AlanFung:LabNotes/CTCF/2010-3-21: Difference between revisions

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==Gel Quantification of ligated product==
==Gel Quantification of ligated product==
[[File:ZhangLab_2 2010-03-21 14hr 21min.jpg]]
[[File:ZhangLab_2 2010-03-21 14hr 21min.jpg]]
*band is relative weak, but seems like it is at the right size, I doubt we can get any thing after bisulfite conversion. Will perform a pcr amplification to amplify ligated product. Also move on to bisulfite conversion with the remaining product.
*Might have overestimated the amount of DNA, although nanodrop shows that the concentration is at 33ng/ul and I used 10ul. It is better to perform a PAGE
*Two bands above 180bp shows that a half ligated product is being developed, hence should double the amount of adapter used
*Low Yield of ligated products, DNA might have lost during washing step, need to save 1/10 after each purification to perform a PAGE. Also skip the washing step between end repair and A-tail.

Latest revision as of 17:32, 22 March 2010

Gel Quantification of ligated product[edit]

File:ZhangLab 2 2010-03-21 14hr 21min.jpg

  • band is relative weak, but seems like it is at the right size, I doubt we can get any thing after bisulfite conversion. Will perform a pcr amplification to amplify ligated product. Also move on to bisulfite conversion with the remaining product.
  • Might have overestimated the amount of DNA, although nanodrop shows that the concentration is at 33ng/ul and I used 10ul. It is better to perform a PAGE
  • Two bands above 180bp shows that a half ligated product is being developed, hence should double the amount of adapter used
  • Low Yield of ligated products, DNA might have lost during washing step, need to save 1/10 after each purification to perform a PAGE. Also skip the washing step between end repair and A-tail.