Noi/NOTES/2011-11-15
Jump to navigation
Jump to search
Normalization of libraries from HL104 run (Library ID: NP-BSPP-Ind1_45-Sep18) to repeat sequencing by GAIIx flowcell[edit]
- Continued from library preparation on 2011/09/18: [[1]] and library normalization on 2011/11/17: [[2]]
- Note: The rest of libraries were normalized and pooled for sequencing (some of them were repeated on 2011/10/17)
- Libraries from two families from HAPMAP plate, the 9 replicates for probe normalization and PGP1iPS treated with different bisulfite conversion kits (Zymoresearch and Imprint from Sigma)
# of reads | Indx | Sample ID | Well ID | Relative ratio to 4 million reads | original volume for 60ng | calculated new volume | Well ID |
3,457,940 | s_7_1_Indx10 | GM11995 (wellID G7) | B3 | 0.864 | 10.80 | 12.49 | B3 |
4,062,805 | s_7_1_Indx11 | GM11993 (wellID F2) | C3 | 1.016 | 11.09 | 10.92 | C3 |
3,733,084 | s_7_1_Indx12 | **GM10861 (wellID A9) | D3 | 0.933 | 11.46 | 12.27 | D3 |
3,663,235 | s_7_1_Indx13 | GM11992 (wellID C2 ) | E3 | 0.916 | 10.32 | 11.27 | E3 |
2,928,739 | s_7_1_Indx14 | GM11994 (wellID G9 ) | F3 | 0.732 | 22.00 | 30.05 | F3 |
7,213,122 | s_7_1_Indx15 | GM10860 (wellID F10) | G3 | 1.803 | 10.99 | 6.09 | G3 |
2,853,891 | s_7_1_Indx16 | GM12813 (wellID E8) | H3 | 0.713 | 6.98 | 9.79 | H3 |
3,678,983 | s_7_1_Indx17 | GM12802 (wellID E7) | A5 | 0.920 | 7.88 | 8.56 | A5 |
3,067,241 | s_7_1_Indx18 | GM12815 (wellID G12) | B5 | 0.767 | 7.48 | 9.75 | B5 |
3,763,585 | s_7_1_Indx19 | GM12812 (wellID F11) | C5 | 0.941 | 10.20 | 10.84 | C5 |
3,246,362 | s_7_1_Indx20 | GM12814 (wellID A7) | D5 | 0.812 | 6.53 | 8.05 | D5 |
3,833,426 | s_7_1_Indx21 | GM12801 (wellID D9) | E5 | 0.958 | 7.08 | 7.39 | E5 |
3,177,943 | s_7_1_Indx22 | NA12156 (wellID B3)-1 | F5 | 0.794 | 7.43 | 9.35 | F5 |
3,349,096 | s_7_1_Indx23 | NA12156 (wellID B3)-2 | G5 | 0.837 | 6.45 | 7.70 | G5 |
3,604,801 | s_7_1_Indx24 | NA12156 (wellID B3)-3 | H5 | 0.901 | 6.49 | 7.21 | H5 |
4,379,684 | s_7_1_Indx25 | NA12156 (wellID B3)-4 | A7 | 1.095 | 8.51 | 7.77 | A7 |
3,557,582 | s_7_1_Indx26 | NA12156 (wellID B3)-5 | B7 | 0.889 | 10.12 | 11.38 | B7 |
4,331,433 | s_7_1_Indx27 | NA12156 (wellID B3)-6 | C7 | 1.083 | 7.49 | 6.92 | C7 |
2,945,843 | s_7_1_Indx28 | NA12156 (wellID B3)-7 | D7 | 0.736 | 7.62 | 10.34 | D7 |
3,444,795 | s_7_1_Indx29 | NA12156 (wellID B3)-8 | E7 | 0.861 | 9.90 | 11.50 | E7 |
3,429,469 | s_7_1_Indx30 | NA12156 (wellID B3)-9 | F7 | 0.857 | 7.39 | 8.62 | F7 |
6,808,403 | s_7_1_Indx41 | **PGP1iPS | A11 | 1.702 | 14.16 | 8.32 | A11 |
5,281,331 | s_7_1_Indx42 | PGP1iPS-IMPRINT | B11 | 1.320 | 17.42 | 13.19 | B11 |
6,256,272 | s_7_1_Indx94 | UCLA-RO_Indx94 | in tube | 1.564 | 4.06 | 2.60 | tube |
- Perform PAGE size selection in 5-well 6% TBE gel (2 5-well gels)
File:ZhangLab 2 2011-11-15 13hr 30min PAGE-SS NP BSPP-HAPMAP-norm.jpg
- Note: The gel had curve while running, so I cut the band following the curve.
- After gel purification resuspend the libraries in total volume 30ul.
File:ZhangLab 2 2011-11-16 12hr 36min.jpg
- 1ul of sequencing libraries were analyzed by PAGE quantification, conc.: ng/ul or nM
- Concentration was also verified by Qubit ds-DNA HS, conc.: ng/ul or nM
- Library ID: NP-BSPP_HAPMAP_Nov15,2011, HL110 run --> PE 100 by GAIIx flowcell
- Note: HL110 run in Zhang's lab failed (in lane 1 & 5), these libraries were sequenced again HL111 run (PE 110) by HiSeq.
- Mapping: [[3]]