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==Quantify libraries with Phi-X ladder qPCR==
==Quantify libraries with Phi-X ladder qPCR==
==AL-Exome-CViB-Jan14-AB w/ 1/10 dilution, AL-Exome-CViB-Jan14-CDE w/ 1/10 dilution, Ida's library==
==Stock Phi-X (1nM),Stock Phi-X (0.1nM), Stock Phi-X (0.05nM), JD-cpg97k+30k-Breast_cancer-01230B09-Jan15,1/10 JD-cpg97k+30k-Breast_cancer-01230B09-Jan15, 1/10 AL-Exome-CViB-Jan14-AB, 1/100 AL-Exome-CViB-Jan14-AB, 1/10 AL-Exome-CViB-Jan14-CDE, 1/100 AL-Exome-CViB-Jan14-CDE==
{| {{table}}
{| {{table}}
| Setup||||
| Setup||||
|-
|-
| 1nm PhiX||AL-Exome-CViB-Jan14-AB ||AL-Exome-CViB-Jan14-CDE
| Stock Phi-X (1nM)||1/10 JD-cpg97k+30k-Breast_cancer-01230B09-Jan15||1/100 AL-Exome-CViB-Jan14-CDE
|-
|-
| 1nm PhiX||AL-Exome-CViB-Jan14-AB ||AL-Exome-CViB-Jan14-CDE
| Stock Phi-X (1nM)||1/10JD-cpg97k+30k-Breast_cancer-01230B09-Jan15||1/100 AL-Exome-CViB-Jan14-CDE
|-
|-
| 1nm PhiX||AL-Exome-CViB-Jan14-AB ||AL-Exome-CViB-Jan14-CDE
| Stock Phi-X (0.1nM)||1/10 AL-Exome-CViB-Jan14-AB||
|-
|-
| 1nm PhiX||AL-Exome-CViB-Jan14-AB ||AL-Exome-CViB-Jan14-CDE
| Stock Phi-X (0.1nM)||1/10 AL-Exome-CViB-Jan14-AB||
|-
|-
| Ida||1/10 AL-Exome-CViB-Jan14-AB ||1/10 AL-Exome-CViB-Jan14-CDE
| Stock Phi-X (0.05nM)||1/100 AL-Exome-CViB-Jan14-AB||
|-
|-
| Ida||1/10 AL-Exome-CViB-Jan14-AB ||1/10 AL-Exome-CViB-Jan14-CDE
| Stock Phi-X (0.05nM)||1/100 AL-Exome-CViB-Jan14-AB||
|-
| Ida||1/10 AL-Exome-CViB-Jan14-AB ||1/10 AL-Exome-CViB-Jan14-CDE
|-
| Ida||1/10 AL-Exome-CViB-Jan14-AB ||1/10 AL-Exome-CViB-Jan14-CDE
|-
|-
|  
|  
|}
|}
{| {{table}}
{| {{table}}
| ||2 Wells||X13
| ||For 2 wells||X10
|-
|-
| DNA||2||26
| DNA||2.000||
|-
|-
| Syb_FP5 (100uM)||0.2||2.6
| Syb_FP5 (100uM)||0.200||2.000
|-
|-
| Syb_RP7 (100uM)||0.2||2.6
| Syb_RP7 (100uM)||0.200||2.000
|-
|-
| 2X Phusion||25|| ,
| 2X Phusion||25.000||250.000
|-
|-
| 50X SYBR Green||0.2||2.6
| 50X SYBR Green I||0.200||2.000
|-
|-
| H2O||24||312
| H20||24.000||240.000
|-
| Total||||345.8
|-
|-
|  
|  
|}
|}
     * Dilute sample, 1ul in 9ul ddh2o
     * Dilute sample, 1ul in 9ul ddh2o
     * mix 2ul 1/10 sample with 98ul mix in non-stick tube
     * mix 2ul 1/10 sample with 98ul mix in non-stick tube
Line 48: Line 40:


98C 30 sec -> 20 cycles of (98C 10sec->64C 20sec->72C 20sec)->72C 5 min
98C 30 sec -> 20 cycles of (98C 10sec->64C 20sec->72C 20sec)->72C 5 min
  [[Media:JD-cpg97k+30k-Breast_cancer-01230B09-Jan15_log.pdf]]
  [[Media:JD-cpg97k+30k-Breast_cancer-01230B09-Jan15_log_4.pdf]]
  [[Media:AL-Exome-CViB-Jan14-AB.pdf]]
  [[Media:AL-Exome-CViB-Jan14-AB_4.pdf]]
  [[Media:AL-Exome-CViB-Jan14-CDE.pdf]]
  [[Media:AL-Exome-CViB-Jan14-CDE_4.pdf]]
==JD-cpg97k+30k-Breast_cancer-01230B09-Jan15==
{| {{table}}
| ||Well / Set||C(t)||||Difference||nM
|-
| PhiX||A1||6.98||7.06||||
|-
| PhiX||B1||7.2||||||
|-
| PhiX||C1||7.16||||||
|-
| PhiX||D1||6.89||||||
|-
| JD-cpg97k+30k-Breast_cancer-01230B09-Jan15||E1||6.82||6.92||0.14||1.1
|-
| JD-cpg97k+30k-Breast_cancer-01230B09-Jan15||F1||7.09||||||
|-
| JD-cpg97k+30k-Breast_cancer-01230B09-Jan15||G1||6.89||||||
|-
| JD-cpg97k+30k-Breast_cancer-01230B09-Jan15||H1||6.86||||||
|-
|
|}
==AL-Exome-CViB-Jan14-AB==
{| {{table}}
| ||Well / Set||C(t)||Ave.||Difference||nM
|-
| ||||||||||
|-
| ||||||||||
|-
| PhiX||A1||7.99||8.11||||
|-
| PhiX||B1||8.33||||||
|-
| PhiX||C1||8.18||||||
|-
| PhiX||D1||7.95||||||
|-
| AL-Exome-CViB-Jan14-AB||B2||4.48||4.51||3.61||12.17
|-
| AL-Exome-CViB-Jan14-AB||C2||4.57||||||
|-
| AL-Exome-CViB-Jan14-AB||D2||4.47||||||
|-
|
|}
==1/10 AL-Exome-CViB-Jan14-AB==
{| {{table}}
| ||Well / Set||C(t)||Ave.||Difference||nM(X10DF.)
|-
| PhiX||A1||8.55||8.7||||
|-
| PhiX||B1||8.96||||||
|-
| PhiX||C1||8.74||||||
|-
| PhiX||D1||8.56||||||
|-
| 1/10 AL-Exome-CViB-Jan14-AB||G2||8.13||7.99||0.71||16.39
|-
| 1/10 AL-Exome-CViB-Jan14-AB||H2||7.85
|-
|
|}


==1/10 AL-Exome-CViB-Jan14-CDE==
{| {{table}}
{| {{table}}
| ||Well / Set||C(t)||Ave.||Difference||nM (X10DF.)
| nM||||
|-
| PhiX||A1||7.66||7.78||||
|-
| PhiX||B1||8||||||
|-
| PhiX||C1||7.86||||||
|-
| PhiX||D1||7.61||||||
|-
|-
| 1/10 AL-Exome-CViB-Jan14-CDE||E3||6.57||6.68||1.1||21.44
| ||0.6215000||0.0165400
|-
|-
| 1/10 AL-Exome-CViB-Jan14-CDE||F3||6.69||||||
| ||0.6598000||0.0178900
|-
|-
| 1/10 AL-Exome-CViB-Jan14-CDE||G3||6.72||||||
| ||0.9573000||
|-
|-
| 1/10 AL-Exome-CViB-Jan14-CDE||H3||6.75||||||
| ||1.3480000||
|-
|-
|  
| ||0.0010940||
|}
==AL-Exome-CViB-Jan14-CDE==
{| {{table}}
| ||Well / Set||C(t)||Ave.||Difference||nM
|-
|-
| PhiX||A1||7.22||7.32||||
| ||0.0011790||
|-
|-
| PhiX||B1||7.49||||||
| 1.5690000||1.7510000||
|-
|-
| PhiX||C1||7.41||||||
| 1.7850000||1.3480000||
|-
|-
| PhiX||D1||7.16||||||
| Average (nM)||||
|-
|-
| AL-Exome-CViB-Jan14-CDE||A3||3.91||4.14||3.19||9.09
| ||0.641||0.017
|-
|-
| AL-Exome-CViB-Jan14-CDE||B3||4.14||||||
| ||1.153||
|-
|-
| AL-Exome-CViB-Jan14-CDE||C3||4.25||||||
| ||0.001||
|-
|-
| AL-Exome-CViB-Jan14-CDE||D3||4.24||||||
| 1.677||1.550||
|-
|-
|  
|  
|}
|}
==Result==
==Result==
X DF
{| {{table}}
{| {{table}}
| ||||nM
| ||||nM
|-
|-
| JD-cpg97k+30k-Breast_cancer-01230B09-Jan15||||1.1
| JD-cpg97k+30k-Breast_cancer-01230B09-Jan15||||1.677
|-
|-
| 1/10 Ida||||
| 1/10JD-cpg97k+30k-Breast_cancer-01230B09-Jan15||||6.41
|-
| ||||
|-
|-
| AL-Exome-CViB-Jan14-AB||||12.17
| 1/10 AL-Exome-CViB-Jan14-AB||||11.530
|-
|-
| 1/10 AL-Exome-CViB-Jan14-AB||||16.39
| 1/100 AL-Exome-CViB-Jan14-AB||||0.110
|-
|-
| ||||
| ||||
|-
|-
| AL-Exome-CViB-Jan14-CDE||||9.09
| 1/10 AL-Exome-CViB-Jan14-CDE||||15.5
|-
|-
| 1/10 AL-Exome-CViB-Jan14-CDE||||21.44
| 1/100 AL-Exome-CViB-Jan14-CDE||||1.72
|-
|-
|  
|  
|}
|}

Latest revision as of 21:43, 21 January 2010

Quantify libraries with Phi-X ladder qPCR[edit]

Stock Phi-X (1nM),Stock Phi-X (0.1nM), Stock Phi-X (0.05nM), JD-cpg97k+30k-Breast_cancer-01230B09-Jan15,1/10 JD-cpg97k+30k-Breast_cancer-01230B09-Jan15, 1/10 AL-Exome-CViB-Jan14-AB, 1/100 AL-Exome-CViB-Jan14-AB, 1/10 AL-Exome-CViB-Jan14-CDE, 1/100 AL-Exome-CViB-Jan14-CDE[edit]

Setup
Stock Phi-X (1nM) 1/10 JD-cpg97k+30k-Breast_cancer-01230B09-Jan15 1/100 AL-Exome-CViB-Jan14-CDE
Stock Phi-X (1nM) 1/10JD-cpg97k+30k-Breast_cancer-01230B09-Jan15 1/100 AL-Exome-CViB-Jan14-CDE
Stock Phi-X (0.1nM) 1/10 AL-Exome-CViB-Jan14-AB
Stock Phi-X (0.1nM) 1/10 AL-Exome-CViB-Jan14-AB
Stock Phi-X (0.05nM) 1/100 AL-Exome-CViB-Jan14-AB
Stock Phi-X (0.05nM) 1/100 AL-Exome-CViB-Jan14-AB
For 2 wells X10
DNA 2.000
Syb_FP5 (100uM) 0.200 2.000
Syb_RP7 (100uM) 0.200 2.000
2X Phusion 25.000 250.000
50X SYBR Green I 0.200 2.000
H20 24.000 240.000
   * Dilute sample, 1ul in 9ul ddh2o
   * mix 2ul 1/10 sample with 98ul mix in non-stick tube
   * aliquot 24ul to each well, for each sample use the same tip for every well (Pipet slowly!)

98C 30 sec -> 20 cycles of (98C 10sec->64C 20sec->72C 20sec)->72C 5 min

Media:JD-cpg97k+30k-Breast_cancer-01230B09-Jan15_log_4.pdf
Media:AL-Exome-CViB-Jan14-AB_4.pdf
Media:AL-Exome-CViB-Jan14-CDE_4.pdf
nM
0.6215000 0.0165400
0.6598000 0.0178900
0.9573000
1.3480000
0.0010940
0.0011790
1.5690000 1.7510000
1.7850000 1.3480000
Average (nM)
0.641 0.017
1.153
0.001
1.677 1.550

Result[edit]

X DF
nM
JD-cpg97k+30k-Breast_cancer-01230B09-Jan15 1.677
1/10JD-cpg97k+30k-Breast_cancer-01230B09-Jan15 6.41
1/10 AL-Exome-CViB-Jan14-AB 11.530
1/100 AL-Exome-CViB-Jan14-AB 0.110
1/10 AL-Exome-CViB-Jan14-CDE 15.5
1/100 AL-Exome-CViB-Jan14-CDE 1.72