Noi/NOTES/2012-6-6: 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) ==
'''Tagging_validation_2012_06_05'''
== 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