Alice:LabNotes/2009-7-6
Jump to navigation
Jump to search
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)