Noi/NOTES/2012-8-23

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Revision as of 01:27, 24 August 2012 by >Noi
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Bisulfite conversion

  • Repeat bisulfite conversion and I will fill more info and reason of repeating
Lab IDs Conc. (ng/ul) Volume for 2000ng LabID ID H2O Total amount (ng) CT conversion reagent (ul) Total volume (ul)
GL-1 295.8 6.76 GL-1 13.24 2000.00 130.00 150.00
GL-2 220.6 9.07 GL-2 10.93 2000.00 130.00 150.00
GL-3 149.7 13.36 GL-3 6.64 2000.00 130.00 150.00
GL-4 172.3 11.61 GL-4 8.39 2000.00 130.00 150.00
GL-5 285.2 7.01 GL-5 12.99 2000.00 130.00 150.00
GL-6 296.6 6.74 GL-6 13.26 2000.00 130.00 150.00
GL-7 320.0 6.25 GL-7 13.75 2000.00 130.00 150.00
GL-8 339.3 5.89 GL-8 14.11 2000.00 130.00 150.00
GL-9 467.5 4.28 GL-9 15.72 2000.00 130.00 150.00
GL-10 431.7 4.63 GL-10 15.37 2000.00 130.00 150.00
GL-11 349.1 5.73 GL-11 14.27 2000.00 130.00 150.00
GL-12 234.5 8.53 GL-12 11.47 2000.00 130.00 150.00
GL-13** 72.2 20.00 GL-13 0.00 1444.80 130.00 150.00
GL-14 137.3 14.56 GL-14 5.44 2000.00 130.00 150.00
GL-15 207.5 9.64 GL-15 10.36 2000.00 130.00 150.00
GL-16 135.5 14.76 GL-16 5.24 2000.00 130.00 150.00
AL-1 226.6 8.83 AL-1 11.17 2000.00 130.00 150.00
AL-2 375.5 5.33 AL-2 14.67 2000.00 130.00 150.00
AL-3 256.8 7.79 AL-3 12.21 2000.00 130.00 150.00
AL-4 142.1 14.08 AL-4 5.92 2000.00 130.00 150.00
AL-5 140.1 14.27 AL-5 5.73 2000.00 130.00 150.00

330k BSPP capture set up

Probe normali
Subset ID Adjusted Multiplier(2012_05_22) Actual amount of probe required (probe:target ratio, 100:1) Multiplier F Probe concentration (ng/ul) Volume (ul) Volume for 75rxn (ul) Subset ID
DMR.s1 0.25 2.24 0.56 26.2 0.02 0.49 DMR.s1
DMR.s2 0.35 2.24 0.78 30.1 0.03 0.60 DMR.s2
DMR.s3 1.15 18.90 21.74 21.15 1.03 23.64 DMR.s3
DMR.s4 1.00 18.90 18.90 22.34 0.85 19.46 DMR.s4
DMR.s5 4.83 18.90 91.29 29 3.15 72.40 DMR.s5
DMR.Exp1 1.00 18.90 18.90 31.88 0.59 13.64 DMR.Exp1
DMR.Exp2 1.00 18.90 18.90 24.11 0.78 18.03 DMR.Exp2
DMR.Exp3 1.00 18.90 18.90 28.9 0.65 15.04 DMR.Exp3
1.05uM Oligo suppressor-set1 0.125 2.88 1.05uM Oligo suppressor-set1
1.05uM Oligo suppressor-set2 0.125 2.88 1.05uM Oligo suppressor-set2
  • This means that the maximum volume of bis-cvt gDNA is 42.15ul in total volume 55ul
Components 1rxn (ul) 23 rxn mix (ul)
10X AmpLigase Buffer 5.50 126.50
DMR330k probe mix (ul) 7.10 163.30
105nM Oligo suppressor 0.25 5.75
Total volume (ul) 12.85 295.55


Sample IDs Conc. (ng/ul) Volume for 250ng (ul) Sample IDs H2O Total amount of
bis-cvt gDNA (ng)
Probe mix (ul) 10X AmpLigase Buffer 1.05uM Oligo suppressor
set1 &2 (ul)
Total volume (ul)
GL-1 6.30 39.68 GL-1 2.47 250.00 7.10 5.50 0.25 55.00
GL-2 5.00 42.15 GL-2 0.00 210.75 7.10 5.50 0.25 55.00
GL-3 8.92 28.03 GL-3 14.12 250.00 7.10 5.50 0.25 55.00
GL-4 7.14 35.01 GL-4 7.14 250.00 7.10 5.50 0.25 55.00
GL-5* 5.34 42.15 GL-5* 0.00 225.08 7.10 5.50 0.25 55.00
GL-6## 3.97 42.15 GL-6## 0.00 167.34 7.10 5.50 0.25 55.00
GL-7* 5.30 42.15 GL-7* 0.00 223.40 7.10 5.50 0.25 55.00
GL-8* 5.08 42.15 GL-8* 0.00 214.12 7.10 5.50 0.25 55.00
GL-9 5.51 42.15 GL-9 0.00 232.25 7.10 5.50 0.25 55.00
GL-10 5.31 42.15 GL-10 0.00 223.82 7.10 5.50 0.25 55.00
GL-11 4.99 42.15 GL-11 0.00 210.33 7.10 5.50 0.25 55.00
GL-12 4.97 42.15 GL-12 0.00 209.49 7.10 5.50 0.25 55.00
GL-13 7.11 35.16 GL-13 6.99 250.00 7.10 5.50 0.25 55.00
GL-14 7.27 34.39 GL-14 7.76 250.00 7.10 5.50 0.25 55.00
GL-15 8.01 31.21 GL-15 10.94 250.00 7.10 5.50 0.25 55.00
GL-16 7.25 34.48 GL-16 7.67 250.00 7.10 5.50 0.25 55.00
AL-1 5.06 42.15 AL-1 0.00 213.28 7.10 5.50 0.25 55.00
AL-2 5.00 42.15 AL-2 0.00 210.75 7.10 5.50 0.25 55.00
AL-3 5.22 42.15 AL-3 0.00 220.02 7.10 5.50 0.25 55.00
AL-4 7.16 34.92 AL-4 7.23 250.00 7.10 5.50 0.25 55.00
AL-5 8.40 29.76 AL-5 12.39 250.00 7.10 5.50 0.25 55.00