Noi/NOTES/2012-8-23: Difference between revisions
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>Noi (Created page with "= Bisulfite conversion = * Repeat bisulfite conversion and I will fill more info and reason of repeating {| {{table}} border = 1 | align="center" style="background:#f0f0f0;"|'...") |
>Noi No edit summary |
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| AL-5||140.1||14.27||AL-5||5.73||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 | |||
{| {{table}} border = 1 | |||
| align="center" style="background:#f0f0f0;"|'''Subset ID''' | |||
| align="center" style="background:#f0f0f0;"|'''Adjusted Multiplier(2012_05_22)''' | |||
| align="center" style="background:#f0f0f0;"|'''Actual amount of probe required (probe:target ratio, 100:1)''' | |||
| align="center" style="background:#f0f0f0;"|'''Multiplier F''' | |||
| align="center" style="background:#f0f0f0;"|'''Probe concentration (ng/ul)''' | |||
| align="center" style="background:#f0f0f0;"|'''Volume (ul)''' | |||
| align="center" style="background:#f0f0f0;"|'''Volume for 75rxn (ul)''' | |||
| align="center" style="background:#f0f0f0;"|'''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 | |||
{| {{table}} border = 1 | |||
| align="center" style="background:#f0f0f0;"|'''Components''' | |||
| align="center" style="background:#f0f0f0;"|'''1rxn (ul)''' | |||
| align="center" style="background:#f0f0f0;"|'''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 | |||
|} | |||
<br> | |||
{| {{table}} border = 1 | |||
| align="center" style="background:#f0f0f0;"|'''Sample IDs''' | |||
| align="center" style="background:#f0f0f0;"|'''Conc. (ng/ul)''' | |||
| align="center" style="background:#f0f0f0;"|'''Volume for 250ng (ul)''' | |||
| align="center" style="background:#f0f0f0;"|'''Sample IDs''' | |||
| align="center" style="background:#f0f0f0;"|'''H2O''' | |||
| align="center" style="background:#f0f0f0;"|'''Total amount of<br> bis-cvt gDNA (ng)''' | |||
| align="center" style="background:#f0f0f0;"|'''Probe mix (ul)''' | |||
| align="center" style="background:#f0f0f0;"|'''10X AmpLigase Buffer''' | |||
| align="center" style="background:#f0f0f0;"|'''1.05uM Oligo suppressor<br> set1 &2 (ul)''' | |||
| align="center" style="background:#f0f0f0;"|'''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 | |||
|} | |} |
Revision as of 01:27, 24 August 2012
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 |