Template:ASUBME103 f2014 L5: Difference between revisions

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{|{{table}} width="800"
{|{{table}} width="800"
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|style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]]<span style="font-size:22px;"> BME 100 Fall 2014</span>
|style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]]<span style="font-size:22px;"> BME 100 Spring 2014</span>
|style="background-color: #F2F2F2" | [[BME100_f2014 | <font face="trebuchet ms" style="color: #808080"> '''Home''' </font>]]<br>[[BME100_f2014:People | <font face="trebuchet ms" style="color: #808080"> '''People''' </font>]]<br>[[BME100_f2014:Projects1 | <font face="trebuchet ms" style="color: #808080"> '''Lab Write-Up 1''' </font>]] | [[BME100_f2014:Projects2 | <font face="trebuchet ms" style="color: #808080"> '''Lab Write-Up 2''' </font>]] | [[BME100_f2014:Projects3 | <font face="trebuchet ms" style="color: #808080"> '''Lab Write-Up 3''' </font>]]<br>[[BME100_f2014:Projects4 | <font face="trebuchet ms" style="color: #808080"> '''Lab Write-Up 4''' </font>]] | [[BME100_f2014:Projects5 | <font face="trebuchet ms" style="color: #808080"> '''Lab Write-Up 5''' </font>]] | [[BME100_f2014:Projects6 | <font face="trebuchet ms" style="color: #808080"> '''Lab Write-Up 6''' </font>]]<br>[[BME100_f2014:Logistics | <font face="trebuchet ms" style="color: #808080"> ''' Course Logistics For Instructors''' </font>]] <br>[[BME100_f2014:Photos | <font face="trebuchet ms" style="color: #808080"> '''Photos''' </font>]] <br>[[BME100_f2014:WikiHelp | <font face="trebuchet ms" style="color: #808080"> '''Wiki Editing Help''' </font>]]  
|style="background-color: #F2F2F2" | [[BME100_s2014 | <font face="trebuchet ms" style="color: #808080"> '''Home''' </font>]]<br>[[BME100_s2014:People | <font face="trebuchet ms" style="color: #808080"> '''People''' </font>]]<br>[[BME100_s2014:Projects1 | <font face="trebuchet ms" style="color: #808080"> '''Lab Write-Up 1''' </font>]] | [[BME100_s2014:Projects2 | <font face="trebuchet ms" style="color: #808080"> '''Lab Write-Up 2''' </font>]] | [[BME100_s2014:Projects3 | <font face="trebuchet ms" style="color: #808080"> '''Lab Write-Up 3''' </font>]]<br>[[BME100_s2014:Projects4 | <font face="trebuchet ms" style="color: #808080"> '''Lab Write-Up 4''' </font>]] | [[BME100_s2014:Projects5 | <font face="trebuchet ms" style="color: #808080"> '''Lab Write-Up 5''' </font>]] | [[BME100_s2014:Projects6 | <font face="trebuchet ms" style="color: #808080"> '''Lab Write-Up 6''' </font>]]<br>[[BME100_s2014:Logistics | <font face="trebuchet ms" style="color: #808080"> ''' Course Logistics For Instructors''' </font>]] <br>[[BME100_s2014:Photos | <font face="trebuchet ms" style="color: #808080"> '''Photos''' </font>]] <br>[[BME100_s2014:WikiHelp | <font face="trebuchet ms" style="color: #808080"> '''Wiki Editing Help''' </font>]]  
|-
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| style="background-color: #ffcc66; padding: 5px;" colspan="2" | [[Image:BME494_Asu_logo.png]]
| style="background-color: #ffcc66; padding: 5px;" colspan="2" | [[Image:BME494_Asu_logo.png]]
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'''SYBR Green Dye'''<br>
'''SYBR Green Dye'''<br>
<!-- Instructions: A short summary describing SYBR green dye. -->
''[Instructions: A short summary describing SYBR green dye]''<br>




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




'''How the Fluorescence Technique Works'''<br>
'''How the Fluorescence Technique Works'''<br>
<!-- Instructions: Write a paragraph about how the fluorescence technique works, in your own words -->
''[Instructions: In your own words]''




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


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


'''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: 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 =
* Distance between the smart phone cradle and drop =
''[Instructions: See worksheet page 6.]''




'''Solutions Used for Calibration'''
'''Solutions Used for Calibration''' ''[Instructions: See worksheet page 6.]''
<!-- Refer to the relevant table in your worksheet -->
{| {{table}} width=700
{| {{table}} width=700
|-
|-
Line 85: Line 73:
| 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 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 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: Show an IMAGE <u>where you drew a circle around the droplet</u> with the freehand tool for a sample with no DNA. -->
 
''[Instructions: Show an IMAGE <u>where you drew a circle around the droplet</u> with the freehand tool for a sample '''with''' DNA (positive signal)]''






'''Image J Values for All Samples'''  
'''Image J Values for All 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: See worksheet page 8. '''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 Excel-to-Wiki Converter]. 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>




<!-- Do not edit below this line -->
<!-- Do not edit below this line -->
|}
|}
<!--
{|{{table}} width="800"
|-
|style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]]<span style="font-size:22px;"> BME 100 Fall 2014</span>
|style="background-color: #F2F2F2" | [[BME100_f2014 | <font face="trebuchet ms" style="color: #808080"> '''Home''' </font>]]<br>[[BME100_f2014:People | <font face="trebuchet ms" style="color: #808080"> '''People''' </font>]]<br>[[BME100_f2014:Projects1 | <font face="trebuchet ms" style="color: #808080"> '''Lab Write-Up 1''' </font>]] | [[BME100_f2014:Projects2 | <font face="trebuchet ms" style="color: #808080"> '''Lab Write-Up 2''' </font>]] | [[BME100_f2014:Projects3 | <font face="trebuchet ms" style="color: #808080"> '''Lab Write-Up 3''' </font>]]<br>[[BME100_f2014:Projects4 | <font face="trebuchet ms" style="color: #808080"> '''Lab Write-Up 4''' </font>]] | [[BME100_f2014:Projects5 | <font face="trebuchet ms" style="color: #808080"> '''Lab Write-Up 5''' </font>]] | [[BME100_f2014:Projects6 | <font face="trebuchet ms" style="color: #808080"> '''Lab Write-Up 6''' </font>]]<br>[[BME100_f2014:Logistics | <font face="trebuchet ms" style="color: #808080"> ''' Course Logistics For Instructors''' </font>]] <br>[[BME100_f2014:Photos | <font face="trebuchet ms" style="color: #808080"> '''Photos''' </font>]] <br>[[BME100_f2014:WikiHelp | <font face="trebuchet ms" style="color: #808080"> '''Wiki Editing Help''' </font>]]
|-
| style="background-color: #ffcc66; padding: 5px;" colspan="2" | [[Image:BME494_Asu_logo.png]]
|-
| colspan="2"|
<!-- ##### DO NOT edit above this line unless you know what you are doing. ##### -->
=OUR TEAM=
{| style="wikitable" width="700px"
|- valign="top"
| [[Image:BME103student.jpg|100px|thumb|Name: student]]
| [[Image:BME103student.jpg|100px|thumb|Name: student]]
| [[Image:BME103student.jpg|100px|thumb|Name: student]]
| [[Image:BME103student.jpg|100px|thumb|Name: student]]
| [[Image:BME103student.jpg|100px|thumb|Name: student]]
| [[Image:BME103student.jpg|100px|thumb|Name: student]]
|}
<!-- Note: Delete any image placeholders that you do not need. -->
=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==
'''Smart Phone Camera Settings'''<br>
PHONE #1
<!-- 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:
** Flash:
** ISO setting:
** White Balance:
** Exposure:
** Saturation:
** Contrast:
'''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. -->
* Distance between the smart phone cradle and drop =
'''Solutions Used for Calibration'''
<!-- Refer to the relevant table in your worksheet -->
{| {{table}} width=700
|-
| 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 ||

Revision as of 08:23, 29 October 2014

BME 100 Spring 2014 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: student
Name: student
Name: student
Name: student
Name: student
Name: student


LAB 5 WRITE-UP

Background Information

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


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


How the Fluorescence Technique Works
[Instructions: In your own words]



Procedure

Smart Phone Camera Settings

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


Calibration

[Instructions: 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 =

[Instructions: See worksheet page 6.]


Solutions Used for Calibration [Instructions: See worksheet page 6.]

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

  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 Samples

[Instructions: 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


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 _____ :



OUR TEAM

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


LAB 5 WRITE-UP

Background Information

SYBR Green Dye


Single-Drop Fluorimeter


How the Fluorescence Technique Works




Procedure

Smart Phone Camera Settings
PHONE #1

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



PHONE #2

  • 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
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