Noi/NOTES/2012-5-14: 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''' == Probe production for the HiResChrPaint project == * Continued from the plan...")
 
>Noi
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'''Program'''<br>  
'''Program'''<br>  
95C 30sec -> (95C 3sec -> 55C 30sec-> 72C 20sec) x 16 -> 72C 2min -> 15C hold.<br>
95C 30sec -> (95C 3sec -> 55C 30sec-> 72C 20sec) x 16 -> 72C 2min -> 15C hold.<br>
#1-V4 -> 16 cycles
#2-V4 -> 16 cycles
#3-V4 -> 14 cycles
#4-V4 -> 15 cycles
*'''V6 pool for all four sets (12 reaction for each set)'''
*'''V6 pool for all four sets (12 reaction for each set)'''
{| {{table}}
{| {{table}}
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'''Program'''<br>
'''Program'''<br>
95C 30sec -> (95C 3sec -> 55C 30sec-> 72C 20sec) x 15 -> 72C 2min -> 15C hold.<br>
95C 30sec -> (95C 3sec -> 55C 30sec-> 72C 20sec) x 15 -> 72C 2min -> 15C hold.<br>
  - Check the size distribution of the amplicons with 6% TBE gels.
#1-V6 -> 15 cycles
#2-V6 -> 14 cycles
#3-V6 -> 14 cycles
#4-V6 -> 14 cycles
   - Ethanol precipitation.
   - Ethanol precipitation.
    - Pool amplified amplicons (total volume 1,200ul each set) into 15mL tube
    - Add 4ul of Glycoblue
    - Add 120ul of 3M NaoAc pH5.5
    - Add 3mL of 100% EtOH
    - Put the tubes at -80C for 1hr
    - Centrifuge at 3,000rmp for 30min, 4C
    - Remove spnt. add 600ul of 75% EtOH and transfer the DNA pellet to 1.5 mL tube
    - Spin at 14,000rmp for 5min
    - Dry the pellet in the hood and resuspend with 100ul H2O
   - Re-purified each amplicon with two Qiaquick columns, eluted with 40ul EB.
   - Re-purified each amplicon with two Qiaquick columns, eluted with 40ul EB.
   - Measure concentration.
   - Measure concentration.

Revision as of 19:19, 14 May 2012

Probe production for the HiResChrPaint project

Production PCR

  • V4 pool for all four sets (12 reaction for each set)
Components Volume (ul) 49x rxn mix
20nM oligo pool 0.20 0.00
2x Kapa SYBG qPCR MM 50.00 2,450.00
100uM pAP1V41U 0.40 19.60
100uM AP2V4 0.40 19.60
2mM aa-dUTP 3.00 147.00
H2O 46.00 2,254.00
Total volume (ul) 100.00 4,900.00

- Aliquot 1197.6 ul in 1.5 mL tube, add 2.4ul of each oligo pool to each tube
Program
95C 30sec -> (95C 3sec -> 55C 30sec-> 72C 20sec) x 16 -> 72C 2min -> 15C hold.

#1-V4 -> 16 cycles
#2-V4 -> 16 cycles
#3-V4 -> 14 cycles
#4-V4 -> 15 cycles 
  • V6 pool for all four sets (12 reaction for each set)
Components Volume (ul) 49x rxn mix
20nM oligo pool 0.20 0.00
2x Kapa SYBG qPCR MM 50.00 2,450.00
100uM pAP1V61U 0.40 19.60
100uM AP2V6 0.40 19.60
2mM aa-dUTP 3.00 147.00
H2O 46.00 2,254.00
Total volume (ul) 100.00 4,900.00

- Aliquot 1197.6 ul in 1.5 mL tube, add 2.4ul of each oligo pool to each tube
Program
95C 30sec -> (95C 3sec -> 55C 30sec-> 72C 20sec) x 15 -> 72C 2min -> 15C hold.

#1-V6 -> 15 cycles
#2-V6 -> 14 cycles
#3-V6 -> 14 cycles
#4-V6 -> 14 cycles
  - Ethanol precipitation.
    - Pool amplified amplicons (total volume 1,200ul each set) into 15mL tube
    - Add 4ul of Glycoblue
    - Add 120ul of 3M NaoAc pH5.5
    - Add 3mL of 100% EtOH
    - Put the tubes at -80C for 1hr
    - Centrifuge at 3,000rmp for 30min, 4C
    - Remove spnt. add 600ul of 75% EtOH and transfer the DNA pellet to 1.5 mL tube
    - Spin at 14,000rmp for 5min
    - Dry the pellet in the hood and resuspend with 100ul H2O
  - Re-purified each amplicon with two Qiaquick columns, eluted with 40ul EB.
  - Measure concentration.