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>
* Note: For N37 sample set, TE buffer was added to bring up volume to 20ul and adjusted the final concentration to ~100ng/ul

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