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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) == | ||
''' | == Tagging_validation_2012_06_05 == | ||
* Note: | |||
** All samples showing ":Spectral Pull-up" are free-relaoded | |||
** From previous result of re-sequencing of the samples showing "Homopolymeric or Repetitive Region", the results were pretty much the same because of the presence of poly N region upstream of the 7T sequences that causes the non-specific signal after that region. Therefore I will not repeat sequencing for those clones, but the sequences are good enough for validation | |||
== 2ul USER/2U == | |||
{| {{table}} border = 1 | |||
| align="center" style="background:#f0f0f0;"|'''Sample IDs''' | |||
| align="center" style="background:#f0f0f0;"|'''Surrounding sequences<br>contain AGAGTG (7A or 7N) GTG''' | |||
| align="center" style="background:#f0f0f0;"|'''7A, AAAAAAA''' | |||
| align="center" style="background:#f0f0f0;"|'''Note:''' | |||
| align="center" style="background:#f0f0f0;"|'''Pass validation''' | |||
|- | |||
| 2U-1||yes||yes||||yes | |||
|- | |||
| 2U-2||yes||yes||||yes | |||
|- | |||
| 2U-3||yes||yes||||yes | |||
|- | |||
| 2U-4||seem to,yes||most likely yes||:Homopolymeric or Repetitive Region||yes | |||
|- | |||
| 2U-5||seem to,yes||yes||:Homopolymeric or Repetitive Region||yes | |||
|- | |||
| 2U-6||yes||yes||:Spectral Pull-up, free-reload||yes | |||
|- | |||
| 2U-7||most likely yes||yes||:Homopolymeric or Repetitive Region||yes | |||
|- | |||
| 2U-8||yes||yes||||yes | |||
|- | |||
| 2U-9||yes||yes||||yes | |||
|- | |||
| 2U-10||yes||yes||:Spectral Pull-up, free-reload||yes | |||
|- | |||
| 2U-11||not clear||yes, peak not clear||:Spectral Pull-up, free-reload||no: need to confirm by reloading | |||
|- | |||
| 2U-12||not clear||yes, peak not clear||:Spectral Pull-up, free-reload||no: need to confirm by reloading | |||
|- | |||
| 2U-13||yes||yes||:Spectral Pull-up, free-reload||yes | |||
|- | |||
| 2U-14||yes||yes||:Spectral Pull-up, free-reload||yes | |||
|- | |||
| 2U-15||seem to,yes||most likely yes||:Homopolymeric or Repetitive Region||yes | |||
|- | |||
| 2U-16||yes||yes||:Spectral Pull-up, free-reload||yes | |||
|} | |||
'''Summary''' | |||
- Total 16 clones | |||
- 14 clones correct | |||
- 2 clones need to be confirmed by re-sequencing | |||
== 5ul USER/5U == | |||
{| {{table}} border = 1 | |||
| align="center" style="background:#f0f0f0;"|'''Sample IDs''' | |||
| align="center" style="background:#f0f0f0;"|'''Surrounding sequences<br>contain AGAGTG (7A or 7N) GTG''' | |||
| align="center" style="background:#f0f0f0;"|'''7A, AAAAAAA''' | |||
| align="center" style="background:#f0f0f0;"|'''Note:''' | |||
| align="center" style="background:#f0f0f0;"|'''Pass validation''' | |||
|- | |||
| 5U-1||seem to,yes||most likely yes||:Homopolymeric or Repetitive Region||yes | |||
|- | |||
| 5U-2||yes||6T in stead of 7T||||* repeat to confirm 7T | |||
|- | |||
| 5U-3||seem to,yes||most likely yes||:Homopolymeric or Repetitive Region||yes | |||
|- | |||
| 5U-4||yes||yes||:poor quality||yes | |||
|- | |||
| 5U-5||yes||TCTTTTT||||* repeat to confirm | |||
|- | |||
| 5U-6||unclear||seem to, ||:poor quality||? * repeat to confirm | |||
|- | |||
| 5U-7||yes||yes||||yes | |||
|- | |||
| 5U-8||seem to,yes||yes||:Homopolymeric or Repetitive Region||yes | |||
|- | |||
| 5U-9||yes||yes||:Spectral Pull-up, free-reload||yes | |||
|- | |||
| 5U-10||yes||yes||||yes | |||
|- | |||
| 5U-11||seem to,yes||most likely yes,||:Homopolymeric or Repetitive Region||yes | |||
|- | |||
| 5U-12||not clear||seem to by sequences but not the peak||:Spectral Pull-up, free-reload||no: need to confirm by reloading | |||
|- | |||
| 5U-13||yes||TTTTCTT||:Spectral Pull-up, free-reload||* repeat to confirm 7T | |||
|- | |||
| 5U-14||yes||yes||:Spectral Pull-up, free-reload||yes | |||
|- | |||
| 5U-15||yes||yes||||yes | |||
|- | |||
| 5U-16||seem to, yes||yes||:Homopolymeric or Repetitive Region||yes | |||
|} | |||
'''Summary''' | |||
- Total 16 clones | |||
- 11 clones correct | |||
- 5 clones were repeated for confirmation |
Revision as of 00:56, 7 June 2012
Sanger sequencing results of the amplicons amplified with randomly tagging primers (with USER)
Tagging_validation_2012_06_05
- Note:
- All samples showing ":Spectral Pull-up" are free-relaoded
- From previous result of re-sequencing of the samples showing "Homopolymeric or Repetitive Region", the results were pretty much the same because of the presence of poly N region upstream of the 7T sequences that causes the non-specific signal after that region. Therefore I will not repeat sequencing for those clones, but the sequences are good enough for validation
2ul USER/2U
Sample IDs | Surrounding sequences contain AGAGTG (7A or 7N) GTG |
7A, AAAAAAA | Note: | Pass validation |
2U-1 | yes | yes | yes | |
2U-2 | yes | yes | yes | |
2U-3 | yes | yes | yes | |
2U-4 | seem to,yes | most likely yes | :Homopolymeric or Repetitive Region | yes |
2U-5 | seem to,yes | yes | :Homopolymeric or Repetitive Region | yes |
2U-6 | yes | yes | :Spectral Pull-up, free-reload | yes |
2U-7 | most likely yes | yes | :Homopolymeric or Repetitive Region | yes |
2U-8 | yes | yes | yes | |
2U-9 | yes | yes | yes | |
2U-10 | yes | yes | :Spectral Pull-up, free-reload | yes |
2U-11 | not clear | yes, peak not clear | :Spectral Pull-up, free-reload | no: need to confirm by reloading |
2U-12 | not clear | yes, peak not clear | :Spectral Pull-up, free-reload | no: need to confirm by reloading |
2U-13 | yes | yes | :Spectral Pull-up, free-reload | yes |
2U-14 | yes | yes | :Spectral Pull-up, free-reload | yes |
2U-15 | seem to,yes | most likely yes | :Homopolymeric or Repetitive Region | yes |
2U-16 | yes | yes | :Spectral Pull-up, free-reload | yes |
Summary - Total 16 clones - 14 clones correct - 2 clones need to be confirmed by re-sequencing
5ul USER/5U
Sample IDs | Surrounding sequences contain AGAGTG (7A or 7N) GTG |
7A, AAAAAAA | Note: | Pass validation |
5U-1 | seem to,yes | most likely yes | :Homopolymeric or Repetitive Region | yes |
5U-2 | yes | 6T in stead of 7T | * repeat to confirm 7T | |
5U-3 | seem to,yes | most likely yes | :Homopolymeric or Repetitive Region | yes |
5U-4 | yes | yes | :poor quality | yes |
5U-5 | yes | TCTTTTT | * repeat to confirm | |
5U-6 | unclear | seem to, | :poor quality | ? * repeat to confirm |
5U-7 | yes | yes | yes | |
5U-8 | seem to,yes | yes | :Homopolymeric or Repetitive Region | yes |
5U-9 | yes | yes | :Spectral Pull-up, free-reload | yes |
5U-10 | yes | yes | yes | |
5U-11 | seem to,yes | most likely yes, | :Homopolymeric or Repetitive Region | yes |
5U-12 | not clear | seem to by sequences but not the peak | :Spectral Pull-up, free-reload | no: need to confirm by reloading |
5U-13 | yes | TTTTCTT | :Spectral Pull-up, free-reload | * repeat to confirm 7T |
5U-14 | yes | yes | :Spectral Pull-up, free-reload | yes |
5U-15 | yes | yes | yes | |
5U-16 | seem to, yes | yes | :Homopolymeric or Repetitive Region | yes |
Summary - Total 16 clones - 11 clones correct - 5 clones were repeated for confirmation