Kun:LabNotes/CpgSeq/2007-12-7: Difference between revisions

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<b>No amplification in both reactions, even after I added another 15 cycles. I then realized that I use the wrong primer AmpF2Sol. so I repeated the experiment using AmpFSol.</b>
<b>No amplification in both reactions, even after I added another 15 cycles. I then realized that I use the wrong primer AmpF2Sol. so I repeated the experiment using AmpFSol.</b>
<b>The second amplification didn't work either, even after 50 cycles.</b>


==Exp.2 Repeat the capturing experiment==
==Exp.2 Repeat the capturing experiment==
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94C 3min -> snap on ice for >1min -> add 2ul 10U/ul DNA Pol I -> 16C 10min -> 37C 10min -> 75C 10min.
94C 3min -> snap on ice for >1min -> add 2ul 10U/ul DNA Pol I -> 16C 10min -> 37C 10min -> 75C 10min.
Purify with MinElute columns.
Purify with MinElute columns, eluted with 22ul ddH2O. Measure concentration.
==Exp.3 Measure the solexa libraries purified today with PicoGreen on Chromo4==
#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
    CpGMIPv2 S2(211nM)        3.3ul
      0ul          12.5ul              12.5ul                  25ul
    CpGMIPv2 L1(243nM)        1.4ul 
      10ul          2.5ul              12.5ul                  25ul
    H2O                      95.3ul
    11.5ul            1ul              12.5ul                  25ul
      12ul          0.5ul              12.5ul                  25ul


     1X TE           sample          Diluted PicoGreen       Total volume
                RL DNA(31ng/ul) Jurkat DNA(32ng/ul)
      10ul          2.5ul               12.5ul                   25ul
    Template      10ul            10ul
     10x buffer  1.5ul           1.5ul
    10nM CpG-MIP  2ul              2ul       (set up another 2 with the v1 probes)
    H2O          1.5ul           1.5ul


Read twice at SYBG I channel.
94C 3min->65C 20h-> add 1ul SLN mix (2U/ul stoffel, 2U/ul AmpLigase, 2mM dNTP) -> 65C 30min -> 15 cycles of (94C 1min -> 65C 1h) -> 65C 4h -> 37C 1min -> add 1ul of exo mix (Exo I, Exo III, T7 exo)->37c 1 hour -> 94C 5min -> 4C hold.

Latest revision as of 22:23, 9 December 2007

Exp.l PCR on the captured CpG islands[edit]

  • Template: two capturing reactions started at 12/05/2007.
  • Primer: Amp_F_sol, Amp_R_sol
                          x 1         x 2
     template:            5ul         10ul
     ABI 10x buffer:    4.5ul          9ul
     25mM MgCl2:          3ul          6ul
     10mM dNTP:           1ul          2ul
     100uM AmpFSol:    0.15ul        0.3ul
     100uM AmpRSol:    0.15ul        0.3ul
     50X SYBG I:        0.4ul        0.8ul
     iTaq:                1ul          2ul
     H2O:              35.3ul       70.6ul

94C 3min -> 10 cycles of (94C 45sec -> 59C 2min -> 72C 1min) -> 20 cycles of (94C 45 sec -> 72C 1min) -> 72C 3min -> 15C hold.

No amplification in both reactions, even after I added another 15 cycles. I then realized that I use the wrong primer AmpF2Sol. so I repeated the experiment using AmpFSol.

The second amplification didn't work either, even after 50 cycles.

Exp.2 Repeat the capturing experiment[edit]

  1. I decided to repeat phosphorylation reaction on the probes by adding 0.5ul 10mM ATP and 1ul T4PNK to the reactions (S1, S2, L), 37C 15min, 85C 10min.
  2. I also decided to do one round of DNA synthesis on the bisulfite converted DNAs to convert them into dsDNA prior to the capturing reactions.
    DNA                 20ul
    10x NEBbuffer2       3ul
    10mM dNTP          1.5ul
    100uM N6             3ul
    

94C 3min -> snap on ice for >1min -> add 2ul 10U/ul DNA Pol I -> 16C 10min -> 37C 10min -> 75C 10min. Purify with MinElute columns, eluted with 22ul ddH2O. Measure concentration.

   CpGMIPv2 S2(211nM)         3.3ul
   CpGMIPv2 L1(243nM)         1.4ul   
   H2O                       95.3ul
               RL DNA(31ng/ul) Jurkat DNA(32ng/ul)
    Template      10ul             10ul
    10x buffer   1.5ul            1.5ul
    10nM CpG-MIP   2ul              2ul       (set up another 2 with the v1 probes)
    H2O          1.5ul            1.5ul

94C 3min->65C 20h-> add 1ul SLN mix (2U/ul stoffel, 2U/ul AmpLigase, 2mM dNTP) -> 65C 30min -> 15 cycles of (94C 1min -> 65C 1h) -> 65C 4h -> 37C 1min -> add 1ul of exo mix (Exo I, Exo III, T7 exo)->37c 1 hour -> 94C 5min -> 4C hold.