BME100 f2016:Group16 W8AM L5: Difference between revisions
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| [[Image:Me1.jpg|100px|thumb|Name: Nandini Sharma]] | | [[Image:Me1.jpg|100px|thumb|Name: Nandini Sharma]] | ||
| [[Image: | | [[Image:Firetruck.jpg|100px|thumb|Name: Christian Forbus]] | ||
| [[Image: | | [[Image:jaredmacanas.jpg|100px|thumb|Name: Jared Macanas]] | ||
| [[Image: | | [[Image:BME_100_Cropped_Picture.jpg|100px|thumb|Name: TJ Smith]] | ||
| [[Image: | | [[Image:Openwetware_profile.JPG|100px|thumb|Name: Brandon Gandolf]] | ||
|} | |} | ||
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'''Imaging set-up'''<br> | '''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. --> | <!-- INSTRUCTIONS: In the space below, describe in detail how your team set up your device to capture images from the fluorimeter. --> | ||
When setting up our device to capture the images, we placed the phone, which in this case was an iPhone 7, in an upright position focused on the drop. We placed the phone approximately 7cm away from the drop and used a timer to capture the image. We used an eraser to help hold it in position while it was in the stand and then we used a folder to cover the back of the fluorimeter to keep all of the light out. | |||
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<!-- INSTRUCTIONS: In the space below, in your own words write the steps you performed to place samples onto the fluorimeter --> | <!-- INSTRUCTIONS: In the space below, in your own words write the steps you performed to place samples onto the fluorimeter --> | ||
# '' | # ''Step 1: First, we placed 80 microliters of SYBR Green 1 and 80 microliters of a calf thymus on the slide.'' | ||
# '' | # ''Step 2: Then, we placed the box over the stand we created to meet up with the height of the camera.'' | ||
# '' | # ''Step 3: Next, we aligned the drop to meet up with the LED light.'' | ||
# '' | # ''Step 4: Then, we focused the camera on the drop.'' | ||
<br> | <br> | ||
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<!-- 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. --> | <!-- 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. --> | ||
(1) 5 μg/mL sample | |||
[[Image:5ug-mL.png]] | |||
(2) 0.5 μg/mL sample | |||
[[Image:0.5ug-mL.png]] | |||
(3) zero DNA | |||
[[Image:0ug-mL.png]] | |||
'''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}} | |||
| align="center" style="background:#f0f0f0;" rowspan="2"|'''Initial Concentration of 2X Calf Thymus DNA solution (μg/mL)''' | |||
| align="center" style="background:#f0f0f0;" rowspan="2"|'''Final DNA concentration in SYBR Green I solution (μg/mL)''' | |||
| align="center" style="background:#f0f0f0;" rowspan="2"|'''Sample Number''' | |||
| align="center" style="background:#f0f0f0;" colspan="3"|'''RAWINTDEN DROP - BACKGROUND''' | |||
| align="center" style="background:#f0f0f0;" rowspan="2"|'''MEAN''' | |||
| align="center" style="background:#f0f0f0;" rowspan="2"|'''Standard Deviation''' | |||
|- | |||
|style="background:#f0f0f0;"|Image 1 | |||
|style="background:#f0f0f0;"|Image 2 | |||
|style="background:#f0f0f0;"|Image 3 | |||
|- | |||
| 0||0||C-6||14278351||13427774||14185926||13964017||466693.702 | |||
|- | |||
| 0.25||0.125||C-5||19226506||17073922||46566069||27622165.67||16441168.13 | |||
|- | |||
| 0.5||0.25||C-4||15721858||48006477||46168607||36632314||18132286.65 | |||
|- | |||
| 1||0.5||C-3||23466266||24932157||225536611||91311678||116244512.5 | |||
|- | |||
| 2||1||C-2||19196572||17899556||21911378||19669168.67||2047239.519 | |||
|- | |||
| 5||2.5||C-1||21911378||21225181||21391583||21509380.67||357943.8481 | |||
|- | |||
|} | |||
'''Calibration curves'''<br> | '''Calibration curves'''<br> | ||
<!-- INSTRUCTIONS: Place images of your Excel plots (2 total) here. --> | <!-- INSTRUCTIONS: Place images of your Excel plots (2 total) here. --> | ||
[[Image:Calibrationcurve1group16.png]] | |||
[[Image:CalibrationCurve2group16.png]] | |||
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<!-- 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. --> | <!-- 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. --> | ||
(1) Negative control PCR sample | |||
[[Image:PCRnegative.png]] | |||
(2) the Positive control PCR sample | |||
[[Image:PCRpositive.png]] | |||
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<!-- 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. --> | <!-- 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}} | |||
| align="center" style="background:#f0f0f0;"|'''PCR Product TUBE LABEL''' | |||
| align="center" style="background:#f0f0f0;"|'''MEAN (of RAWINTDEN DROP - BACKGROUND)''' | |||
| align="center" style="background:#f0f0f0;"|'''PCR Product Concentration (µg /mL)''' | |||
(Step 5 calculation) | |||
| align="center" style="background:#f0f0f0;"|'''Total Dilution''' | |||
| align="center" style="background:#f0f0f0;"|'''Initial PCR Product Concentration (µg /mL)''' | |||
(Step 6 calculation) | |||
|- | |||
| G16P||17325033.67||-2.112494389||12||-25.34993267 | |||
|- | |||
| G16N||9674297.333||-3.387617111||12||-40.65140533 | |||
|- | |||
| G161-1||11230618.75||-3.128230208||12||-37.5387625 | |||
|- | |||
| G161-2||25825943.33||-0.695676111||12||-8.348113333 | |||
|- | |||
| G161-3||12141144||-2.976476||12||-35.717712 | |||
|- | |||
| G162-1||15417670||-2.430388333||12||-29.16466 | |||
|- | |||
| G162-2||16374828.67||-2.270861889||12||-27.25034267 | |||
|- | |||
| G162-3||10571880.33||-3.238019944||12||-38.85623933 | |||
|- | |||
|} | |||
'''PCR Results: Summary''' | '''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.--> | <!-- 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 | * Our positive control PCR result was -25.34993267 μg/mL | ||
* Our negative control PCR result was | * Our negative control PCR result was -40.65140533 μg/mL | ||
<u>Observed results</u> | <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 --> | <!-- 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 30857 : This patient appeared to be negative because the sample was clear, just like the negative control. | ||
* Patient | * Patient 75331 : This patient appeared to be positive because the sample was fluorescent green, just like the positive control. | ||
<u>Conclusions</u> | <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. --> | <!-- 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 30857 :Patients initial concentration values were closest to positive control. So, the patients results are positive. | ||
* Patient | * Patient 75331: Patients intial concentration values were closest to negative control. So, the patients results are negative. | ||
Latest revision as of 23:39, 8 November 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
LAB 5 WRITE-UPPCR Reaction ReportFor Part C of the lab, our group prepped our samples for the Polymerase Chain Reaction. To complete this we needed to know proper lab procedure such as how to pipette and label. The pre-lab was helpful in informing us of the steps in the process of pipetting. The first step was to label the tubes. We were able to maintain the labeling structure that we established in the initial parts of this lab. Once we had the pipette it was easy to fell the difference between the first and second stop. It takes more force to get to the second stop than it does to get to the first stop. While pipetting, it was difficult to ensure that all the liquid was all collected. It took a few tries on the first few tubes to ensure all the liquid was empties. By the end we were able to ensure that majority of the 50 microliters of the PCR mix and each sample were pipetted into the tubes. The overall process was tedious because of the amount of time it took but it was fairly simple and easy to understand. Fluorimeter ProcedureImaging set-up
Placing Samples onto the Fluorimeter
Data Collection and AnalysisImages of High, Low, and Zero Calf Thymus DNA (1) 5 μg/mL sample (2) 0.5 μg/mL sample (3) zero DNA
Calibration curves
Images of Our PCR Negative and Positive Controls (1) Negative control PCR sample (2) the Positive control PCR sample
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