row 1 cell 2 || row 1 cell 3 || row 1 cell 4
| row 1 cell 1 || row 1 cell 2 || row 1 cell 3 || row 1 cell 4
|-
|-
| row 2 cell 1 || row 2 cell 2 || row 2 cell 3 || row 2 cell 4
| row 2 cell 1 || row 2 cell 2 || row 2 cell 3 || row 2 cell 4
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|-
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| row 3 cell 1 || row 3 cell 2 || row 3 cell 3 || row 3 cell 4
|}
|}
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''[Add more rows as needed]''
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'''DNA Sample Set-up Procedure'''
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'''Placing Samples onto the Fluorimeter'''
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# Step 1
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* ''[Step one, in your OWN words]''
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# Step 2
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* ''[Step two, in your own words]''
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# Step 3...
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* ''[Step three, in your own words]''
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* ''[etc.]''
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<br>
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<!-- Note: Be sure to delete the text in brackets: ''[ ]'' -->
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'''PCR Reaction Mix'''
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==Data Analysis==
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* What is in the PCR reaction mix?
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'''Representative Images of Samples'''
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'''DNA/ primer mix'''
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''[Show an IMAGE <u>where you drew a circle around the droplet</u> with the freehand tool for a sample with no DNA]''
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* What is in the DNA/ primer mix?
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''[Show an IMAGE <u>where you drew a circle around the droplet</u> with the freehand tool for a sample '''with''' DNA (positive signal)]''
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<br><br>
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'''Image J Values for All Samples''' ''[See worksheet page 5]''
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{| {{table}} width=700
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==Research and Development==
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|-
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| row 1 cell 1 || row 1 cell 2 || row 1 cell 3 || row 1 cell 4 || row 1 cell 5
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|-
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| row 2 cell 1 || row 2 cell 2 || row 2 cell 3 || row 2 cell 4 || row 2 cell 5
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|-
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| row 3 cell 1 || row 3 cell 2 || row 3 cell 3 || row 3 cell 4 || row 2 cell 5
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|}
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''[Add more rows as needed]''
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'''Specific Cancer Marker Detection - The Underlying Technology'''<br>
 
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(Add a write-up of the information discussed in Week 3's class)<br>
 
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(BONUS points: Use a program like Powerpoint, Word, Illustrator, Microsoft Paint, etc. to illustrate how primers bind to the cancer DNA template, and how Taq polymerases amplify the DNA. Screen-captures from the OpenPCR tutorial might be useful. Be sure to credit the source if you borrow images.)
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'''Fitting a Straight Line'''<br>
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''[Place an IMAGE of your Excel plot with a line of best fit here. See worksheet page 8]''
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<br><br>
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<br>
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<!-- Note: Be sure to delete the text in brackets: ''[ ]'' -->

Current revision

BME 103 Spring 2013 Home
People
Lab Write-Up 1
Lab Write-Up 2
Lab Write-Up 3
Course Logistics For Instructors
Photos
Wiki Editing Help
Image:BME494_Asu_logo.png


Contents

OUR TEAM

Name: student
Name: student
Name: student
Name: student
Name: student
Name: student
Name: student
Name: student
Name: student
Name: student
Name: student
Name: student


LAB 2 WRITE-UP

Background Information

SYBR Green Dye
[A short summary describing SYBR green dye]


Single-Drop Fluorimeter
[A description of the single-drop fluorimeter device. Add a PHOTO for bonus points]


How the Fluorescence Technique Works
[In your own words, a summary of the information from page 9 of the worksheet]



Procedure

Smart Phone Camera Settings

  • [The type of smart phone you used and how you adjusted the camera settings, if applicable (see worksheet page 4).]
    • Flash:
    • ISO setting:
    • White Balance:
    • Exposure:
    • Saturation:
    • Contrast:
  • [If you used an additional phone, describe the other type of smart phone you used and how you adjusted the camera settings, if applicable (see worksheet page 4).]
    • Flash:
    • ISO setting:
    • White Balance:
    • Exposure:
    • Saturation:
    • Contrast:


Calibration

[Describe how to set up your camera in front of the fluorimeter. Add a PHOTO of this set-up for bonus points.]

  • Distance between the smart phone cradle and drop =

[See worksheet page 5]


Solutions Used for Calibration [See worksheet page 5]

row 1 cell 1 row 1 cell 2 row 1 cell 3 row 1 cell 4
row 2 cell 1 row 2 cell 2 row 2 cell 3 row 2 cell 4
row 3 cell 1 row 3 cell 2 row 3 cell 3 row 3 cell 4

[Add more rows as needed]


Placing Samples onto the Fluorimeter

  • [Step one, in your OWN words]
  • [Step two, in your own words]
  • [Step three, in your own words]
  • [etc.]


Data Analysis

Representative Images of Samples

[Show an IMAGE where you drew a circle around the droplet with the freehand tool for a sample with no DNA]

[Show an IMAGE where you drew a circle around the droplet with the freehand tool for a sample with DNA (positive signal)]


Image J Values for All Samples [See worksheet page 5]

row 1 cell 1 row 1 cell 2 row 1 cell 3 row 1 cell 4 row 1 cell 5
row 2 cell 1 row 2 cell 2 row 2 cell 3 row 2 cell 4 row 2 cell 5
row 3 cell 1 row 3 cell 2 row 3 cell 3 row 3 cell 4 row 2 cell 5

[Add more rows as needed]


Fitting a Straight Line
[Place an IMAGE of your Excel plot with a line of best fit here. See worksheet page 8]




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