Noi/NOTES/2011-11-15

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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]]