Noi/NOTES/2014-5-23: Difference between revisions
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>Noi (Created page with "= BSPP capture of amplified DNA from Illumina using different 3 enzymes for polymerization = [[http://genome-tech.ucsd.edu/LabNotes/index.php/noi:DMR220k_LabNotes#2014 Link to...") |
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** Illumina Polymerase (black color) | ** Illumina Polymerase (black color) | ||
* I include sample C1, A1, and A2 in capture reaction, but not include GP1V4. This is may not necessary, but I want to make sure that there is no any background from the template itself. | * I include sample C1, A1, and A2 in capture reaction, but not include GP1V4. This is may not necessary, but I want to make sure that there is no any background from the template itself. | ||
* For cancer samples, I performed bisulfite conversion 6tubes of C1 and 3tubes of C2 samples (600ng gDNA for each tube). I used bisulfite treated DNA from different tubes for each reaction. There might me some variations of DNA amount in each reaction based on accuracy of DNA concentration quantification or pipetting. |
Revision as of 21:15, 26 May 2014
BSPP capture of amplified DNA from Illumina using different 3 enzymes for polymerization
- From previous experiment on 2014-05-13 [[1]], the results were inconclusive, and I lacked positive control. Dr. Zhang suggested to repeat experiment on few samples from Illumina and include cancer sample DNA as control.
- I need to prepare more GP1V4 BSPP.
Sample list and experimental design
- Cancer sample #1 or C1 (BXPC3)
- Cancer sample #2 or C2 (U87MG)
- Illumina amplified DNA, A1
- Illumina amplifed DNA, A2
- Capture with 500:1 GP1V4:target ratio (total amount in each reaction ~13ng)
- Bisulfite treated DNA/amplified DNA amount 200ng
- Add different enzyme in SLN mix,
- Stoffel (blue color)
- Hemo KlenTaq (red color)
- Illumina Polymerase (black color)
- I include sample C1, A1, and A2 in capture reaction, but not include GP1V4. This is may not necessary, but I want to make sure that there is no any background from the template itself.
- For cancer samples, I performed bisulfite conversion 6tubes of C1 and 3tubes of C2 samples (600ng gDNA for each tube). I used bisulfite treated DNA from different tubes for each reaction. There might me some variations of DNA amount in each reaction based on accuracy of DNA concentration quantification or pipetting.