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.