Kun:LabNotes/CpgSeq: Difference between revisions

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*Probe design: [[Kun:LabNotes/CpgSeq/2007-10-12]]
Probe design:  
*[[Kun:LabNotes/CpgSeq/2007-10-12]]: probe = revcomp(RP) + linker + FP
*Just realized that there was a mistake in probe design (11-20-2007). I assumed that after bisulfite treatment, the two strands are still complementary, which is not true. The probes have to be designed based on one strand only. If the forward PCR primers contain no "C" and the reverse primers contain no "G", that means the target strand is the forward strand. In that case, the padlock probes should be: revcomp(FP) + linker + RP. Here are the revised perl scripts: [[Media: CpG_primer2padlock_v2.txt | first 24 primers]]; [[Media: CpG_primer2padlock2_v2.txt | second 12 primers]]. Here is the new [[Media: CpG_probes_v2.txt | probe file]].

Revision as of 01:58, 21 November 2007

<calendar> name=Kun:LabNotes/CpgSeq format=%name/%year-%month-%day date=2007/11/01 view=threemonths </calendar>


Probe design:

  • Kun:LabNotes/CpgSeq/2007-10-12: probe = revcomp(RP) + linker + FP
  • Just realized that there was a mistake in probe design (11-20-2007). I assumed that after bisulfite treatment, the two strands are still complementary, which is not true. The probes have to be designed based on one strand only. If the forward PCR primers contain no "C" and the reverse primers contain no "G", that means the target strand is the forward strand. In that case, the padlock probes should be: revcomp(FP) + linker + RP. Here are the revised perl scripts: first 24 primers; second 12 primers. Here is the new probe file.