Noi/NOTES/2013-4-25: Difference between revisions

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* Jeff suggested not go over 15 cycles. I stopped reaction for 10ng UDG at 13 cycles and the rest at 15 cycles to make sure that I would see amplification.  
* Jeff suggested not go over 15 cycles. I stopped reaction for 10ng UDG at 13 cycles and the rest at 15 cycles to make sure that I would see amplification.  
  '''qPCR curve'''
  '''qPCR curve'''
  [[File:20130425_lowinput_CGI.png| 650px]]
  [[File:20130425_lowinput_CGI.png| 650px]]
* The qPCR curve of NTC was lower than other samples. This was not as usual since I expected to see high background of adapters especially in NTC.  
* The qPCR curve of NTC was lower than other samples. This was not as usual since I expected to see high background of adapters especially in NTC.  
* PAGE analysis to verify the PCR products by loading 5 ul of PCR product without bead purification (1/10 of total volume)
* PAGE analysis to verify the PCR products by loading 5 ul of PCR product without bead purification (1/10 of total volume)
  [[File:ZhangLab_2 2013-04-25 18hr 24min_lowinput_CGI_e.jpg| 520px]] [[File:ZhangLab_2 2013-04-25 18hr 16min_lowinput_CGI_e.jpg| 330px]]
  [[File:ZhangLab_2 2013-04-25 18hr 24min_lowinput_CGI_e.jpg| 520px]] [[File:ZhangLab_2 2013-04-25 18hr 16min_lowinput_CGI_e.jpg| 330px]]
S and L: with USER
UDG = Uracil DNA glycosylase
* Will add more info
* Will add more info

Revision as of 03:38, 26 April 2013

  • [Link to calendar]
  • Continued from: http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2013-4-24
  • Received 12 positive control samples using the CGI protocol from Jeff (check details of his experiment in his page)
  • Note from Jeff: I amplified e. coli gDNA using standard in tube MDA, with the addition of diluted dUTP at a very low concentration. I then purified, and diluted the amplicons to 1 ng and 10 ng. I then used USER/Uracil DNA glycosylase (UDG) to remove the dUTPs incorporated during MDA, and used Exo - klenow for nick translation and A tailing.
Sample list (4ul each)
2 10 ng, high USER conc.
2 10 ng, low USER conc.
2 1 ng, high USER conc.
2 1 ng, low USER conc.
2 1ng, UDG
2 10ng, UDG
  • To process these samples
    • Do adapter ligation, bead purification, and PCR
    • Require at least 10X dilution of original volume (4ul --> need minimum ligation reaction 40ul)
    • If the reaction works, we expected to see a smear from ~500 -1500bp
    • Since the length of a smear is large, I would increase extension time during amplification to be longer (1min)
    • Since DNA input is in the range of 1-10ng, I will used the same condition I tried on 2013_04_23 but using 50ul ligation reaction
Order of the tubes (need to check more info with Jeff)
1. 1ng high/low? USER short incubation
2. 1ng high/low? USER short incubation
3. 10ng high/low? USER short incubation
4. 10ng high/low? USER short incubation
5. 1ng high/low? USER long incubation
6. 1ng high/low? USER long incubation
7. 10ng high/low? USER long incubation
8. 10ng high/low? USER long incubation
9. 1ng UDG
10. 1ng UDG
11. 10ng UDG
12. 10ng UDG
13 . NTC

Adapter ligation

  • Adapter ligation mix (Total 50ul) : Ligation reaction mix 49.2ul/reaction & 0.8ul of 3uM adapters (Diluted 30uM adapters 10X with cold 1X Stoffel buffer)
Ligation reaction mix 1x rxn 13x rxn mix
KAPA 5X Ligation buffer 10.00 130.00
KAPA DNA ligase 5.00 65.00
H2O 20.20 262.60
Total 35.20 457.60
  • Aliquot 35.2 ul of ligation reaction mix to each tube
  • Transfer 4ul of sample to reaction tubes
  • Rinse the tube with 10ul H2O and transfer all to reaction tube (total volume now is 49.2ul)
  • Note: for NTC, I accidentally added too much H2O, so total of reaction of NTC was 60.8ul
  • Add 0.8ul of 3uM adapters
  • 20C for 15min (no shaking)
  • Bead purification: 50ul 20% PEG/5M NaCl, wait 10min (no shaking), sit on magnet 5min, wash twice with fresh 80% EtOH, dry for 3 min
  • Eluted with 15ul H2O (used all for PCR)

Amplification

Components 1x rxn 13.5 rxn mix
adapter ligated DNA 15.00 0.00
PCR_F(10uM) 1.00 13.50
PCR_R.N2IndX(10uM) 1.00 0.00
H2O 8.00 108.00
2X KAPA SYBR MM 25.00 337.50
Total volume 50.00 675.00
  • Aliquot 34ul, add 1ul of PCR_R.N2Indx, 15ul of adapter ligated DNA
Samples Indx
1. 1ng high/low? USER short incubation PCR_R.N2Indx1
2. 1ng high/low? USER short incubation PCR_R.N2Indx2
3. 10ng high/low? USER short incubation PCR_R.N2Indx3
4. 10ng high/low? USER short incubation PCR_R.N2Indx4
5. 1ng high/low? USER long incubation PCR_R.N2Indx5
6. 1ng high/low? USER long incubation PCR_R.N2Indx6
7. 10ng high/low? USER long incubation PCR_R.N2Indx7
8. 10ng high/low? USER long incubation PCR_R.N2Indx8
9. 1ng UDG PCR_R.N2Indx21
10. 1ng UDG PCR_R.N2Indx22
11. 10ng UDG PCR_R.N2Indx23
12. 10ng UDG PCR_R.N2Indx24
12. NTC PCR_R.N2Indx24
Program (Eppendorf Realplex)
98C - 30s, (98C - 10s, 62C - 30s, 72C - 60s)x15, 72C - 2min, hold at 15C
  • Jeff suggested not go over 15 cycles. I stopped reaction for 10ng UDG at 13 cycles and the rest at 15 cycles to make sure that I would see amplification.
qPCR curve

File:20130425 lowinput CGI.png
  • The qPCR curve of NTC was lower than other samples. This was not as usual since I expected to see high background of adapters especially in NTC.
  • PAGE analysis to verify the PCR products by loading 5 ul of PCR product without bead purification (1/10 of total volume)
File:ZhangLab 2 2013-04-25 18hr 24min lowinput CGI e.jpg File:ZhangLab 2 2013-04-25 18hr 16min lowinput CGI e.jpg

S and L: with USER
UDG = Uracil DNA glycosylase
  • Will add more info