Kun:LabNotes/CpgSeq/2007-10-12

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Revision as of 06:58, 16 October 2007 by KunZhang (talk | contribs) (New page: ===Fri.Exp.Design: Design padlock probes to capture CpG islands=== I'm starting from the primers used in Taylor et al. Cancer Research, 2007, 67:8511-8. To convert these sequencing into pa...)
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Fri.Exp.Design: Design padlock probes to capture CpG islands

I'm starting from the primers used in Taylor et al. Cancer Research, 2007, 67:8511-8. To convert these sequencing into padlock probes, I need to do the followning:

  • Remove the barcodes at the end of the primers;
  • Convert the right primers to their reverse complementary sequences, add Gs to the end so that the total length of the forward and reverse sequences are the same for all targets;
  • Add common linkers to the two capturing arms.
  • It turned out that the padlock probes are pretty long, getting 24 probes cost > $1000. Decided to make 10 shorter ones only. I also manually remove 4 bps from the PCDGHA12 primers to make them shorter.
  • Synthesizing 10 padlock probes in tubes are not cheap either. After confirm the discount pricing with IDT, I decided to get 24 probes in the plate format.
  • Starting primer file and the actual input file.
  • Perl script to convert primers to padlocks.
  • The first set of padlock probes.