Kun:LabNotes/ASE/2007-12-7

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Exp.1 Measure the solexa libraries purified today with PicoGreen on Chromo4[edit]

  • Make 500ul of 1:200 diluted PicoGreen: 2.5ul PicoGreen + 497.5ul 1X TE.
  • Make serial dilution of DNA standard:
     1X TE        2ng/ul DNA       Diluted PicoGreen       Total volume
      0ul           12.5ul               12.5ul                   25ul 
      10ul           2.5ul               12.5ul                   25ul 
    11.5ul             1ul               12.5ul                   25ul 
      12ul           0.5ul               12.5ul                   25ul 
     1X TE        2ng/ul ssDNA       Diluted PicoGreen       Total volume
      0ul           12.5ul               12.5ul                   25ul 
      10ul           2.5ul               12.5ul                   25ul 
    11.5ul             1ul               12.5ul                   25ul 
      12ul           0.5ul               12.5ul                   25ul 
    1X TE            sample          Diluted PicoGreen       Total volume
      10ul           2.5ul               12.5ul                   25ul 

Read twice at SYBG I channel.

Sample layout:

Ds-ref Ss-ref Samples Samples Samples(11/21)
1ng/ul 1ng/ul H1c(12/03) Bjg(12/07) 5
0.2ng/ul 0.2ng/ul H2c(12/03) Bjc(12/07) 6
0.08ng/ul 0.08ng/ul Hues6(12/03) Bjg(11/29) 7
0.04ng/ul 0.04ng/ul H1c(12/07) Bjc(11/29) 8
1ng/ul 1ng/ul H2g(12/07) CES22k#2 9
0.2ng/ul 0.2ng/ul H2c(12/07) CES22k#4 10
0.08ng/ul 0.08ng/ul Hues6g(12/07) CES22k#5 11
0.04ng/ul 0.04ng/ul Huestc(12/07) 12


Chromo4 reads

Ds-ref Ss-ref Samples Samples Samples
A 1.48 0.23 0.13 0.45 0.17
B 0.42 0.14 0.13 0.13 0.35
C 0.24 0.12 0.19 0.81 0.44
D 0.17 0.13 0.13 0.25 0.65
E 1.62 0.21 0.27 0.13 0.52
F 0.41 0.13 0.14 0.14 0.35
G 0.24 0.13 0.25 0.14 0.15
H 0.16 0.12 0.15 0.09 0.35

Calculated DNA concentration:

Samples ng/ul nM Gel quant (ng/ul)
H1c(12/03) 0.13 1.49 0.18
H2c(12/03) 0.1 1.21 0.13
Hues6(12/03) 0.53 6.17 0.82
H1c(12/07) 0.12 1.44 0.11
H2g(12/07) 1.08 12.51 0.98
H2c(12/07) 0.13 1.52 0.13
Hues6g(12/07) 0.9 10.51
Hues6c(12/07) 0.25 2.85
Bjg(12/07) 2.3 26.78
Bjc(12/07) 0.09 1.1
Bjg(11/29) 4.82 56.07
Bjc(11/29) 0.93 10.81
Hues6 gDNA(11/20) 0.35 4.03 1.2
Hues6 cDNA(11/20) 1.6 18.59 2.8
H1 gDNA(222ng/ul) 2.27 26.41 4.5
H1 cDNA(11/20) 3.69 42.91 4.6
H2 gDNA(200ng/ul) 2.84 32.99 3.7
H2 cDNA(11/20) 1.65 19.15 3.2
BJ MDA DNA(11/20) 0.27 3.11 0.34
BJ cDNA(11/20l) 1.59 18.55 3