AlanFung:LabNotes/CTCF/2011-5-10: Difference between revisions

From ZhangLabWiki
Jump to navigation Jump to search
>Alan6017518
>Alan6017518
Line 4: Line 4:
[[File:ZhangLab_2 2011-05-10 10hr 40min.jpg|500px]]
[[File:ZhangLab_2 2011-05-10 10hr 40min.jpg|500px]]
* Need to purify CHR8, CHR21, and CHR22.
* Need to purify CHR8, CHR21, and CHR22.
** Then need to estimate the concentration
**Qubit Results
*CHR8-3.25ng/ul
*CHR21-4.39ng/ul
*CHR22-4.77ng/ul
 
** Need amplicon length (~200)
** Need amplicon length (~200)
* Run an experiment where we do PCR on both Bisulfite-converted DNA and the three controls
* Run an experiment where we do PCR on both Bisulfite-converted DNA and the three controls

Revision as of 21:22, 24 May 2011

Bisulfite Conversion DNA Damage Estimation

  • Perform PCR with CHR8, CHR21 and CHR22
  • These will be our standards

File:ZhangLab 2 2011-05-10 10hr 40min.jpg

  • Need to purify CHR8, CHR21, and CHR22.
    • Qubit Results
  • CHR8-3.25ng/ul
  • CHR21-4.39ng/ul
  • CHR22-4.77ng/ul
    • Need amplicon length (~200)
  • Run an experiment where we do PCR on both Bisulfite-converted DNA and the three controls
    • Want to make sure number of starting molecules is the same.
  • With normal DNA, 5 pg ~= 2 molecules
  • With PCR product, X pg ~= 2 molecules; X << 5
  • Need to run a PCR reaction using 500 pg of bisulfite converted DNA and X pg of PCR product as templates, with X such that the number of molecules in each tube is the same.
    • Can run QPCR to check for DNA damage; only hot-start for 30 seconds instead of 3 minutes.