BME100 f2016:Group2 W8AM L5: Difference between revisions

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Materials:
{|{{table}} width="800"
*Lab coat
*Safety goggles
*Disposable gloves
*CR reaction mix, 8 tubes, 50 µL each (mix contains Taq DNA polymerase, MgCl2, and dNTP’s)
*DNA/ primer mix, 8 tubes, 50 µL each (each mix contains a different template DNA all tubes have the same forward primer and reverse primer)
*A strip of empty PCR tubes
*Disposable pipette tips
*Cup for discarded tips
*Micropipettor
*OpenPCR machine
 
 
{| {{table}}
|-
|-
| Tube Label || PCR Reaction Sample || Patient ID
|style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]]<span style="font-size:22px;"> BME 100 Fall 2016</span>
|style="background-color: #F2F2F2" | [[BME100_f2016 | <font face="trebuchet ms" style="color: #808080"> '''Home''' </font>]]<br>[[BME100_f2016:People | <font face="trebuchet ms" style="color: #808080"> '''People''' </font>]]<br>[[BME100_f2016:Projects1 | <font face="trebuchet ms" style="color: #808080"> '''Lab Write-Up 1''' </font>]] | [[BME100_f2016:Projects2 | <font face="trebuchet ms" style="color: #808080"> '''Lab Write-Up 2''' </font>]] | [[BME100_f2016:Projects3 | <font face="trebuchet ms" style="color: #808080"> '''Lab Write-Up 3''' </font>]]<br>[[BME100_f2016:Projects4 | <font face="trebuchet ms" style="color: #808080"> '''Lab Write-Up 4''' </font>]] | [[BME100_f2016:Projects5 | <font face="trebuchet ms" style="color: #808080"> '''Lab Write-Up 5''' </font>]] | [[BME100_f2016:Projects6 | <font face="trebuchet ms" style="color: #808080"> '''Lab Write-Up 6''' </font>]]<br>[[BME100_f2016:Logistics | <font face="trebuchet ms" style="color: #808080"> '''Course Logistics For Instructors''' </font>]] <br>[[BME100_f2016:Photos | <font face="trebuchet ms" style="color: #808080"> '''Photos''' </font>]] <br>[[BME100_f2016:WikiHelp | <font face="trebuchet ms" style="color: #808080"> '''Wiki Editing Help''' </font>]]
|-
|-
| G2 P || Positive Control || none
| style="background-color: #ffcc66; padding: 5px;" colspan="2" | [[Image:BME494_Asu_logo.png]]
|-
| G2 N || Negative Control || none
|-
| G2 1-1 || Patient 1, replicate 1 ||
|-
G2 1-2 || Patient 1, replicate 2 ||
|-
| G2 1-3 || Patient 1, replicate 3 ||
|-
| G2 2-1 || Patient 2, replicate 1 ||
|-
G2 2-2 || Patient 2, replicate 2 ||
|-
| G2 2-3 || Patient 2, replicate 3 ||
|-
|-
| 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|Yesenia Barrera Millan]]
| [[Image:BME103student.jpg|100px|thumb|Mariam El Sheikha]]
| [[Image:BME103student.jpg|100px|thumb|Tori Johnson]]
| [[Image:BME103student.jpg|100px|thumb|Vishvak Rangarajan]]
|}
<!-- 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 labeling scheme? -->
==Fluorimeter Procedure==
'''Imaging set-up'''<br>
<!-- INSTRUCTIONS: In the space below, describe in detail how your team set up your device to capture images from the fluorimeter. -->
'''Placing Samples onto the Fluorimeter'''
<!-- INSTRUCTIONS: In the space below, in your own words write the steps you performed to place 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 _____ :
<!-- Do not edit below this line -->
|}
|}

Revision as of 17:38, 25 October 2016

BME 100 Fall 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
Photos
Wiki Editing Help

OUR TEAM

Yesenia Barrera Millan
Mariam El Sheikha
Tori Johnson
Vishvak Rangarajan


LAB 5 WRITE-UP

PCR Reaction Report

Fluorimeter Procedure

Imaging set-up



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 Collection and Analysis

Images of High, Low, and Zero Calf Thymus DNA


Calibrator Mean Values


TABLE GOES HERE


Calibration curves


Images of Our PCR Negative and Positive Controls


PCR Results: PCR concentrations solved

TABLE GOES HERE


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 _____ :



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