Noi/NOTES/2011-5-28: Difference between revisions
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= BSPP DMR330k capture of HIV patients samples and N37 = | = BSPP DMR330k capture of HIV patients samples and N37 = | ||
* May 19, 2011, received 39 gDNA from the blood samples of HIV patients form Tropher's lab, Medical School, UCSD | * May 19, 2011, received 39 gDNA from the blood samples of HIV patients form Tropher's lab, Medical School, UCSD | ||
* Ma7 25, 2011, received 10 gDNA from all tissues of N37 donor from Jin Billy Li, Standford Univ | * Ma7 25, 2011, received 10 gDNA from all tissues of N37 donor from Jin Billy Li, Standford Univ<br> | ||
{| {{table}} border = 1 | |||
| align="center" style="background:#f0f0f0;"|'''Sample ID''' | |||
| align="center" style="background:#f0f0f0;"|'''PID''' | |||
| align="center" style="background:#f0f0f0;"|'''New order in Zhang lab''' | |||
| align="center" style="background:#f0f0f0;"|'''Place in 96plate''' | |||
| align="center" style="background:#f0f0f0;"|'''Volume (ul)''' | |||
| align="center" style="background:#f0f0f0;"|'''Conc. (ng/ul)''' | |||
| align="center" style="background:#f0f0f0;"|'''Total amount (ug)''' | |||
|- | |||
| 3||26406 102||1||A1||21||100||2.1 | |||
|- | |||
| 4||26406 108||2||A2||21||100||2.1 | |||
|- | |||
| 5||26604 054||3||A3||21||100||2.1 | |||
|- | |||
| 6||26604 066||4||A4||21||100||2.1 | |||
|- | |||
| 11||NW578 000||5||A5||21||100||2.1 | |||
|- | |||
| 12||NW578 012||6||A6||21||100||2.1 | |||
|- | |||
| 13||58346 006||7||A7||21||100||2.1 | |||
|- | |||
| 14||58346 012||8||A8||21||100||2.1 | |||
|- | |||
| 15||CA198 006||9||A9||21||100||2.1 | |||
|- | |||
| 16||CA198 C12||10||A10||21||100||2.1 | |||
|- | |||
| 17||CA219 000||11||A11||21||100||2.1 | |||
|- | |||
| 18||CA219 006||12||A12||21||100||2.1 | |||
|- | |||
| 19||CA275 000||13||B1||21||100||2.1 | |||
|- | |||
| 20||CA275 006||14||B2||21||100||2.1 | |||
|- | |||
| 21||CB252 000||15||B3||21||100||2.1 | |||
|- | |||
| 22||CB252 006||16||B4||21||100||2.1 | |||
|- | |||
| 24||CC182 012||17||B5||21||100||2.1 | |||
|- | |||
| 25||24371 000||18||B6||21||100||2.1 | |||
|- | |||
| 26||24371 012||19||B7||21||100||2.1 | |||
|- | |||
| 27||NW470 012||20||B8||21||100||2.1 | |||
|- | |||
| 28||NW470 024||21||B9||21||100||2.1 | |||
|- | |||
| 30||27054 012||22||B10||21||100||2.1 | |||
|- | |||
| 31||CA239 000||23||B11||21||100||2.1 | |||
|- | |||
| 33||CE214 000||24||B12||21||100||2.1 | |||
|- | |||
| 34||CE214 006||25||C1||21||100||2.1 | |||
|- | |||
| 35||CB255 000||26||C2||21||100||2.1 | |||
|- | |||
| 36||CB255 006||27||C3||21||100||2.1 | |||
|- | |||
| 37||21003 000||28||C4||21||100||2.1 | |||
|- | |||
| 38||21003 012||29||C5||21||100||2.1 | |||
|- | |||
| 39||CG139 006||30||C6||21||100||2.1 | |||
|- | |||
| 40||CG139 018||31||C7||21||100||2.1 | |||
|- | |||
| 41||NM633 012||32||C8||21||100||2.1 | |||
|- | |||
| 42||NM633 024||33||C9||21||100||2.1 | |||
|- | |||
| 43||NM805 012||34||C10||21||100||2.1 | |||
|- | |||
| 44||NM805 024||35||C11||21||100||2.1 | |||
|- | |||
| 45||CB199 000||36||C12||21||100||2.1 | |||
|- | |||
| 46||26592 060||37||D1||21||100||2.1 | |||
|- | |||
| 47||24054 030||38||D2||21||100||2.1 | |||
|- | |||
| 48||24054 036||39||D3||21||100||2.1 | |||
|}<br> | |||
{| {{table}} border = 1 | {| {{table}} border = 1 | ||
Line 35: | Line 120: | ||
|- | |- | ||
| 10.00||Stomach||1.17||1.71||2.00||N37-10||18.29||20.00||100.04 | | 10.00||Stomach||1.17||1.71||2.00||N37-10||18.29||20.00||100.04 | ||
|} | |||
* Note: For N37 sample set, TE buffer was added to bring up volume to 20ul and adjusted the final concentration to ~100ng/ul<br> | |||
=Bisulfite conversion = | |||
* Plate layout | |||
{| {{table}} border = 1 | |||
| align="center" style="background:#f0f0f0;"|'''Plat layout''' | |||
| align="center" style="background:#f0f0f0;"|'''1''' | |||
| align="center" style="background:#f0f0f0;"|'''2''' | |||
| align="center" style="background:#f0f0f0;"|'''3''' | |||
| align="center" style="background:#f0f0f0;"|'''4''' | |||
| align="center" style="background:#f0f0f0;"|'''5''' | |||
| align="center" style="background:#f0f0f0;"|'''6''' | |||
| align="center" style="background:#f0f0f0;"|'''7''' | |||
| align="center" style="background:#f0f0f0;"|'''8''' | |||
| align="center" style="background:#f0f0f0;"|'''9''' | |||
| align="center" style="background:#f0f0f0;"|'''10''' | |||
| align="center" style="background:#f0f0f0;"|'''11''' | |||
| align="center" style="background:#f0f0f0;"|'''12''' | |||
|- | |||
| A '''A'''||A1||A2||A3||A4||A5||A6||A7||A8||A9||A10||A11||A12 | |||
|- | |||
| B|||||||||||||||||||||||| | |||
|- | |||
| C '''B'''||B1||B2||B3||B4||B5||B6||B7||B8||B9||B10||B11||B12 | |||
|- | |||
| D|||||||||||||||||||||||| | |||
|- | |||
| E '''C'''||C1||C2||C3||C4||C5||C6||C7||C8||C9||C10||C11||C12 | |||
|- | |||
| F|||||||||||||||||||||||| | |||
|- | |||
| G '''D'''||D1||D2||D3|||||||||||||||||| | |||
|- | |||
| H||N37-1 ||N37-2||N37-3||N37-4||N37-5||N37-6||N37-7||N37-8||N37-9||N37-10|||| | |||
|}<br> | |}<br> | ||
Revision as of 15:09, 28 May 2011
BSPP DMR330k capture of HIV patients samples and N37
- May 19, 2011, received 39 gDNA from the blood samples of HIV patients form Tropher's lab, Medical School, UCSD
- Ma7 25, 2011, received 10 gDNA from all tissues of N37 donor from Jin Billy Li, Standford Univ
Sample ID | PID | New order in Zhang lab | Place in 96plate | Volume (ul) | Conc. (ng/ul) | Total amount (ug) |
3 | 26406 102 | 1 | A1 | 21 | 100 | 2.1 |
4 | 26406 108 | 2 | A2 | 21 | 100 | 2.1 |
5 | 26604 054 | 3 | A3 | 21 | 100 | 2.1 |
6 | 26604 066 | 4 | A4 | 21 | 100 | 2.1 |
11 | NW578 000 | 5 | A5 | 21 | 100 | 2.1 |
12 | NW578 012 | 6 | A6 | 21 | 100 | 2.1 |
13 | 58346 006 | 7 | A7 | 21 | 100 | 2.1 |
14 | 58346 012 | 8 | A8 | 21 | 100 | 2.1 |
15 | CA198 006 | 9 | A9 | 21 | 100 | 2.1 |
16 | CA198 C12 | 10 | A10 | 21 | 100 | 2.1 |
17 | CA219 000 | 11 | A11 | 21 | 100 | 2.1 |
18 | CA219 006 | 12 | A12 | 21 | 100 | 2.1 |
19 | CA275 000 | 13 | B1 | 21 | 100 | 2.1 |
20 | CA275 006 | 14 | B2 | 21 | 100 | 2.1 |
21 | CB252 000 | 15 | B3 | 21 | 100 | 2.1 |
22 | CB252 006 | 16 | B4 | 21 | 100 | 2.1 |
24 | CC182 012 | 17 | B5 | 21 | 100 | 2.1 |
25 | 24371 000 | 18 | B6 | 21 | 100 | 2.1 |
26 | 24371 012 | 19 | B7 | 21 | 100 | 2.1 |
27 | NW470 012 | 20 | B8 | 21 | 100 | 2.1 |
28 | NW470 024 | 21 | B9 | 21 | 100 | 2.1 |
30 | 27054 012 | 22 | B10 | 21 | 100 | 2.1 |
31 | CA239 000 | 23 | B11 | 21 | 100 | 2.1 |
33 | CE214 000 | 24 | B12 | 21 | 100 | 2.1 |
34 | CE214 006 | 25 | C1 | 21 | 100 | 2.1 |
35 | CB255 000 | 26 | C2 | 21 | 100 | 2.1 |
36 | CB255 006 | 27 | C3 | 21 | 100 | 2.1 |
37 | 21003 000 | 28 | C4 | 21 | 100 | 2.1 |
38 | 21003 012 | 29 | C5 | 21 | 100 | 2.1 |
39 | CG139 006 | 30 | C6 | 21 | 100 | 2.1 |
40 | CG139 018 | 31 | C7 | 21 | 100 | 2.1 |
41 | NM633 012 | 32 | C8 | 21 | 100 | 2.1 |
42 | NM633 024 | 33 | C9 | 21 | 100 | 2.1 |
43 | NM805 012 | 34 | C10 | 21 | 100 | 2.1 |
44 | NM805 024 | 35 | C11 | 21 | 100 | 2.1 |
45 | CB199 000 | 36 | C12 | 21 | 100 | 2.1 |
46 | 26592 060 | 37 | D1 | 21 | 100 | 2.1 |
47 | 24054 030 | 38 | D2 | 21 | 100 | 2.1 |
48 | 24054 036 | 39 | D3 | 21 | 100 | 2.1 |
Number | Sample | Concentration (ug/ul) | Volume (ul) | Total amount (ug) | NewID | TE buffer (ul) | Total volume (ul) | Final conc. (ng/ul) |
1.00 | Cerebellum | 1.38 | 1.45 | 2.00 | N37-1 | 18.55 | 20.00 | 100.05 |
2.00 | Colon | 1.44 | 1.39 | 2.00 | N37-2 | 18.61 | 20.00 | 100.08 |
3.00 | Frontal lobe | 0.91 | 2.20 | 2.00 | N37-3 | 17.80 | 20.00 | 100.10 |
4.00 | Heart | 0.73 | 2.74 | 2.00 | N37-4 | 17.26 | 20.00 | 100.01 |
5.00 | Small intestine | 1.09 | 1.83 | 1.99 | N37-5 | 18.17 | 20.00 | 99.74 |
6.00 | Liver | 0.93 | 2.15 | 2.00 | N37-6 | 17.85 | 20.00 | 99.98 |
7.00 | Lung | 0.50 | 4.00 | 2.00 | N37-7 | 16.00 | 20.00 | 100.00 |
8.00 | Skeletal muscle | 0.57 | 3.51 | 2.00 | N37-8 | 16.49 | 20.00 | 100.04 |
9.00 | Pancrease | 1.48 | 1.35 | 2.00 | N37-9 | 18.65 | 20.00 | 99.90 |
10.00 | Stomach | 1.17 | 1.71 | 2.00 | N37-10 | 18.29 | 20.00 | 100.04 |
- Note: For N37 sample set, TE buffer was added to bring up volume to 20ul and adjusted the final concentration to ~100ng/ul
Bisulfite conversion
- Plate layout
Plat layout | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 |
A A | A1 | A2 | A3 | A4 | A5 | A6 | A7 | A8 | A9 | A10 | A11 | A12 |
B | ||||||||||||
C B | B1 | B2 | B3 | B4 | B5 | B6 | B7 | B8 | B9 | B10 | B11 | B12 |
D | ||||||||||||
E C | C1 | C2 | C3 | C4 | C5 | C6 | C7 | C8 | C9 | C10 | C11 | C12 |
F | ||||||||||||
G D | D1 | D2 | D3 | |||||||||
H | N37-1 | N37-2 | N37-3 | N37-4 | N37-5 | N37-6 | N37-7 | N37-8 | N37-9 | N37-10 |