Noi/NOTES/2012-6-5: Difference between revisions

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== Sanger sequencing results of the amplicons amplified with randomly tagging primers (with USER)==
== Sanger sequencing results of the amplicons amplified with randomly tagging primers (with USER)==
'''Check Sanger's sequencing result roughly before sending more clones'''
'''Check Sanger's sequencing result roughly before sending more clones'''
* Primimg with Syb_RP-7: read reverse complementary of the AmpFA/NU.Sol strand
         qs (quality score) Sequence correct            7nt=AAAAAAA    Note
         qs (quality score) Sequence correct            7nt=AAAAAAA    Note
                           contain AGAGTG(7)GTG       
                           contain AGAGTG(7)GTG       
  1U-1  29                seem to (overlapping peaks)  yes,          :Homopolymeric or Repetitive Region                 
  1U-1  29                seem to (overlapping peaks)  yes,          :Homopolymeric or Repetitive Region, **request for free repeat                
  1U-2  29                yes                          yes,          :Homopolymeric or Repetitive Region
  1U-2  29                yes                          yes,          :Homopolymeric or Repetitive Region
  1U-3  33                yes                          yes,          chromatogram very clear even the peak very low
  1U-3  33                yes                          yes,          chromatogram very clear even the peak very low
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  1U-6  43                yes                          yes,       
  1U-6  43                yes                          yes,       
  1U-7  42                yes                          yes,          chromatogram very clear even the peak very low
  1U-7  42                yes                          yes,          chromatogram very clear even the peak very low
  1U-8  14                seem to (overlapping peaks)  yes          Non-specific, request for free repeat
  1U-8  14                seem to (overlapping peaks)  yes          Non-specific, **request for free repeat
  1U-9  31                yes                          yes,                           
  1U-9  31                yes                          yes,                           
  1U-10  43                no                          no,          This clone has a shift band higher than other positive clones on E-gel
  1U-10  43                no                          no,          This clone has a shift band higher than other positive clones on E-gel
                                                                       will look closer to the sequences (seem to be neither AmpFNU.Sol nor AmpFAU.Sol)
                                                                       will look closer to the sequences (seem to be neither AmpFNU.Sol nor AmpFAU.Sol)
* Summary: From 10 clones sequences by Sanger's sequencing
** 7 clones are clearly correct and all contain 7T
** 2 clones clearly showed 7T but show overlapping of the peaks surrounding 7T sequences --> request for free repeat
** 1 clone showed unrelated sequences of the clone amplified by AmpFNU.Sol or AmpFAU.Sol
* Images of trace file will be uploaded later

Revision as of 16:00, 5 June 2012

Randomly tagging primer experiment

Sanger sequencing results of the amplicons amplified with randomly tagging primers (with USER)

Check Sanger's sequencing result roughly before sending more clones

  • Primimg with Syb_RP-7: read reverse complementary of the AmpFA/NU.Sol strand
       qs (quality score) Sequence correct             7nt=AAAAAAA    Note
                          contain AGAGTG(7)GTG      
1U-1   29                 seem to (overlapping peaks)  yes,          :Homopolymeric or Repetitive Region, **request for free repeat                
1U-2   29                 yes                          yes,          :Homopolymeric or Repetitive Region
1U-3   33                 yes                          yes,          chromatogram very clear even the peak very low
1U-4   32                 yes                          yes,          
1U-5   42                 yes                          yes,          
1U-6   43                 yes                          yes,      
1U-7   42                 yes                          yes,          chromatogram very clear even the peak very low
1U-8   14                 seem to (overlapping peaks)  yes           Non-specific, **request for free repeat
1U-9   31                 yes                          yes,                           
1U-10  43                 no                           no,           This clone has a shift band higher than other positive clones on E-gel
                                                                     will look closer to the sequences (seem to be neither AmpFNU.Sol nor AmpFAU.Sol)
  • Summary: From 10 clones sequences by Sanger's sequencing
    • 7 clones are clearly correct and all contain 7T
    • 2 clones clearly showed 7T but show overlapping of the peaks surrounding 7T sequences --> request for free repeat
    • 1 clone showed unrelated sequences of the clone amplified by AmpFNU.Sol or AmpFAU.Sol
  • Images of trace file will be uploaded later