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

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** 2 clones clearly showed 7T but show overlapping of the peaks surrounding 7T sequences --> request for free repeat
** 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
** 1 clone showed unrelated sequences of the clone amplified by AmpFNU.Sol or AmpFAU.Sol
== Screen more clone for Sanger sequencing ==
== Screen more clones for Sanger sequencing ==
  Perform size screen of the PCR products from 2012_06_03 in 2% agarose gel, load sample 5ul each well (24 clones from each 2U or 5U)
  Perform size screen of the PCR products from 2012_06_03 in 2% agarose gel, load sample 5ul each well (24 clones from each 2U or 5U)
    
    
Line 37: Line 37:
  - Measured DNA conc. by Nanodrop
  - Measured DNA conc. by Nanodrop
== DNA preparation for Sanger sequencing at GENEWIZ ==
== DNA preparation for Sanger sequencing at GENEWIZ ==
{| {{table}} border = 3, style="text-align: center;"
| align="center" style="background:#f0f0f0;"|'''Sample IDs'''
| align="center" style="background:#f0f0f0;"|'''Conc. (ng/ul)'''
| align="center" style="background:#f0f0f0;"|'''~ Volume for 50ng (ul)'''
| align="center" style="background:#f0f0f0;"|'''H2O (ul)'''
| align="center" style="background:#f0f0f0;"|'''10uM Syb_RP7 (ul)'''
| align="center" style="background:#f0f0f0;"|'''Total volume (ul)'''
|-
| 2U-1||41.30||1.25||11.25||2.50||15.00
|-
| 2U-2||41.30||1.25||11.25||2.50||15.00
|-
| 2U-3||28.10||2.00||10.50||2.50||15.00
|-
| 2U-4||39.50||1.25||11.25||2.50||15.00
|-
| 2U-5||47.40||1.25||11.25||2.50||15.00
|-
| 2U-6||26.30||2.00||10.50||2.50||15.00
|-
| 2U-7||19.10||2.50||10.00||2.50||15.00
|-
| 2U-8||16.20||3.00||9.50||2.50||15.00
|-
| 2U-9||39.90||1.25||11.25||2.50||15.00
|-
| 2U-10||42.20||1.25||11.25||2.50||15.00
|-
| 2U-11||35.70||1.50||11.00||2.50||15.00
|-
| 2U-12||32.20||1.50||11.00||2.50||15.00
|-
| 2U-13||36.20||1.50||11.00||2.50||15.00
|-
| 2U-14||45.80||1.25||11.25||2.50||15.00
|-
| 2U-15||33.50||1.50||11.00||2.50||15.00
|-
| 2U-16||35.20||1.50||11.00||2.50||15.00
|-
| 5U-1||33.50||1.50||11.00||2.50||15.00
|-
| 5U-2||26.00||2.00||10.50||2.50||15.00
|-
| 5U-3||22.70||2.00||10.50||2.50||15.00
|-
| 5U-4||26.10||2.00||10.50||2.50||15.00
|-
| 5U-5||42.00||1.25||11.25||2.50||15.00
|-
| 5U-6||41.00||1.25||11.25||2.50||15.00
|-
| 5U-7||34.90||1.25||11.25||2.50||15.00
|-
| 5U-8||38.10||1.50||11.00||2.50||15.00
|-
| 5U-9||46.30||1.25||11.25||2.50||15.00
|-
| 5U-10||41.80||1.25||11.25||2.50||15.00
|-
| 5U-11||41.20||1.25||11.25||2.50||15.00
|-
| 5U-12||30.20||1.50||11.00||2.50||15.00
|-
| 5U-13||27.50||2.00||10.50||2.50||15.00
|-
| 5U-14||35.70||1.50||11.00||2.50||15.00
|-
| 5U-15||38.00||1.25||11.25||2.50||15.00
|-
| 5U-16||33.30||1.50||11.00||2.50||15.00
|}

Revision as of 01:21, 6 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(7A or7N)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)

1ul USER/1U

File:1U-1.png File:1U-2.png File:1U-3.png File:1U-4.png File:1U-5.png File:1U-6.png File:1U-7.png File:1U-8.png File:1U-9.png File:1U-10.png

  • Summary: From 10 clones sequenced by Sanger 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

Screen more clones for Sanger sequencing

Perform size screen of the PCR products from 2012_06_03 in 2% agarose gel, load sample 5ul each well (24 clones from each 2U or 5U)
  
File:2012 06 05 size-screening-2U.png
  
File:2012 06 05 size-screening-5U.png
 
Note: Loading 5ul of PCR product is overloaded in a small well (26-well comb, 2% SYBR safe gel)
  
- Purified 35ul PCR products with 1vol. AmPure beads and eluted with 30ul EB buffer
- Measured DNA conc. by Nanodrop

DNA preparation for Sanger sequencing at GENEWIZ

Sample IDs Conc. (ng/ul) ~ Volume for 50ng (ul) H2O (ul) 10uM Syb_RP7 (ul) Total volume (ul)
2U-1 41.30 1.25 11.25 2.50 15.00
2U-2 41.30 1.25 11.25 2.50 15.00
2U-3 28.10 2.00 10.50 2.50 15.00
2U-4 39.50 1.25 11.25 2.50 15.00
2U-5 47.40 1.25 11.25 2.50 15.00
2U-6 26.30 2.00 10.50 2.50 15.00
2U-7 19.10 2.50 10.00 2.50 15.00
2U-8 16.20 3.00 9.50 2.50 15.00
2U-9 39.90 1.25 11.25 2.50 15.00
2U-10 42.20 1.25 11.25 2.50 15.00
2U-11 35.70 1.50 11.00 2.50 15.00
2U-12 32.20 1.50 11.00 2.50 15.00
2U-13 36.20 1.50 11.00 2.50 15.00
2U-14 45.80 1.25 11.25 2.50 15.00
2U-15 33.50 1.50 11.00 2.50 15.00
2U-16 35.20 1.50 11.00 2.50 15.00
5U-1 33.50 1.50 11.00 2.50 15.00
5U-2 26.00 2.00 10.50 2.50 15.00
5U-3 22.70 2.00 10.50 2.50 15.00
5U-4 26.10 2.00 10.50 2.50 15.00
5U-5 42.00 1.25 11.25 2.50 15.00
5U-6 41.00 1.25 11.25 2.50 15.00
5U-7 34.90 1.25 11.25 2.50 15.00
5U-8 38.10 1.50 11.00 2.50 15.00
5U-9 46.30 1.25 11.25 2.50 15.00
5U-10 41.80 1.25 11.25 2.50 15.00
5U-11 41.20 1.25 11.25 2.50 15.00
5U-12 30.20 1.50 11.00 2.50 15.00
5U-13 27.50 2.00 10.50 2.50 15.00
5U-14 35.70 1.50 11.00 2.50 15.00
5U-15 38.00 1.25 11.25 2.50 15.00
5U-16 33.30 1.50 11.00 2.50 15.00