BME100 s2015:Group17 12pmL5: Difference between revisions
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'''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. --> | ||
*CALIBRATION | |||
**PART 1 | |||
[[Image:part1calibration.png]] | |||
**PART 2 | |||
[[Image:part2calibration.png]] | |||
*PCR REACTION | |||
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'''Image J Values for All Calibrator Samples''' | '''Image J Values for All Calibrator Samples''' | ||
<!-- INSTRUCTIONS: Show a table for the ImageJ calf thymus DNA data. '''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 a table for the ImageJ calf thymus DNA data. '''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 1 | |||
[[Image:TABLE1CALIBRATION.png]] | |||
*TABLE2 | |||
[[Image:TABLE2CALIBRATION.png]] | |||
'''Calibration curve'''<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. --> | ||
[[Image:CALIBRATIONGRAPH.png]] | |||
'''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 561 μg/mL | ||
* Our negative control PCR result was | * Our negative control PCR result was -357 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 48611 : | ||
* Patient | **Qualitative - The images looked like a bubble in the distance. Compared to the positive control the images were darker, and more similar to the negative control image. | ||
**Quantitative: These numbers are negative values, which is very obscure. This may have been a result from poor calibration. | |||
* Patient 56653 : | |||
**Qualitative: Much like patient 1, this patient had images similar to the negative control than the positive control. | |||
**Quantitative: These numbers are also very obscure, demonstrating negative concentration values. | |||
<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 48611 : This patient is more similar to the negative control than the positive control once the qualitative and quantitative values were taken into consideration. | ||
* Patient | * Patient 56653 : Much like patient 48611, the data demonstrates that this patient is also closer to the negative control. | ||
Revision as of 16:00, 1 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
Calibration curve
Observed results
Conclusions
SNP Information & Primer DesignBackground: About the Disease SNP SNP, single nucleotide polymorphism is a DNA sequence variation occurring within a small population where a single base, A, T, C, or G differs between paired chromosomes or biological species. SNP are one of the most important genetic mutations that impact common disease. SNP results from replication errors and DNA damage, this phenomenon occurs exactly once in human evolution. Only sometimes does SNP have a correlation to a certain disease or trait. SNP has several applications in medicine such as gene discovery, allele mapping, and drug response prediction. Primer Design and Testing Results obtained from this lab were used to analyze the DNA sequence of two patients, one with a disease and the other without a disease. This lab demonstrated that primers bind to a certain region of a DNA sequence in order for the amplification of a small sample of DNA. Amplification occurs in two different directions on the DNA strand, the 5` and 3` ends. The 5` primers begins its sequence at the origin of the disease SNP variation location of 34370656. This was the location in the human genome where a thymine nucleotide has been mutated to a cytosine nucleotide, such a mutation results in the SNP disease that is seen in one of the patients. We used the UCSC In-Silico PCR website to test the non-disease primer to match the rs19956218 sequence.
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