Noi/NOTES/2014-5-23

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Revision as of 21:15, 26 May 2014 by >Noi
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BSPP capture of amplified DNA from Illumina using different 3 enzymes for polymerization

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  • 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.