Noi/NOTES/2014-5-23: Difference between revisions

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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

[Link to calendar]

  • 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.