BME103 s2013:TEMPwu2: Difference between revisions

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<!-- Note: Delete any image placeholders that you do not need. -->


=LAB 2 WRITE-UP=
=LAB 2 WRITE-UP=


==Initial Machine Testing==
==Background Information==




'''The Original Design'''<br>
'''SYBR Green Dye'''<br>
(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>
''[A short summary describing SYBR green dye]''<br>




'''Experimenting With the Connections'''<br>
'''Single-Drop Fluorimeter'''<br>
''[A description of the single-drop fluorimeter device. Add a PHOTO for bonus points]''<br>


When we unplugged (part 3) from (part 6), the machine ... (did what? fill in your answer)


When we unplugged the white wire that connects (part 6) to (part 2), the machine ... (did what? fill in your answer)
'''How the Fluorescence Technique Works'''<br>
''[In your own words, a summary of the information from page 9 of the worksheet]''




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


(Write the date you first tested Open PCR and your experience(s) with the machine)<br>
==Procedure==


'''Smart Phone Camera Settings'''<br>
* ''[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:


<br><br>


==Protocols==
'''Calibration'''<br>


'''Thermal Cycler Program'''<br>
''[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]''


'''DNA Sample Set-up'''<br>


{| {{table}}
'''Solutions Used for Calibration''' ''[See worksheet page 5]''
{| {{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
|-
| row 3 cell 1 || row 3 cell 2 || row 3 cell 3 || row 3 cell 4
|}
|}
''[Add more rows as needed]''




'''DNA Sample Set-up Procedure'''
'''Placing Samples onto the Fluorimeter'''
# Step 1
* ''[Step one, in your OWN words]''
# Step 2
* ''[Step two, in your own words]''
# Step 3...
* ''[Step three, in your own words]''
* ''[etc.]''


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


'''PCR Reaction Mix'''
==Data Analysis==
* What is in the PCR reaction mix?


'''Representative Images of Samples'''


'''DNA/ primer mix'''
''[Show an IMAGE <u>where you drew a circle around the droplet</u> with the freehand tool for a sample with no DNA]''
* What is in the DNA/ primer mix?


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






<br><br>
'''Image J Values for All Samples''' ''[See worksheet page 5]''
 
{| {{table}} width=700
==Research and Development==
|-
| 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]''


'''Specific Cancer Marker Detection - The Underlying Technology'''<br>


(Add a write-up of the information discussed in Week 3's class)<br>


(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.)
'''Fitting a Straight Line'''<br>
''[Place an IMAGE of your Excel plot with a line of best fit here. See worksheet page 8]''




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




Latest revision as of 16:05, 26 March 2013

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


OUR TEAM

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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