Noi/NOTES/2011-1-20

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DMR220k capture and library construction of normal/tumor samples from JHU[edit]

continued from 2010_12_18: [[1]]

Prepared new multiplexed libraries with normalized amount of each individual library based on the number of reads from SE sequencing (HL086)[edit]

Library stats deconvoluted data by Dr. Zhang[edit]

Samples # reads
s_6_Ind10.txt 999702.00
s_6_Ind11.txt 648307.00
s_6_Ind12.txt 730823.00
s_6_Ind13.txt 613427.00
s_6_Ind14.txt 542208.00
s_6_Ind15.txt 715812.00
s_6_Ind16.txt 713672.00
s_6_Ind17.txt 668289.00
s_6_Ind18.txt 755716.00
s_6_Ind19.txt 922611.00
s_6_Ind1.txt 931078.00
s_6_Ind20.txt 991341.00
s_6_Ind21.txt 1276771.00
s_6_Ind22.txt 823874.00
s_6_Ind23.txt 874307.00
s_6_Ind24.txt 937769.00
s_6_Ind25.txt 664256.00
s_6_Ind26.txt 1119454.00
s_6_Ind27.txt 703026.00
s_6_Ind28.txt 554901.00
s_6_Ind29.txt 665564.00
s_6_Ind2.txt 853815.00
s_6_Ind30.txt 894323.00
s_6_Ind31.txt 724070.00
s_6_Ind32.txt 705601.00
s_6_Ind33.txt 635324.00
s_6_Ind34.txt 641013.00
s_6_Ind35.txt 553429.00
s_6_Ind36.txt 746503.00
s_6_Ind37.txt 501745.00
s_6_Ind38.txt 421420.00
s_6_Ind39.txt 474684.00
s_6_Ind3.txt 751752.00
s_6_Ind40.txt 158.00
s_6_Ind41.txt 4239.00
s_6_Ind42.txt 399683.00
s_6_Ind43.txt 598741.00
s_6_Ind44.txt 976630.00
s_6_Ind45.txt 401621.00
s_6_Ind46.txt 769589.00
s_6_Ind47.txt 607350.00
s_6_Ind48.txt 850211.00
s_6_Ind4.txt 408868.00
s_6_Ind5.txt 874586.00
s_6_Ind6.txt 844143.00
s_6_Ind7.txt 807345.00
s_6_Ind8.txt 912227.00
s_6_Ind9.txt 633534.00


Normalized Ratio[edit]

  • Note: normalized to 700,000 reads
  • IndX4 (D1) was purified more and re-estimated concentration
SampleID IndX Samples #reads relative ratio normalized amount (ng) Concentration (ng/ul) volume (ul) SampleID
A1 R6.3IndX1 s_6_Ind1.txt 931078.00 0.75 18.80 7.46 2.52 A1
B1 R6.3IndX2 s_6_Ind2.txt 853815.00 0.82 20.50 6.50 3.15 B1
C1 R6.3IndX3 s_6_Ind3.txt 751752.00 0.93 23.28 6.63 3.51 C1
D1* R6.3IndX4 s_6_Ind4.txt 408868.00 1.71 42.80 1.58 27.09 D1
E1 R6.3IndX5 s_6_Ind5.txt 874586.00 0.80 20.01 6.91 2.90 E1
F1 R6.3IndX6 s_6_Ind6.txt 844143.00 0.83 20.73 7.62 2.72 F1
G1 R6.3IndX7 s_6_Ind7.txt 807345.00 0.87 21.68 9.15 2.37 G1
H1 R6.3IndX8 s_6_Ind8.txt 912227.00 0.77 19.18 5.39 3.56 H1
A2 R6.3IndX9 s_6_Ind9.txt 633534.00 1.10 27.62 5.29 5.22 A2
B2 R6.3IndX10 s_6_Ind10.txt 999702.00 0.70 17.51 3.51 4.99 B2
C2 R6.3IndX11 s_6_Ind11.txt 648307.00 1.08 26.99 4.70 5.74 C2
D2 R6.3IndX12 s_6_Ind12.txt 730823.00 0.96 23.95 4.35 5.50 D2
E2 R6.3IndX13 s_6_Ind13.txt 613427.00 1.14 28.53 6.10 4.68 E2
F2 R6.3IndX14 s_6_Ind14.txt 542208.00 1.29 32.28 5.60 5.76 F2
G2 R6.3IndX15 s_6_Ind15.txt 715812.00 0.98 24.45 3.36 7.28 G2
H2 R6.3IndX16 s_6_Ind16.txt 713672.00 0.98 24.52 9.02 2.72 H2
A3 R6.3IndX17 s_6_Ind17.txt 668289.00 1.05 26.19 5.81 4.51 A3
B3 R6.3IndX18 s_6_Ind18.txt 755716.00 0.93 23.16 4.53 5.11 B3
C3 R6.3IndX19 s_6_Ind19.txt 922611.00 0.76 18.97 4.80 3.95 C3
D3 R6.3IndX20 s_6_Ind20.txt 991341.00 0.71 17.65 3.61 4.89 D3
E3 R6.3IndX21 s_6_Ind21.txt 1276771.00 0.55 13.71 2.09 6.56 E3
F3 R6.3IndX22 s_6_Ind22.txt 823874.00 0.85 21.24 4.22 5.03 F3
G3 R6.3IndX23 s_6_Ind23.txt 874307.00 0.80 20.02 3.63 5.51 G3
H3 R6.3IndX24 s_6_Ind24.txt 937769.00 0.75 18.66 2.39 7.81 H3
A4 R6.3IndX25 s_6_Ind25.txt 664256.00 1.05 26.35 4.83 5.45 A4
B4 R6.3IndX26 s_6_Ind26.txt 1119454.00 0.63 15.63 9.92 1.58 B4
C4 R6.3IndX27 s_6_Ind27.txt 703026.00 1.00 24.89 4.01 6.21 C4
D4 R6.3IndX28 s_6_Ind28.txt 554901.00 1.26 31.54 4.53 6.96 D4
E4 R6.3IndX29 s_6_Ind29.txt 665564.00 1.05 26.29 4.57 5.75 E4
F4 R6.3IndX30 s_6_Ind30.txt 894323.00 0.78 19.57 2.34 8.36 F4
G4 R6.3IndX31 s_6_Ind31.txt 724070.00 0.97 24.17 4.40 5.49 G4
H4 R6.3IndX32 s_6_Ind32.txt 705601.00 0.99 24.80 3.63 6.83 H4
A5 R6.3IndX33 s_6_Ind33.txt 635324.00 1.10 27.55 5.11 5.39 A5
B5 R6.3IndX34 s_6_Ind34.txt 641013.00 1.09 27.30 4.21 6.48 B5
C5 R6.3IndX35 s_6_Ind35.txt 553429.00 1.26 31.62 3.19 9.91 C5
D5 R6.3IndX36 s_6_Ind36.txt 746503.00 0.94 23.44 3.77 6.22 D5
E5 R6.3IndX37 s_6_Ind37.txt 501745.00 1.40 34.88 5.82 5.99 E5
F5 R6.3IndX38 s_6_Ind38.txt 421420.00 1.66 41.53 6.55 6.34 F5
G5 R6.3IndX39 s_6_Ind39.txt 474684.00 1.47 36.87 6.35 5.81 G5
H5 R6.3IndX40 s_6_Ind40.txt 158.00 H5
A6 R6.3IndX41 s_6_Ind41.txt 4239.00 A6
B6 R6.3IndX42 s_6_Ind42.txt 399683.00 1.75 43.78 5.73 7.64 B6
C6 R6.3IndX43 s_6_Ind43.txt 598741.00 1.17 29.23 4.29 6.81 C6
D6 R6.3IndX44 s_6_Ind44.txt 976630.00 0.72 17.92 2.58 6.95 D6
E6 R6.3IndX45 s_6_Ind45.txt 401621.00 1.74 43.57 5.75 7.58 E6
F6 R6.3IndX46 s_6_Ind46.txt 769589.00 0.91 22.74 3.46 6.57 F6
G6 R6.3IndX47 s_6_Ind47.txt 607350.00 1.15 28.81 4.10 7.03 G6
H6 R6.3IndX48 s_6_Ind48.txt 850211.00 0.82 20.58 3.33 6.18 H6


PAGE size selection
File:ZhangLab 2 2011-01-20 22hr 15min JHUSeqLib new-1.jpgFile:ZhangLab 2 2011-01-20 22hr 17min JHUSeqLib new-2.jpg

DMR220k capture and library construction of African's gDNA from UPENN[edit]

continued from 2011_01_03: [[2]]

Prepared new multiplexed libraries with normalized amount of each individual library based on the number of reads from SE sequencing (HL086)[edit]

Library stats deconvoluted data by Dr. Zhang[edit]

Samples # reads
s_7_Ind10.txt 435937.00
s_7_Ind11.txt 1170860.00
s_7_Ind12.txt 428963.00
s_7_Ind13.txt 382010.00
s_7_Ind14.txt 406986.00
s_7_Ind15.txt 411352.00
s_7_Ind16.txt 401840.00
s_7_Ind17.txt 1766313.00
s_7_Ind18.txt 444570.00
s_7_Ind19.txt 417023.00
s_7_Ind1.txt 719787.00
s_7_Ind20.txt 1319691.00
s_7_Ind21.txt 346315.00
s_7_Ind22.txt 409111.00
s_7_Ind23.txt 1535886.00
s_7_Ind24.txt 334978.00
s_7_Ind25.txt 705539.00
s_7_Ind26.txt 404335.00
s_7_Ind27.txt 668036.00
s_7_Ind28.txt 610378.00
s_7_Ind29.txt 847850.00
s_7_Ind2.txt 875926.00
s_7_Ind30.txt 753242.00
s_7_Ind31.txt 685115.00
s_7_Ind32.txt 665399.00
s_7_Ind33.txt 944028.00
s_7_Ind34.txt 445650.00
s_7_Ind35.txt 733397.00
s_7_Ind36.txt 813140.00
s_7_Ind37.txt 992650.00
s_7_Ind38.txt 603606.00
s_7_Ind39.txt 774346.00
s_7_Ind3.txt 703529.00
s_7_Ind40.txt 1027525.00
s_7_Ind41.txt 1153812.00
s_7_Ind42.txt 928359.00
s_7_Ind43.txt 1148342.00
s_7_Ind44.txt 1098551.00
s_7_Ind45.txt 836268.00
s_7_Ind46.txt 416424.00
s_7_Ind47.txt 491180.00
s_7_Ind48.txt 1315177.00
s_7_Ind4.txt 430378.00
s_7_Ind5.txt 548028.00
s_7_Ind6.txt 874813.00
s_7_Ind7.txt 811884.00
s_7_Ind8.txt 625083.00
s_7_Ind9.txt 398720.00


Normalized Ratio[edit]

  • Note: normalized to 700,000 reads
  • IndX26(B4) and IndX28(D4)has less amount of DNA then they were purified more and re-estimated concentration.
SampleID IndX Samples #reads relative ratio normalized amount (ng) Concentration (ng/ul) volume (ul)
A1 R6.3IndX1 s_7_Ind1.txt 719787.00 0.97 24.31 2.69 9.04
B1 R6.3IndX2 s_7_Ind2.txt 875926.00 0.80 19.98 2.26 8.84
C1 R6.3IndX3 s_7_Ind3.txt 703529.00 0.99 24.87 2.30 10.82
D1 R6.3IndX4 s_7_Ind4.txt 430378.00 1.63 40.66 2.92 13.93
E1 R6.3IndX5 s_7_Ind5.txt 548028.00 1.28 31.93 3.67 8.70
F1 R6.3IndX6 s_7_Ind6.txt 874813.00 0.80 20.00 1.88 10.64
G1 R6.3IndX7 s_7_Ind7.txt 811884.00 0.86 21.55 2.19 9.84
H1 R6.3IndX8 s_7_Ind8.txt 625083.00 1.12 28.00 1.65 16.97
A2 R6.3IndX9 s_7_Ind9.txt 398720.00 1.76 43.89 5.21 8.42
B2 R6.3IndX10 s_7_Ind10.txt 435937.00 1.61 40.14 3.83 10.48
C2 R6.3IndX11 s_7_Ind11.txt 1170860.00 0.60 14.95 1.35 11.07
D2 R6.3IndX12 s_7_Ind12.txt 428963.00 1.63 40.80 2.65 15.39
E2 R6.3IndX13 s_7_Ind13.txt 382010.00 1.83 45.81 3.04 15.07
F2 R6.3IndX14 s_7_Ind14.txt 406986.00 1.72 43.00 3.25 13.23
G2 R6.3IndX15 s_7_Ind15.txt 411352.00 1.70 42.54 3.11 13.68
H2 R6.3IndX16 s_7_Ind16.txt 401840.00 1.74 43.55 3.83 11.37
A3 R6.3IndX17 s_7_Ind17.txt 1766313.00 0.40 9.91 1.51 6.56
B3 R6.3IndX18 s_7_Ind18.txt 444570.00 1.57 39.36 4.64 8.48
C3 R6.3IndX19 s_7_Ind19.txt 417023.00 1.68 41.96 3.49 12.02
D3 R6.3IndX20 s_7_Ind20.txt 1319691.00 0.53 13.26 1.49 8.90
E3 R6.3IndX21 s_7_Ind21.txt 346315.00 2.02 50.53 3.85 13.13
F3 R6.3IndX22 s_7_Ind22.txt 409111.00 1.71 42.78 3.38 12.66
G3 R6.3IndX23 s_7_Ind23.txt 1535886.00 0.46 11.39 1.40 8.14
H3 R6.3IndX24 s_7_Ind24.txt 334978.00 2.09 52.24 5.17 10.10
A4 R6.3IndX25 s_7_Ind25.txt 705539.00 0.99 24.80 3.75 6.61
B4 R6.3IndX26 s_7_Ind26.txt 404335.00 1.73 43.28 2.56 16.91
C4 R6.3IndX27 s_7_Ind27.txt 668036.00 1.05 26.20 3.15 8.32
D4 R6.3IndX28 s_7_Ind28.txt 610378.00 1.15 28.67 3.46 8.29
E4 R6.3IndX29 s_7_Ind29.txt 847850.00 0.83 20.64 2.57 8.03
F4 R6.3IndX30 s_7_Ind30.txt 753242.00 0.93 23.23 2.57 9.04
G4 R6.3IndX31 s_7_Ind31.txt 685115.00 1.02 25.54 2.69 9.50
H4 R6.3IndX32 s_7_Ind32.txt 665399.00 1.05 26.30 3.02 8.71
A5 R6.3IndX33 s_7_Ind33.txt 944028.00 0.74 18.54 2.33 7.96
B5 R6.3IndX34 s_7_Ind34.txt 445650.00 1.57 39.27 5.39 7.29
C5 R6.3IndX35 s_7_Ind35.txt 733397.00 0.95 23.86 2.69 8.87
D5 R6.3IndX36 s_7_Ind36.txt 813140.00 0.86 21.52 2.37 9.08
E5 R6.3IndX37 s_7_Ind37.txt 992650.00 0.71 17.63 2.05 8.60
F5 R6.3IndX38 s_7_Ind38.txt 603606.00 1.16 28.99 3.11 9.32
G5 R6.3IndX39 s_7_Ind39.txt 774346.00 0.90 22.60 2.53 8.93
H5 R6.3IndX40 s_7_Ind40.txt 1027525.00 0.68 17.03 2.13 8.00
A6 R6.3IndX41 s_7_Ind41.txt 1153812.00 0.61 15.17 1.80 8.43
B6 R6.3IndX42 s_7_Ind42.txt 928359.00 0.75 18.85 2.35 8.02
C6 R6.3IndX43 s_7_Ind43.txt 1148342.00 0.61 15.24 1.58 9.65
D6 R6.3IndX44 s_7_Ind44.txt 1098551.00 0.64 15.93 1.44 11.06
E6 R6.3IndX45 s_7_Ind45.txt 836268.00 0.84 20.93 2.29 9.14
F6 R6.3IndX46 s_7_Ind46.txt 416424.00 1.68 42.02 3.29 12.77
G6 R6.3IndX47 s_7_Ind47.txt 491180.00 1.43 35.63 4.79 7.44
H6 R6.3IndX48 s_7_Ind48.txt 1315177.00 0.53 13.31 1.52 8.75


  • Note: for AfricanUPenn libraries, 300ul out of 486ul was used for PAGE size selection

PAGE size selection

File:ZhangLab 2 2011-01-20 23hr 31min UPennSeqLib new-1.jpgFile:ZhangLab 2 2011-01-20 23hr 33min UPennSeqLib new-2.jpg

PAGE quantification of TumorJHU and AfricanUPenn libraries

  • perform PAGE analysis to check the size and conc. of sequencing library.

File:ZhangLab 2 2011-01-21 18hr 01min PQ SeqLib final.jpg

  • 0.6 and 0.3ul of DNA was analyzed by PAGE quantification
  • TumorJHU libraries: conc.= 9.4ng/ul or 46.0nM (yield : 9.4ng/ul x 80ul = 752ng)
  • Quantification by Alan (Qubic) : 19.99nM
  • AfricanUPenn libraries: conc.= 7.8ng/ul or 38.0nM (yield : 7.8ng/ul x 80ul = 486ng
  • Quantification by Alan (Qubic) : 18.42nM
  • Note: yield of AfricanUPenn libraries was low because used lower amount for PAGE size selection
  • Note: The extra band above the expected band showed up in this gel. From my experience, this band is possible the expected band that shifts sometime. I used to load DNA with this extra band in denaturing gel, it's gone.