Revision as of 01:37, 13 July 2009 by >Jie deng
The detailed capture reaction setup can be found under LabNotes 6/28/09
Pooled all the captured product based on the following table:
sample
|
a1
|
a2
|
a3
|
a4
|
'
|
b1
|
b2
|
b3
|
b4
|
concentration (ng/ul) |
16 |
9.7 |
6.7 |
12.3 |
|
9.4 |
7.6 |
5.1 |
9.8
|
volume (ul) |
10 |
8.2 |
17 |
9.5 |
|
15 |
9.3 |
20 |
10.5
|
total (ng) |
160 |
80 |
115.2 |
116.8 |
|
141 |
70.5 |
101.5 |
103
|
|
sample
|
c1
|
c2
|
c3
|
c4
|
'
|
d1
|
d2
|
d3
|
d4
|
concentration (ng/ul) |
13 |
7.2 |
4.9 |
5.4 |
|
14 |
7.8 |
6.6 |
7.4
|
volume (ul) |
10 |
9 |
19 |
17.5 |
|
10 |
9 |
15 |
14
|
total (ng) |
130 |
65 |
93.6 |
95 |
|
140 |
70 |
100.8 |
102.2
|
|
sample
|
e1
|
e2
|
e3
|
e4
|
'
|
f1
|
f2
|
f3
|
f4
|
concentration (ng/ul) |
11 |
3.1 |
3.4 |
4.7 |
|
9.5 |
5.5 |
2.2 |
4.6
|
volume (ul) |
7.3 |
13 |
17 |
12.5 |
|
2.9 |
2.5 |
9 |
4.4
|
total (ng) |
80.3 |
40.15 |
57.8 |
58.6 |
|
27.5 |
13.8 |
19.8 |
20
|
|
sample
|
DF1
|
DF2
|
DF3
|
DF4
|
'
|
FS1
|
FS2
|
FS3
|
FS4
|
concentration (ng/ul) |
17.7 |
10.1 |
6.2 |
11.7 |
|
15.3 |
4.1 |
5.4 |
5.2
|
volume (ul) |
9.2 |
8.1 |
19 |
10.2 |
|
8.6 |
16 |
18 |
18.5
|
total (ng) |
163.6 |
81.8 |
117.8 |
119.4 |
|
131.8 |
65.9 |
95 |
111.7
|
|
perform E-gel size selection after pooling all the samples together (8 total):
assume 70% recovery rate, the total amount of DNA in each sample set is:
PGP1_070809: 25ul (330.4ng)
PGP2_070809: 30ul (291ng)
PGP3_070809: 32ul (269ng)
NA12878_070809: 26ul (289ng)
PGP5_070809: 31ul (166ng)
PGP7_070809: 17ul (65ng)
DF6-9-9_070809: 33ul (177ng)
foreskin_070809: 44ul (283ng)
Since PGP7 had very little amount of DNA, it was not send out for shearing. And I will need to repeat the capture on sample f3.
Sent out the following tubes for Covaris shearing to Dr. Billy Li (Harvard) on 7/8/09
PGP1_070809: 25ul (13ng/ul)
PGP2_070809: 30ul (9.7ng/ul)
PGP3_070809: 32ul (8.4ng/ul)
NA12878_070809: 26ul (11ng/ul)
PGP5_070809: 31ul (5.5ng/ul)
DF6-9-9_070809: 33ul (5.4ng/ul)
foreskin_070809: 44ul (6.4ng/ul)