Template:ASUBME103 f2014 L5: Difference between revisions

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=LAB 5 WRITE-UP=
=LAB 5 WRITE-UP=
==Background Information==
'''SYBR Green Dye'''<br>
<!-- Instructions: A short summary describing SYBR green dye. -->
'''Single-Drop Fluorimeter'''<br>
<!-- Instructions: A description of the single-drop fluorimeter device. Add a PHOTO for bonus points. -->
'''How the Fluorescence Technique Works'''<br>
<!-- Instructions: Write a paragraph about how the fluorescence technique works, in your own words -->
<br><br>


==Procedure==
==Procedure==


'''Smart Phone Camera Settings'''<br>
'''Smart Phone Camera Settings'''<br>
PHONE #1
<!-- 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. -->
<!-- Instructions: The type of smart phone you used and how you adjusted the camera settings, if applicable (see worksheet page 4). -->
* Type of Smartphone:
** Flash:
** ISO setting:
** White Balance:
** Exposure:
** Saturation:
** Contrast:
<br><br>
 
<!-- Instructions: If you used an additional phone, describe the other type of smart phone you used and how you adjusted the camera settings, if applicable. If not, delete the following list. -->
PHONE #2
* Type of Smartphone:
* Type of Smartphone:
** Flash:
** Flash:
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'''Calibration'''<br>
'''Calibration'''<br>
<!-- Instructions: 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. Add a PHOTO of this set-up for bonus points. -->


<!-- INSTRUCTIONS: Type the distance between your phone cradle and the drop after the equal sign. -->
* Distance between the smart phone cradle and drop =
* Distance between the smart phone cradle and drop =




'''Solutions Used for Calibration'''
'''Solutions Used for Calibration'''
<!-- Refer to the relevant table in your worksheet -->
{| {{table}} width=700
{| {{table}} width=700
|-
|-
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| row 3 cell 1 || row 3 cell 2 || row 3 cell 3 || row 3 cell 4
| row 3 cell 1 || row 3 cell 2 || row 3 cell 3 || row 3 cell 4
|}
|}
<!-- Add more rows to this table as needed -->
 
<!-- Add more rows and cells as needed. -->
 




'''Placing Samples onto the Fluorimeter'''
'''Placing Samples onto the Fluorimeter'''
<!-- Make a numbered list of steps in your own words. The hashtag symbol (Wiki code) will automatically add a number to each list item -->
# ''[Instructions: Step one, in your OWN words]''
# Step 1
# ''[Instructions: Step two, in your own words]''
# Step 2
# ''[Instructions: Step three, in your own words]''
# Step 3
# ''[Instructions: Step etc., in your own words]''
# Step 4


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


==Data Analysis==
==Data Analysis==


'''Representative Images of Samples'''
'''Representative Images of Negative and Positive Samples'''
<!-- Instructions: (1) Show an IMAGE where you drew a circle around the droplet with the freehand tool for a sample with no DNA. Instructions: (2) Show an IMAGE <u>where you drew a circle around the droplet</u> with the freehand tool for just one sample '''with''' DNA (positive signal) -->
<!-- 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 J Values for All Samples'''  
'''Image J Values for All Calibrator Samples'''  
<!-- Instructions: Refer to the appropriate worksheet page. 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 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. -->




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'''Fitting a Straight Line'''<br>
'''Calibration curve'''<br>
<!-- Instructions: Place an IMAGE of your Excel plot with a line of best fit here. -->
<!-- INSTRUCTIONS: Place an image of your Excel plot with a line of best fit here. -->
 
 
'''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 claculated initial concentration values.-->
* Our positive control PCR result was ____ μg/mL
* Our negative control PCR result was ____ μg/mL
 
<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 -->
* Patient _____ :
* Patient _____ :
 
<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. -->
* Patient _____ :
* Patient _____ :
 
 
 
<br><br>
 
==SNP Information & Primer Design==
 
'''Background: About the Disease SNP'''
<!-- INSTRUCTIONS: This content is from PCR Lab D. Write a summary, at least five sentences long, about the disease SNP in your own words. -->
 
 
'''Primer Design and Testing'''
<!-- INSTRUCTIONS: Write a short summary of the results of your primer test. Underneath your summary, include a screen capture of the results web page. You may crop the image so that it only includes the relevant information. -->
 




<br>




<!-- Do not edit below this line -->
<!-- Do not edit below this line -->
|}
|}

Latest revision as of 09:30, 29 October 2014

BME 100 Fall 2014 Home
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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: student
Name: student
Name: student
Name: student
Name: student
Name: student


LAB 5 WRITE-UP

Procedure

Smart Phone Camera Settings

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


Calibration

  • Distance between the smart phone cradle and drop =


Solutions Used for Calibration

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



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 Analysis

Representative Images of Negative and Positive Samples


Image J Values for All Calibrator Samples


TABLE GOES HERE


Calibration curve


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 _____ :




SNP Information & Primer Design

Background: About the Disease SNP


Primer Design and Testing



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