Alice:LabNotes/2009-7-21

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Test the PCR-free library construction protocol[edit]

NA12878_070809: 100ul (7.08ng/ul)
volume were added up to 100ul total with ddH2O (required by Covaris)
Pos. CTRL: 107bp spacer (30ng/ul)

End repair (Enzymatic End-repair Mix)[edit]

                      PGP5     Pos. CTRL
   Sonicated DNA     100ul     25ulDNA + 75ul of H2O
   dNTP                5ul
   10x buffer         12ul
   Enzyme mix          5ul

   Incubate at RT for 30-min
   Purified with QiqQuick columns, eluted with 38ul EB
Nanodrop:
NA12878: 20.5ng/ul
positive control: 7ng/ul

A-tail addition[edit]

   Blunt-ended DNA        35ul
   10X Klenow buffer       5ul
   1mM dATP               10ul
   Klenow fragment (exo-)  1ul
   37C 30min, purified with MinElute columns, eluted with 12ul EB. 

TA ligation[edit]

  • Prepare 20uM adaptor oligo duplex.
     100uM A_adaptor_t         20ul
     100uM A_adaptor_b         20ul
     10x T4 ligase buffer       5ul
     H2O                       55ul
     94C 3min -> cool down to 20C at the rate of 0.05C/sec. 
  • TA ligation:
    • Adaptor/insert ratio should be ~10:1, which would be roughly 2ul per 400ng sonicated DNA.
                                        PGP5       Pos. CTRL     Neg. CTRL
     DNA  (~500ng)                      11ul         11ul         11ul H2O  
     2x QuickLigase buffer (NEB)        16ul         16ul         16ul
     20uM Adaptor oligo mix              3ul          3ul          3ul
     T4 DNA QuickLigase (NEB)            2ul          2ul          2ul
     extra ATP                           5ul          5ul          5ul
     Incubate at RT for 15 minutes.
     Purified with MinElute columns, eluted with 20ul EB

PCR of sequencing library[edit]

                                   x3
   Template                 5ul       
   2x iProof mix           50ul       
   Solexa_PCR_up (10uM)     2ul      
   Solexa_PCR_lo_PE (10uM)  2ul        
   H2O                     41ul     
   50X SYBG I             0.2ul     
 98C 30sec -> 5 cycles of (98C 10sec -> 65C 20sec -> 72C 15 sec) -> 11 cycles of (98C 10sec -> 72C 15 sec)-> 
 72C 3min -> 15C hold.
File:ZhangLab 2 2009-07-21 21hr 02min.jpg
Qiaquick column purification, elute in 30ul EB
Nanodrop: 274ng/ul (260/280: 1.91)
Egel size selection at around 200-225bp
gel quantification: 2.5ng/ul (estimated as 10ng/ul)
Qubit: 27ng/ul

sequencing run[edit]

' Sample Amount loaded Library conc.
Lane 1 phiX 3pmole
Lane 2 phiX 4pmole
Lane 3 NA12878 4pmole 10nM
Lane 4 Hues6ES-DSp 5pmole 38nM
Lane 5 HUES6ES-tRp 5pmole 28nM
Lane 6 Hybrid1-EB 5pmole 606nM
Lane 7 Hybrid2-ES 5pmole 395nM
Lane 8 Hybrid2-EB 5pmole 303nM