Alice:LabNotes/2010-1-21

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MmeI digestion on CViB sequencing libraries

  • Previous library construction protocol can be found under labnotes 1-9-10
  • size selection protocol can found under labnotes 1-15-10
setup:
DNA(15nM)                   10ul
10x buffer 4                2ul
1mM SAM                     2ul
MmeI(2U/ul)                 2ul
37C 1hr, 80C 20min

RE-amplify CViB sets for Covaris shearing

  • previously captured libraries on CViB and PGP7 sets
  • the protocol used for the previous steps can be found under labnotes 12-18-09 and 1-5-10 (for CViB sets) and 8-31-09 (for PGP7)
  • for PGP7, capture products with Jan06 and Jan07 probes were disregarded
     PGP7                   1             2            3          
concnetration(ng/ul): 4.4ng/ul      4.5ng/ul      2.9ng/ul  
volume needed (ul):   2.5ul         1.2ul         2.75ul            
CViB-ab:
(a)1.5ul + (b)1.5ul
CViB-cde:
(c)1ul + (d)1.6ul + (e)1.5ul
PCR
Template:                   0.25ul
2x Phusion master mix:      50ul    
100uM AmpF6.3NH2            0.2ul    
100uM AmpR6.3NH2            0.2ul    
50X SYBG I:                 0.4ul    
H2O                         50ul    
98C 30sec -> (98C 10sec -> 58C 20sec -> 72C 20sec) x 6 -> 72C 3min -> 4C hold.