Noi/NOTES/2012-6-5: Difference between revisions
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>Noi (Created page with "* http://genome-tech.ucsd.edu/LabNotes/index.php/noi:DMR220k_LabNotes '''Link to calendar''' = Randomly tagging primer experiment = * Continued from: http://genome-tech.uc...") |
>Noi No edit summary |
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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