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= Normalization of libraries from HL104 run (Library ID: NP-BSPP-Ind1_45-Sep18) to repeat sequencing by GAIIx flowcell = * Continued from library preparation on 2011/09/18: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-9-18#PCR_Amplification_with_barcoded_primers_.28AmpF6.4Sol_and_AmpR6.3_IndX_No.1-46.29]] and library normalization on 2011/11/17: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-10-17]] *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)<br> {| {{table}} border = 1 | align="center" style="background:#f0f0f0;"|'''# of reads''' | align="center" style="background:#f0f0f0;"|'''Indx''' | align="center" style="background:#f0f0f0;"|'''Sample ID''' | align="center" style="background:#f0f0f0;"|'''Well ID''' | align="center" style="background:#f0f0f0;"|'''Relative ratio to 4 million reads''' | align="center" style="background:#f0f0f0;"|'''original volume for 60ng''' | align="center" style="background:#f0f0f0;"|'''calculated new volume''' | align="center" style="background:#f0f0f0;"|'''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 |}<br> * 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| 400px]] * 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| 300px]] * 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: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-12-25]]
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