Noi/NOTES/2012-5-31

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Sequencing libraries of Sergio's samples and Harvard's samples[edit]

- [[1]]  Sergio's samples   : Index 61,62, 65-72
- [[2]]  Harvard's samples  : Index 73-80
  • Pooled equal molar ratio of each library (100ng each)
Well ID conc. (ng/ul) Total amount in 60ul (ng) Volume for 100ng (ul) Well ID
E8** 2.68 160.74 37.31 E8**
F8** 4.95 297.18 20.20 F8**
A9 8.36 501.4 11.96 A9
B9 7.97 478.09 12.55 B9
C9 8.74 524.33 11.44 C9
D9 7.7 461.86 12.99 D9
E9 6.27 376.26 15.95 E9
F9 7.92 474.91 12.63 F9
G9 4.52 270.94 22.12 G9
H9 7.51 450.74 13.32 H9
Sample ID Conc. (ng/ul) Total amount in 80ul (ng) Volume for 100ng (ul) Sample ID
GM12878 3.77 301.51 26.53 GM
P10E3 2.03 162.17 49.26 P10E3
DF2 5.51 440.42 18.15 DF2
H0 7.49 599.2 13.35 H0
H7 5.42 433.83 18.45 H7
H14 3.46 276.75 28.90 H14
H16 5.64 451.17 17.73 H16
GM12878:H0 1:1 5.51 440.87 18.15 GM:H0 1:1
  • Performed PAGE size-selection with 6% TBE 5-well gel (2 gels)
  • Added 80ul 6x loading, load 55ul per well
File:ZhangLab 2 2012-05-31 12hr 22min PAGE-SS SR-HV.jpg
  • Resuspended with H2O, total volume 36ul
  • Quantified concentration by Qubit dsDNA assay by Alan
  • Performed PAGE quantification to verify the size and concentration of sequencing libraries. Concentration by PQ is 17.5ng/ul
File:ZhangLab 2 2012-05-31 12hr 22min PAGE-quan SR-HV.jpg 

Library IDs: NP_BSPP_SR_HV_Ind61.62.65-80_May31,2012, sequenced on HiSeq 120608_SN1001 run at Biogem (Lane: 8)

Sample indexes[edit]

Sample IDs Lab IDs Well IDs IndX
Old bis-cvt gDNA by Dinh (09/01/2010)
Astrocytes D10 SRB_1 A9 AmpR6.3.Ind65
AstiPS4F4 D11 SRB_2 B9 AmpR6.3.Ind66
AstiPS4F5 D9 SRB_3 C9 AmpR6.3.Ind67
HUVEC D12 SRB_4 D9 AmpR6.3.Ind68
HUViPS4F1 D13 SRB_5 E9 AmpR6.3.Ind69
HUViPS4F3 D14 SRB_6 F9 AmpR6.3.Ind70
HFF-XF D3 SRB_7 G9 AmpR6.3.Ind71
hNSC D1 SRB_8 H9 AmpR6.3.Ind72
gDNA samples from Harvard (ASM ASCM project)
GM12878 gDNA 4-5-12 GM AmpR6.3.Ind73
P10E3 gDNA 4-5-12 P10E3 AmpR6.3.Ind74
DF2 gDNA 4-5-12 DF2 AmpR6.3.Ind75
H0 gDNA 4-5-12 H0 AmpR6.3.Ind76
H7 gDNA 4-5-12 H7 AmpR6.3.Ind77
H14 gDNA 4-5-12 H14 AmpR6.3.Ind78
H16 gDNA 4-5-12 H16 AmpR6.3.Ind79
GM12878:H0:: 1:1 GM:H0 1:1 AmpR6.3.Ind80