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 |
- Mapping of samples from harvard to hg19 continued on: http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-6-27