Noi/NOTES/2011-8-14: Difference between revisions

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| G7*||53.66||20.00||G7*||0.00||1073.20||130.00||150.00
| G7*||53.66||20.00||G7*||0.00||1073.20||130.00||150.00
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| H7*||55.88||20.00||H8*||0.00||1117.60||130.00||150.00
| H7*||55.88||20.00||H7*||0.00||1117.60||130.00||150.00
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| A8*||59.88||20.00||A8*||0.00||1197.60||130.00||150.00
| A8*||59.88||20.00||A8*||0.00||1197.60||130.00||150.00

Revision as of 21:46, 14 August 2011

BSPP DMR330k capture of brain sample from Dr. Ophoff's lab (UCLA)

  • August 1, 2011, received 96 samples from Dr. Ophoff's lab
  • Tina Wang confirmed the concentration of each sample was about 50ng/ul
  • The concentrations were determined again by Nanadrop, and it turned out that the concentrations were vere varied. The volume of the gDNA needed to be adjust when perform bisulfite conversion
  • Note: The ratio of 260/230nm of most of the samples were very low, so I assumed higj salt contamination.

Nanodrop measurement

Well ID ng/ul Well ID ng/ul Well ID ng/ul Well ID ng/ul Well ID ng/ul Well ID ng/ul Well ID ng/ul Well ID ng/ul Well ID ng/ul Well ID ng/ul Well ID ng/ul Well ID ng/ul
A1 127.53 A2 101.77 A3 104.16 A4 89.42 A5 108.53 A6 98.50 A7 71.86 A8 59.88 A9 76.42 A10 59.93 A11 152.47 A12 74.20
B1 214.10 B2 109.05 B3 128.33 B4 80.22 B5 108.85 B6 74.95 B7 39.82 B8 85.67 B9 228.10 B10 72.25 B11 90.51 B12 92.20
C1 98.39 C2 106.42 C3 90.52 C4 114.26 C5 100.28 C6 91.90 C7 79.72 C8 96.65 C9 119.19 C10 69.85 C11 106.38 C12 46.85
D1 102.29 D2 94.38 D3 75.38 D4 119.02 D5 109.51 D6 63.31 D7 100.77 D8 128.37 D9 269.45 D10 129.33 D11 88.70 D12 68.39
E1 90.70 E2 84.67 E3 139.81 E4 90.16 E5 98.92 E6 76.35 E7 197.06 E8 89.01 E9 49.91 E10 62.05 E11 78.12 E12 83.77
F1 55.57 F2 108.48 F3 67.75 F4 117.73 F5 114.30 F6 77.34 F7 60.37 F8 95.33 F9 86.00 F10 139.09 F11 61.46 F12 53.64
G1 111.01 G2 62.01 G3 98.83 G4 133.36 G5 166.66 G6 100.09 G7 53.66 G8 84.04 G9 593.63 G10 189.64 G11 111.77 G12 106.40
H1 108.95 H2 57.54 H3 83.68 H4 90.89 H5 100.31 H6 76.76 H7 55.88 H8 144.05 H9 51.54 H10 70.48 H11 125.43 H12 74.57


Bisulfite conversion

  • Used EZ-96 DNA Methylation-Gold™ Kit (deep well format) Cat#D5008
Sample ID ng/ul Volume for 1200ng Sample ID H2O Total amount (ng) CT conversion reagent (ul) Total volume (ul)
A1 127.53 9.41 A1 10.59 1200.00 130.00 150.00
B1 214.10 5.60 B1 14.40 1200.00 130.00 150.00
C1 98.39 12.20 C1 7.80 1200.00 130.00 150.00
D1 102.29 11.73 D1 8.27 1200.00 130.00 150.00
E1 90.70 13.23 E1 6.77 1200.00 130.00 150.00
F1* 55.57 20.00 F1* 0.00 1111.40 130.00 150.00
G1 111.01 10.81 G1 9.19 1200.00 130.00 150.00
H1 108.95 11.01 H1 8.99 1200.00 130.00 150.00
A2 101.77 11.79 A2 8.21 1200.00 130.00 150.00
B2 109.05 11.00 B2 9.00 1200.00 130.00 150.00
C2 106.42 11.28 C2 8.72 1200.00 130.00 150.00
D2 94.38 12.71 D2 7.29 1200.00 130.00 150.00
E2 84.67 14.17 E2 5.83 1200.00 130.00 150.00
F2 108.48 11.06 F2 8.94 1200.00 130.00 150.00
G2 62.01 19.35 G2 0.65 1200.00 130.00 150.00
H2* 57.54 20.00 H2* 0.00 1150.80 130.00 150.00
A3 104.16 11.52 A3 8.48 1200.00 130.00 150.00
B3 128.33 9.35 B3 10.65 1200.00 130.00 150.00
C3 90.52 13.26 C3 6.74 1200.00 130.00 150.00
D3 75.38 15.92 D3 4.08 1200.00 130.00 150.00
E3 139.81 8.58 E3 11.42 1200.00 130.00 150.00
F3 67.75 17.71 F3 2.29 1200.00 130.00 150.00
G3 98.83 12.14 G3 7.86 1200.00 130.00 150.00
H3 83.68 14.34 H3 5.66 1200.00 130.00 150.00
A4 89.42 13.42 A4 6.58 1200.00 130.00 150.00
B4 80.22 14.96 B4 5.04 1200.00 130.00 150.00
C4 114.26 10.50 C4 9.50 1200.00 130.00 150.00
D4 119.02 10.08 D4 9.92 1200.00 130.00 150.00
E4 90.16 13.31 E4 6.69 1200.00 130.00 150.00
F4 117.73 10.19 F4 9.81 1200.00 130.00 150.00
G4 133.36 9.00 G4 11.00 1200.00 130.00 150.00
H4 90.89 13.20 H4 6.80 1200.00 130.00 150.00
A5 108.53 11.06 A5 8.94 1200.00 130.00 150.00
B5 108.85 11.02 B5 8.98 1200.00 130.00 150.00
C5 100.28 11.97 C5 8.03 1200.00 130.00 150.00
D5 109.51 10.96 D5 9.04 1200.00 130.00 150.00
E5 98.92 12.13 E5 7.87 1200.00 130.00 150.00
F5 114.30 10.50 F5 9.50 1200.00 130.00 150.00
G5 166.66 7.20 G5 12.80 1200.00 130.00 150.00
H5 100.31 11.96 H5 8.04 1200.00 130.00 150.00
A6 98.50 12.18 A6 7.82 1200.00 130.00 150.00
B6 74.95 16.01 B6 3.99 1200.00 130.00 150.00
C6 91.90 13.06 C6 6.94 1200.00 130.00 150.00
D6 63.31 18.95 D6 1.05 1200.00 130.00 150.00
E6 76.35 15.72 E6 4.28 1200.00 130.00 150.00
F6 77.34 15.52 F6 4.48 1200.00 130.00 150.00
G6 100.09 11.99 G6 8.01 1200.00 130.00 150.00
H6 76.76 15.63 H6 4.37 1200.00 130.00 150.00
A7 71.86 16.70 A7 3.30 1200.00 130.00 150.00
B7** 39.82 20.00 B7** 0.00 796.40 130.00 150.00
C7 79.72 15.05 C7 4.95 1200.00 130.00 150.00
D7 100.77 11.91 D7 8.09 1200.00 130.00 150.00
E7 197.06 6.09 E7 13.91 1200.00 130.00 150.00
F7 60.37 19.88 F7 0.12 1200.00 130.00 150.00
G7* 53.66 20.00 G7* 0.00 1073.20 130.00 150.00
H7* 55.88 20.00 H7* 0.00 1117.60 130.00 150.00
A8* 59.88 20.00 A8* 0.00 1197.60 130.00 150.00
B8 85.67 14.01 B8 5.99 1200.00 130.00 150.00
C8 96.65 12.42 C8 7.58 1200.00 130.00 150.00
D8 128.37 9.35 D8 10.65 1200.00 130.00 150.00
E8 89.01 13.48 E8 6.52 1200.00 130.00 150.00
F8 95.33 12.59 F8 7.41 1200.00 130.00 150.00
G8 84.04 14.28 G8 5.72 1200.00 130.00 150.00
H8 144.05 8.33 H8 11.67 1200.00 130.00 150.00
A9 76.42 15.70 A9 4.30 1200.00 130.00 150.00
B9 228.10 5.26 B9 14.74 1200.00 130.00 150.00
C9 119.19 10.07 C9 9.93 1200.00 130.00 150.00
D9 269.45 4.45 D9 15.55 1200.00 130.00 150.00
E9* 49.91 20.00 E9* 0.00 998.20 130.00 150.00
F9 86.00 13.95 F9 6.05 1200.00 130.00 150.00
G9*** 593.63 2.02 G9*** 17.98 1200.00 130.00 150.00
H9* 51.54 20.00 H9* 0.00 1030.80 130.00 150.00
A10 59.93 20.00 A10 0.00 1198.60 130.00 150.00
B10 72.25 16.61 B10 3.39 1200.00 130.00 150.00
C10 69.85 17.18 C10 2.82 1200.00 130.00 150.00
D10 129.33 9.28 D10 10.72 1200.00 130.00 150.00
E10 62.05 19.34 E10 0.66 1200.00 130.00 150.00
F10 139.09 8.63 F10 11.37 1200.00 130.00 150.00
G10 189.64 6.33 G10 13.67 1200.00 130.00 150.00
H10 70.48 17.03 H10 2.97 1200.00 130.00 150.00
A11 152.47 7.87 A11 12.13 1200.00 130.00 150.00
B11 90.51 13.26 B11 6.74 1200.00 130.00 150.00
C11 106.38 11.28 C11 8.72 1200.00 130.00 150.00
D11 88.70 13.53 D11 6.47 1200.00 130.00 150.00
E11 78.12 15.36 E11 4.64 1200.00 130.00 150.00
F11 61.46 19.52 F11 0.48 1200.00 130.00 150.00
G11 111.77 10.74 G11 9.26 1200.00 130.00 150.00
H11 125.43 9.57 H11 10.43 1200.00 130.00 150.00
A12 74.20 16.17 A12 3.83 1200.00 130.00 150.00
B12 92.20 13.02 B12 6.98 1200.00 130.00 150.00
C12** 46.85 20.00 C12* 0.00 937.00 130.00 150.00
D12 68.39 17.55 D12 2.45 1200.00 130.00 150.00
E12 83.77 14.32 E12 5.68 1200.00 130.00 150.00
F12* 53.64 20.00 F12* 0.00 1072.80 130.00 150.00
G12 106.40 11.28 G12 8.72 1200.00 130.00 150.00
H12 74.57 16.09 H12 3.91 1200.00 130.00 150.00
  • Eluted volume 20ul with Elution buffer. After Qubit ss-DNA assay the total yields will be calculated based on ~16ul left in the well.
  • Note:
    • *= Total amount in bis-cvt lower than 1200ng, but still above 1000ng
    • ** or ***= Performed two bis-cvt (one in the plate and one in the column (B7 (conc, too low, G9 (conc. too high)
    • ***= conc. too high