BME100 s2015:Group8 12pmL5: Difference between revisions
(26 intermediate revisions by 3 users not shown) | |||
Line 14: | Line 14: | ||
{| style="wikitable" width="700px" | {| style="wikitable" width="700px" | ||
|- valign="top" | |- valign="top" | ||
| [[Image: | | [[Image:BME100Priscilla.png|100px|thumb|Name: Priscilla Hernandez]] | ||
| [[Image:BME100Group8w.jpg|100px|thumb|Name: Alwaleed Alsahafi]] | |||
| [[Image: | | [[Image:BME103Vicky.jpg|100px|thumb|Name: Victoria Sanford]] | ||
| [[Image: | | [[Image:Sarah9551.jpg|100px|thumb|Name: Sarah Soaf]] | ||
| [[Image: | | [[Image:Me_and_me.jpg|100px|thumb|Name: Taylor Simone Woods]] | ||
| [[Image: | |||
|} | |} | ||
<!-- Note: Delete any image placeholders that you do not need. --> | <!-- Note: Delete any image placeholders that you do not need. --> | ||
Line 30: | Line 30: | ||
'''Smart Phone Camera Settings'''<br> | '''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. --> | <!-- 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: | * Type of Smartphone: Samsung Galaxy SIII | ||
** Flash: | ** Flash: off | ||
** ISO setting: | ** ISO setting: auto | ||
** White Balance: | ** White Balance: auto | ||
** Exposure: | ** Exposure: 0 | ||
** Saturation: | ** Saturation: 0 | ||
** Contrast: | ** Contrast: 0 | ||
Line 43: | Line 43: | ||
<!-- INSTRUCTIONS: Type the distance between your phone cradle and the drop after the equal sign. --> | <!-- 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 = 10 cm | ||
Line 49: | Line 49: | ||
{| {{table}} width=700 | {| {{table}} width=700 | ||
|- | |- | ||
| | | Initial Concentration of 2X Calf Thymus DNA Solution (μg/mL) || Volume of the 2X DNA Solution (μL) || Volume of the SYBR Green I Solution (μL) || Final Concentration of 2X Calf Thymus DNA Solution (μg/mL) | ||
|- | |||
| 0 || 80 || 80 || 0 | |||
|- | |||
| 0.25 || 80 || 80 || 0.125 | |||
|- | |- | ||
| | | 0.5 || 80 || 80 || 0.25 | ||
|- | |- | ||
| | | 1 || 80 || 80 || 0.5 | ||
|- | |||
| 2 || 80 || 80 || 1 | |||
|- | |||
| 5 || 80 || 80 || 2.5 | |||
|} | |} | ||
Line 61: | Line 69: | ||
'''Placing Samples onto the Fluorimeter''' | '''Placing Samples onto the Fluorimeter''' | ||
# ' | # Put on gloves. Then find the smooth side of the slide. | ||
# | # Retrieve a fluorimeter from the TA and take it to your group's table. | ||
# | # Put the slide from before in its place on the fluorimeter, making sure the smooth side is facing down. | ||
# ' | # Open the camera app, turn on the timer for 3-5 seconds, and put it on the craddle. | ||
# Make sure the camera has a good view of the slide by adjusting either the height of the fluorimeter or the camera. | |||
# Using a micropipette, take 80 micro liters of SYBR Green I solution and carefully put it between the front two clear circles of the slide. | |||
# Now put 80 micro liters of the sample/calibration over the SYBR Green I drop. | |||
# Make sure the that the light is hitting the drop in the middle and goes through the other side by adjust the slide. | |||
# The camera should be at closest 4 centimeters and focused. Record how far the camera is from the fluorimeter. | |||
# Cover the fluorimeter with the lightbox with one of the flaps up. | |||
# Double check that the camera is focused on the drop. | |||
# Start the camera's timer and take the last flap down. | |||
# Once the picture is taken, dispose of the 160 micro liter drop. | |||
# Move on to the next position on the slide. | |||
# Repeat all the steps for each sample. | |||
<br> | <br> | ||
Line 73: | Line 92: | ||
'''Representative Images of Negative and Positive Samples''' | '''Representative Images of Negative and Positive Samples''' | ||
<!-- 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. --> | <!-- 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: Pic7.jpg]] | |||
[[Image: Pic8.jpg]] | |||
Line 80: | Line 102: | ||
{| | |||
| align="center" style="background:#f0f0f0;"|'''Sample''' | |||
| align="center" style="background:#f0f0f0;"|'''Area''' | |||
| align="center" style="background:#f0f0f0;"|'''Mean''' | |||
| align="center" style="background:#f0f0f0;"|'''Min''' | |||
| align="center" style="background:#f0f0f0;"|'''Max''' | |||
| align="center" style="background:#f0f0f0;"|'''IntDen''' | |||
|- | |||
| H2O||122472||22.478||0||255||2752947 | |||
|- | |||
| 0.25||334592||33.476||0||255||11200689 | |||
|- | |||
| 0.5||193988||44.834||0||255||8697194 | |||
|- | |||
| 1||117636||55.702||0||255||6552507 | |||
|- | |||
| 2||189104||71.432||0||255||13506310 | |||
|- | |||
| 5||147412||73.233||0||255||10795378 | |||
|- | |||
| Negative||98980||70.295||0||255||6957848 | |||
|- | |||
| Positive||84628||73.603||0||255||6228875 | |||
|- | |||
| Patient2A||73900||37.997||0||255||2807950 | |||
|- | |||
| Patient2B||76620||41.83||0||255||3205014 | |||
|- | |||
| Patient2C||184944||84.546||0||255||15636268 | |||
|- | |||
| Patient1A||183223||61.598||0||255||11286081 | |||
|- | |||
| Patient1B||107880||39.85||0||255||4299046 | |||
|- | |||
| Patient1C||90812||65.6||0||255||5957275 | |||
|} | |||
[[Image: Pic1.jpg]] | |||
[[Image: Pic2.jpg]] | |||
[[Image: Pic3.jpg]] | |||
[[Image: Pic4.jpg]] | |||
[[Image: Pic5.jpg]] | |||
[[Image: Pic6.jpg]] | |||
[[Image: Pic9.jpg]] | |||
[[Image: Pic10.jpg]] | |||
[[Image: Pic11.jpg]] | |||
[[Image: Pic12.jpg]] | |||
[[Image: Pic13.jpg]] | |||
[[Image: Pic14.jpg]] | |||
'''Calibration curve'''<br> | '''Calibration curve'''<br> | ||
[[Image:Group_8_noon.jpg]] | |||
'''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 claculated 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 claculated initial concentration values.--> | ||
* Our positive control PCR result was | * Our positive control PCR result was 80 μg/mL | ||
* Our negative control PCR result was | * Our negative control PCR result was 80 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 1 (ID: 62525): The one sample with fluorescence seemed similar to the 2 μg/mL sample | ||
* Patient | * Patient 2 (ID: 86787): There was a slight observance of SYBR Green which seemed to range from nothing to .5 | ||
<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 1 (ID: 62525) : This patient possibly has SNP. The first two samples were cracked and the third appeared much more fluorescent so perhaps the amount of sample was not enough for detection when diluted. | ||
* Patient | * Patient 2 (ID: 86787) : This patient does not have SNP. | ||
Line 111: | Line 181: | ||
'''Background: About the Disease SNP''' | '''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. --> | <!-- INSTRUCTIONS: This content is from PCR Lab D. Write a summary, at least five sentences long, about the disease SNP in your own words. --> | ||
The Single Nucleotide Polymorphism (SNP) is a DNA sequence variation. One of the known SNPs is rs268 in the lipoprotein lipase (LPL) gene. rs268 is found in a species called Germline, which is a series of germ cells. This variation is located in chromosome 8: 19956018. It is considered as a pathogenic SNP and is associated with Coronary Heart disease. | |||
'''Primer Design and Testing''' | '''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. --> | <!-- 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. --> | ||
After testing the Non-disease primer, both forward and backward, we got successful results assuming calculating it with 50mM salt and 50nM annealing oligo concentration. However, the disease primer testing was not successful where there was " no match found." | |||
Non-disease reverse and forward primer: | |||
[[image:Non Disease.jpg]] | |||
[[image:Non-Disease_temp.jpg]] | |||
Disease reverse and forward primer: | |||
[[image:Disease_no_match.jpg]] | |||
[[image:Disease_temp.jpg]] | |||
<!-- Do not edit below this line --> | <!-- Do not edit below this line --> | ||
|} | |} |
Latest revision as of 00:10, 8 April 2015
BME 100 Spring 2015 | 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-UPProcedureSmart Phone Camera Settings
Data AnalysisRepresentative Images of Negative and Positive Samples
Image J Values for All Calibrator Samples
Observed results
Conclusions
SNP Information & Primer DesignBackground: About the Disease SNP The Single Nucleotide Polymorphism (SNP) is a DNA sequence variation. One of the known SNPs is rs268 in the lipoprotein lipase (LPL) gene. rs268 is found in a species called Germline, which is a series of germ cells. This variation is located in chromosome 8: 19956018. It is considered as a pathogenic SNP and is associated with Coronary Heart disease. Primer Design and Testing After testing the Non-disease primer, both forward and backward, we got successful results assuming calculating it with 50mM salt and 50nM annealing oligo concentration. However, the disease primer testing was not successful where there was " no match found."
Disease reverse and forward primer: |