Noi/NOTES/2011-8-9

From ZhangLabWiki
Revision as of 21:39, 12 August 2011 by >Noi
Jump to navigation Jump to search

Repeat BSPP DMR330k capture of GA and control gDNA from blood sample

  • 2011_08_08: received new plate of GA sample plate1 (so called GA plate1-2) from Ling. She prepared gDNA concentration 100ng/ul and volume ~10-15ul)
  • However, after measured the conc. by Nanodrop the conc. of the samples were very varied and were not enough for bisulfite conversion. The concentrations in plate 1-1 were verified by Nanodrop again. Then I calculated the volume required for 1200ng. I didn't pool the gDNA from the two plates because they have different conc. and some sample has too low conc.
  • Used EZ-96 DNA Methylation-Gold™ Kit (deep well format) Cat#D5008
  • Eluted volume 20ul with Elution buffer. After Qubit ss-DNA assay the total yields will be calculated based on ~16ul left in the well.
Sample ID Conc. (ng/ul) Volume plate1-2 enough? Volume plate1-2 (ul) Amount plate1-2 Conc. plate#1-1 (ng/ul) Volume plate 1-1 Sample ID H2O (ul) Total volume (ul) CT conversion reagent (ul) Total volume (ul)
A1 177.30 6.77 1200.00 A1 13.23 20.00 130.00 150.00
B1 104.91 11.44 1200.00 B1 8.56 20.00 130.00 150.00
C1 108.20 11.09 1200.00 C1 8.91 20.00 130.00 150.00
D1 95.30 12.59 1200.00 D1 7.41 20.00 130.00 150.00
E1 142.71 8.41 1200.00 E1 11.59 20.00 130.00 150.00
F1 130.28 9.21 1200.00 F1 10.79 20.00 130.00 150.00
G1 195.56 6.14 1200.00 G1 13.86 20.00 130.00 150.00
H1 126.34 9.50 1200.00 H1 10.50 20.00 130.00 150.00
A2 119.33 10.06 1200.00 A2 9.94 20.00 130.00 150.00
B2 135.56 8.85 1200.00 B2 11.15 20.00 130.00 150.00
C2 48.65 no 10.00 486.50 94.48 7.55 C2 2.45 20.00 130.00 150.00
D2 242.84 4.94 1200.00 D2 15.06 20.00 130.00 150.00
E2 109.93 10.92 1200.00 E2 9.08 20.00 130.00 150.00
F2 139.81 8.58 1200.00 F2 11.42 20.00 130.00 150.00
G2 87.91 13.65 1200.00 G2 6.35 20.00 130.00 150.00
H2 64.74 no 15.00 971.10 138.55 1.65 H2 3.35 20.00 130.00 150.00
A3 121.07 9.91 1200.00 A3 10.09 20.00 130.00 150.00
B3 103.64 11.58 1200.00 B3 8.42 20.00 130.00 150.00
C3 76.09 no 12.00 913.08 144.84 1.98 C3 6.02 20.00 130.00 150.00
D3 154.51 7.77 1200.00 D3 12.23 20.00 130.00 150.00
E3 198.30 6.05 1200.00 E3 13.95 20.00 130.00 150.00
F3 138.66 8.65 1200.00 F3 11.35 20.00 130.00 150.00
G3 163.20 7.35 1200.00 G3 12.65 20.00 130.00 150.00
H3 56.20 no 10.00 562.00 124.85 5.11 H3 4.89 20.00 130.00 150.00
A4 98.78 12.15 1200.00 A4 7.85 20.00 130.00 150.00
B4 60.47 no 12.00 725.64 151.88 3.12 B4 4.88 20.00 130.00 150.00
C4 66.43 no 12.00 797.16 119.93 3.36 C4 4.64 20.00 130.00 150.00
D4 119.64 10.03 1200.00 D4 9.97 20.00 130.00 150.00
E4 208.77 5.75 1200.00 E4 14.25 20.00 130.00 150.00
F4 83.48 no 12.00 1001.76 58.64 3.38 F4 4.62 20.00 130.00 150.00
G4 71.01 no 12.00 852.12 36.48 9.54 G4 0.00 21.54 130.00 151.54
H4 210.32 5.71 1200.00 H4 14.29 20.00 130.00 150.00
A5 266.74 4.50 1200.00 A5 15.50 20.00 130.00 150.00
B5 105.58 11.37 1200.00 B5 8.63 20.00 130.00 150.00
C5 89.41 13.42 1200.00 C5 6.58 20.00 130.00 150.00
D5 61.84 no 15.00 927.60 177.45 1.54 D5 3.46 20.00 130.00 150.00
E5 66.71 no 12.00 800.52 135.97 2.94 E5 5.06 20.00 130.00 150.00
F5 125.29 9.58 1200.00 F5 10.42 20.00 130.00 150.00
G5 121.31 9.89 1200.00 G5 10.11 20.00 130.00 150.00
H5 88.27 13.59 1200.00 H5 6.41 20.00 130.00 150.00
A6 134.70 8.91 1200.00 A6 11.09 20.00 130.00 150.00
B6 62.68 no 12.00 752.16 154.46 2.90 B6 5.10 20.00 130.00 150.00
C6 141.72 8.47 1200.00 C6 11.53 20.00 130.00 150.00
D6 187.04 6.42 1200.00 D6 13.58 20.00 130.00 150.00
E6 64.02 no 12.00 768.24 138.92 3.11 E6 4.89 20.00 130.00 150.00
F6 58.78 no 12.00 705.36 188.15 2.63 F6 5.37 20.00 130.00 150.00
G6 170.00 7.06 1200.00 G6 12.94 20.00 130.00 150.00
H6 111.00 10.81 1200.00 H6 9.19 20.00 130.00 150.00
A7 320.17 3.75 1200.00 A7 16.25 20.00 130.00 150.00
B7 162.36 7.39 1200.00 B7 12.61 20.00 130.00 150.00
C7 126.32 9.50 1200.00 C7 10.50 20.00 130.00 150.00
D7 368.67 3.25 1200.00 D7 16.75 20.00 130.00 150.00
E7 117.82 10.19 1200.00 E7 9.81 20.00 130.00 150.00
F7 84.38 no 12.00 1012.56 107.02 1.75 F7 6.25 20.00 130.00 150.00
G7 105.04 11.42 1200.00 G7 8.58 20.00 130.00 150.00
H7 86.61 13.86 1200.00 H7 6.14 20.00 130.00 150.00
A8 95.35 12.59 1200.00 A8 7.41 20.00 130.00 150.00
B8 98.32 12.21 1200.00 B8 7.79 20.00 130.00 150.00
C8 129.29 9.28 1200.00 C8 10.72 20.00 130.00 150.00
D8 100.98 11.88 1200.00 D8 8.12 20.00 130.00 150.00
E8 73.13 no 12.00 877.56 132.82 2.43 E8 5.57 20.00 130.00 150.00
F8 111.10 10.80 1200.00 F8 9.20 20.00 130.00 150.00
G8 30.00 no 10.00 300.00 162.10 5.55 G8 4.45 20.00 130.00 150.00
H8 82.39 no 12.00 988.68 182.77 1.16 H8 6.84 20.00 130.00 150.00
A9 61.85 no 12.00 742.20 136.13 3.36 A9 4.64 20.00 130.00 150.00
B9 110.49 10.86 1200.00 B9 9.14 20.00 130.00 150.00
C9 62.30 no 12.00 747.60 123.23 3.67 C9 4.33 20.00 130.00 150.00
D9 118.40 10.14 1200.00 D9 9.86 20.00 130.00 150.00
E9 75.01 16.00 1200.00 E9 4.00 20.00 130.00 150.00
F9 (tube 49.9) 60.63 no 15.00 909.45 38.24 7.60 F9 (tube 49.9) 0.00 22.60 130.00 152.60
G9 91.20 no 12.00 1094.40 142.40 0.74 G9 7.26 20.00 130.00 150.00
H9 90.62 13.24 1200.00 H9 6.76 20.00 130.00 150.00
A10 83.92 no 13.00 1090.96 193.87 0.56 A10 6.44 20.00 130.00 150.00
B10 120.56 9.95 1200.00 B10 10.05 20.00 130.00 150.00
C10 86.38 no 12.00 1036.56 168.48 0.97 C10 7.03 20.00 130.00 150.00
D10 49.85 no 12.00 598.20 172.60 3.49 D10 4.51 20.00 130.00 150.00
E10 123.63 9.71 1200.00 E10 10.29 20.00 130.00 150.00
F10 14.38 no 12.00 172.56 89.90 11.43 F10 0.00 23.43 130.00 153.43
G10 60.43 no 12.00 725.16 163.82 2.90 G10 5.10 20.00 130.00 150.00
H10 71.01 no 12.00 852.12 251.70 1.38 H10 6.62 20.00 130.00 150.00
A11 71.94 no 12.00 863.28 96.54 3.49 A11 4.51 20.00 130.00 150.00
B11 72.80 no 12.00 873.60 181.22 1.80 B11 6.20 20.00 130.00 150.00
C11 43.85 no 12.00 526.20 192.17 3.51 C11 4.49 20.00 130.00 150.00
D11 201.88 5.94 1200.00 D11 14.06 20.00 130.00 150.00
E11 221.63 5.41 1200.00 E11 14.59 20.00 130.00 150.00
F11 68.94 no 12.00 827.28 139.05 2.68 F11 5.32 20.00 130.00 150.00
G11 76.28 no 12.00 915.36 137.85 2.06 G11 5.94 20.00 130.00 150.00
H11 73.95 no 12.00 887.40 126.45 2.47 H11 5.53 20.00 130.00 150.00
A12 88.25 no 12.00 1059.00 126.33 1.12 A12 6.88 20.00 130.00 150.00
B12 (tube 94.9) 109.45 10.96 1200.00 B12 (tube 94.9) 9.04 20.00 130.00 150.00
C12 59.30 no 12.00 711.60 147.66 3.31 C12 4.69 20.00 130.00 150.00
D12 42.39 no 12.00 508.68 153.07 4.52 D12 3.48 20.00 130.00 150.00
E12 63.68 no 12.00 764.16 138.06 3.16 E12 4.84 20.00 130.00 150.00
F12 26.25 no 12.00 315.00 144.07 6.14 F12 1.86 20.00 130.00 150.00
G12 59.01 no 12.00 708.12 123.67 3.98 G12 4.02 20.00 130.00 150.00
H12 142.64 8.41 1200.00 H12 11.59 20.00 130.00 150.00


Qubit ssDNA assay

  • Took 1ul of bis-cvt DNA into 9ul of H2O, then add the diluted DNA to 190ul Qubit reagentC (dilution factor = 200)
Order Well ID Conc. in Qubit (ng/mL) Volume (ul) Final conc. (ng/ul) Yields (ng)
1.00 A1 217.00 16.00 43.40 694.40
2.00 B1 180.00 16.00 36.00 576.00
3.00 C1 204.00 16.00 40.80 652.80
4.00 D1 211.00 16.00 42.20 675.20
5.00 E1 201.00 16.00 40.20 643.20
6.00 F1 150.00 16.00 30.00 480.00
7.00 G1 135.00 16.00 27.00 432.00
8.00 H1 219.00 16.00 43.80 700.80
9.00 A2 190.00 16.00 38.00 608.00
10.00 B2 170.00 16.00 34.00 544.00
11.00 C2 151.00 16.00 30.20 483.20
12.00 D2 153.00 16.00 30.60 489.60
13.00 E2 292.00 16.00 58.40 934.40
14.00 F2 112.00 16.00 22.40 358.40
15.00 G2 160.00 16.00 32.00 512.00
16.00 H2 105.00 16.00 21.00 336.00
17.00 A3 176.00 16.00 35.20 563.20
18.00 B3 137.00 16.00 27.40 438.40
19.00 C3 119.00 16.00 23.80 380.80
20.00 D3 128.00 16.00 25.60 409.60
21.00 E3* 40.20 16.00 8.04 128.64
22.00 F3 134.00 16.00 26.80 428.80
23.00 G3 176.00 16.00 35.20 563.20
24.00 H3 112.00 16.00 22.40 358.40
25.00 A4 144.00 16.00 28.80 460.80
26.00 B4 135.00 16.00 27.00 432.00
27.00 C4 133.00 16.00 26.60 425.60
28.00 D4 139.00 16.00 27.80 444.80
29.00 E4 133.00 16.00 26.60 425.60
30.00 F4 189.00 16.00 37.80 604.80
31.00 G4 88.60 16.00 17.72 283.52
32.00 H4* 47.10 16.00 9.42 150.72
33.00 A5 148.00 16.00 29.60 473.60
34.00 B5 127.00 16.00 25.40 406.40
35.00 C5 83.70 16.00 16.74 267.84
36.00 D5 120.00 16.00 24.00 384.00
37.00 E5 117.00 16.00 23.40 374.40
38.00 F5* 34.40 16.00 6.88 110.08
39.00 G5 104.00 16.00 20.80 332.80
40.00 H5 112.00 16.00 22.40 358.40
41.00 A6 125.00 16.00 25.00 400.00
42.00 B6 126.00 16.00 25.20 403.20
43.00 C6 149.00 16.00 29.80 476.80
44.00 D6 135.00 16.00 27.00 432.00
45.00 E6 110.00 16.00 22.00 352.00
46.00 F6 102.00 16.00 20.40 326.40
47.00 G6 127.00 16.00 25.40 406.40
48.00 H6 59.40 16.00 11.88 190.08
49.00 A7 161.00 16.00 32.20 515.20
50.00 B7 146.00 16.00 29.20 467.20
51.00 C7 160.00 16.00 32.00 512.00
52.00 D7 135.00 16.00 27.00 432.00
53.00 E7 146.00 16.00 29.20 467.20
54.00 F7 133.00 16.00 26.60 425.60
55.00 G7 143.00 16.00 28.60 457.60
56.00 H7 85.20 16.00 17.04 272.64
57.00 A8 141.00 16.00 28.20 451.20
58.00 B8 147.00 16.00 29.40 470.40
59.00 C8 119.00 16.00 23.80 380.80
60.00 D8 81.40 16.00 16.28 260.48
61.00 E8 120.00 16.00 24.00 384.00
62.00 F8 62.20 16.00 12.44 199.04
63.00 G8 106.00 16.00 21.20 339.20
64.00 H8 135.00 16.00 27.00 432.00
65.00 A9 110.00 16.00 22.00 352.00
66.00 B9 147.00 16.00 29.40 470.40
67.00 C9 127.00 16.00 25.40 406.40
68.00 D9 95.70 16.00 19.14 306.24
69.00 E9 99.80 16.00 19.96 319.36
70.00 F9 104.00 16.00 20.80 332.80
71.00 G9 92.50 16.00 18.50 296.00
72.00 H9 116.00 16.00 23.20 371.20
73.00 A10 103.00 16.00 20.60 329.60
74.00 B10 69.70 16.00 13.94 223.04
75.00 C10 121.00 16.00 24.20 387.20
76.00 D10 141.00 16.00 28.20 451.20
77.00 E10 114.00 16.00 22.80 364.80
78.00 F10 154.00 16.00 30.80 492.80
79.00 G10 124.00 16.00 24.80 396.80
80.00 H10 111.00 16.00 22.20 355.20
81.00 A11 82.20 16.00 16.44 263.04
82.00 B11 112.00 16.00 22.40 358.40
83.00 C11 109.00 16.00 21.80 348.80
84.00 D11 61.50 16.00 12.30 196.80
85.00 E11 65.20 16.00 13.04 208.64
86.00 F11 148.00 16.00 29.60 473.60
87.00 G11 133.00 16.00 26.60 425.60
88.00 H11 200.00 16.00 40.00 640.00
89.00 A12 114.00 16.00 22.80 364.80
90.00 B12 149.00 16.00 29.80 476.80
91.00 C12 164.00 16.00 32.80 524.80
92.00 D12 142.00 16.00 28.40 454.40
93.00 E12 145.00 16.00 29.00 464.00
94.00 F12 137.00 16.00 27.40 438.40
95.00 G12 177.00 16.00 35.40 566.40
96.00 H12 202.00 16.00 40.40 646.40


  • Note: * = samples which total yields < 200ng