BME100 s2016:Projects5: Difference between revisions

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<!-- Note: Delete any image placeholders that you do not need. -->
=LAB 5 WRITE-UP=
==PCR Reaction Report==
<!-- Write a summary of your team's experience with pipetting the samples to set up the reaction. Did the pre-lab reading help you? Did you understand the difference between the first and second stop on the pipettor? Did the final reactions have exactly the same amount of liquid? Was there any liquid left in the tubes that the DNA samples and PCR reaction mix? Did you have to change your
'''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. -->
* Type of Smartphone:
** Flash:
** ISO setting:
** White Balance:
** Exposure:
** Saturation:
** Contrast:
'''Camera set-up'''<br>
<!-- 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. -->
* Distance between the smart phone cradle and drop =
'''Placing Samples onto the Fluorimeter'''
# ''[Instructions: Step one, in your OWN words]''
# ''[Instructions: Step two, in your own words]''
# ''[Instructions: Step three, in your own words]''
# ''[Instructions: Step etc., in your own words]''
<br>
<!-- Note: Be sure to delete the instruction text in brackets: ''[ ]'' -->
==Data Collection and Analysis==
'''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. -->
'''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.  -->
TABLE GOES HERE
'''Calibration curves'''<br>
<!-- INSTRUCTIONS: Place images of your Excel plots (2 total) here. -->
'''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.  -->
'''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
'''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.-->
* 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 _____ :




Revision as of 08:54, 23 March 2016

BME 100 Spring 2016 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
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Wiki Editing Help


Lab 5: “PCR and Fluorescence Detection of DNA”

  • Content from PCR Lab C and Lab D
    • PCR Reactions
    • Procedure
    • Data Analysis

HW: Lab Report 5 (due 11/03/15 at 11:59 pm through OpenWetWare)

Grading Scheme:
10 points – Overall layout: Our Team section, grammar, style
10 points - Lab C content - PCR reaction report
15 points – Lab D content - Procedure: camera settings, calibration & solutions used for calibration, placing samples onto the fluorimeter
15 points – Lab D content - Data Analysis: representative images of samples, Image J values for all samples, fitting a straight line, PCR results summary
50 points – Peer Assessment

Rubric

    EXCELLENT ACCEPTABLE WEAK*
OVERALL LAYOUT OUR TEAM section 5 pts = Original & non-offensive images; real names 3 pts = More than half original images & information 1 pt = All default green & white avatars; default text
Grammar & style 5 pts = Composition & layout perfect throughout 3 pts = Few spelling errors; images too big or small 1 pt = Many errors
PCR REACTION REPORT Summary 10 pts = Complete description, good text formatting 5 pts = Poor composition 1 pt = Missing (only default text)
FLUORIMETER PROCEDURE Camera settings 5 pts = Type of smartphone; settings where applicable, or "N/A" 3 pt = Brand name only; vague 1 pts = Missing all info
Camera set-up 5 pts = Clear description; distance btwn. camera & drop included 3 pts = Missing one part of the information 2 pts = Only one sentence, missing distance
Placing samples onto the fluorimeter 5 pts = Steps are thorough, clear, and easy to follow 3 pts = Run-on paragraphs 1 pt = Instructions are vague/ incomplete
DATA COLLECTION & ANALYSIS Callibration: 3 drop images, data table, 2 plots with best fit lines 7 pts = Complete 5 pts = Missing one part, somewhat unorganized 3 pts = Missing two or more parts, very unorganized
PCR results: 2 drop images, data table, final results 8 pts = Complete 6 pts = Missing one part, somewhat unorganized 4 pts = Missing two or more parts, very unorganized

Note: *Empty/ plagiarized sections or borrowed images without references receive zero points


Important Information About Grading:

  • Plagiarism: Any images that are copy-pasted from the BME 100 workbook, from another group's Wiki page, or from the internet are considered as plaigiarism. Lab reports that contain any plagiarism will receive a zero and will be reported to James Collofello, Associate Dean for Academic and Student Affairs. Internet images (that are NOT from another group's or previous class's Wiki report) may be used as long as the source is properly cited.
  • Do not wait until the last minute to finish your report. Wiki pages are time-stamped after each "save". Only the version of your page that was saved by the deadline will be graded. Any changes made after the deadline will be ignored, no exceptions. Technical problems with the Wiki website must be reported at least 10 hours before the submission deadline.



Look for your Group's lab report link in the list of links on the right. If it is RED instead of blue, DO NOT CLICK ON IT!

If the link is red, type the name of your Group's lab report link exactly as shown in the following text field and click the Create Page button.

This should open up an Edit page that is pre-populated with a lab report template code.

<createbox> preload=Template:ASUBME100_s2016_L4 prefix=BME100_s2016: width=25 buttonlabel=Create Page </createbox>

Group1_W1030AM_L5 Group2_ W1030AM_L5 Group3_W1030AM_L5 Group4_W1030AM_L5 Group5_W1030AM_L5
Group6_W1030AM_L5 Group7_W1030AM_L5 Group8_W1030AM_L5 Group9_W1030AM_L5 Group10_W1030AM_L5
Group11_W1030AM_L5 Group12_W1030AM_L5 Group13_W1030AM_L5 Group14_W1030AM_L5 Group15_W1030AM_L5
Group16_W1030AM_L5 Group17_W1030AM_L5
 



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