Noi/NOTES/2012-5-24

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Revision as of 22:19, 24 May 2012 by >Noi (Created page with "* http://genome-tech.ucsd.edu/LabNotes/index.php/noi:DMR220k_LabNotes '''Link to calendar''' = DMR 330k BSPP capture of samples from Harvard's group, ASM and ASCM in human...")
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DMR 330k BSPP capture of samples from Harvard's group, ASM and ASCM in human cells project

  • Will be using gDNA sent by Anwesha on 2012_05_24
Sample IDs Conc. (ng.ul) by Nanodrop
(from Harvard)
Amount (ug) in 40ul
GM gDNA 4-5-12 64.52 2.58
P10E3 gDNA 4-5-12 37.86 1.51
DF2 gDNA 4-5-12 70.00 2.80
H0 gDNA 4-5-12 84.52 3.38
H7 gDNA 4-5-12 184.33 7.37
H14 gDNA 4-5-12 167.18 6.69
H16 gDNA 4-5-12 120.60 4.82
  • After confirming concentration by Nanodrop, the conc. I got pretty close to the conc. they labeled.

Bisulfite conversion

Reagent prep
Add the following reagents to CT Conversion Reagent (1tube)
 - H2O                            900ul
 - M-Dissolving Buffer      50ul
 - M-Dilution Buffer       300ul
Mix at room temperature with frequent vortexing or shaking for 15 minutes
Sample IDs Conc. (ng/ul) Volume for 1200ng LabID ID H2O Total amount (ng) CT conversion reagent (ul) Total volume (ul)
GM gDNA 4-5-12 64.52 18.60 GM 1.40 1200.00 130.00 150.00
P10E3 gDNA 4-5-12 37.86 20.00 P10E 0.00 757.20 130.00 150.00
DF2 gDNA 4-5-12 70.00 17.14 DF2 2.86 1200.00 130.00 150.00
H0 gDNA 4-5-12 84.52 14.20 H0 5.80 1200.00 130.00 150.00
H7 gDNA 4-5-12 184.33 6.51 H7 13.49 1200.00 130.00 150.00
H14 gDNA 4-5-12 167.18 7.18 H14 12.82 1200.00 130.00 150.00
H16 gDNA 4-5-12 120.60 9.95 H16 10.05 1200.00 130.00 150.00
GM+H0:: 1:1 9.3 (GM)+ 7.1 (H0) GM+H0 3.60 1200.13 130.00 150.00
Program
  98°C for 10 minutes
  64°C for 2.5 hours
  4°C storage up to 20 hours
Measure conc. with ssDNA Qubit assay (used 1ul of bis-cvt gDNA)