Kun:LabNotes/ASE
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2008 <calendar> name=Kun:LabNotes/ASE format=%name/%year-%month-%day date=2008/02/01 view=oneyear </calendar> 2007 <calendar> name=Kun:LabNotes/ASE format=%name/%year-%month-%day date=2007/11/01 view=threemonths </calendar>
Design of the CES27K9bp probe set (Aug. 2008)
- This is the second probe set that has a gap larger than 1bp. The major differences between CES27K9bp and CES27K are:
- The gap size is 9bp, and the SNPs are 2bp away from the ligation arms (H1) and 6bp away from the extension arms (H2). The reason to place the SNPs further way from the extension arms is to increase the annealing stability of the extension arm with the extension of 6bp before the SNPs are filled. Hopefully this will reduce the allelic difference of circularization efficiency for the probes.
- The annealing temperature was increase to ~65C for the ligation arms and ~53C for the extension arms.
Design of the CES27K probe set
- This is the probe set following the CES22k set. The major differences are:
- The SNPs were chosen based on RefSeq gene instead of the knowngenes table in the GoldenPath database.
- SNPs with MAF>0.05 are included.
- I decided to extend the gap size from 1bp to 10bp, which will allow the exclusion of some non-specific circularization products.
- The capturing arms are Tm normalized with the exception of some SNPs in regions with extreme GC content.
- Codes for getting SNP flanking sequences
- Codes for generating capturing sequences
- Amplification adaptors: Version 6.
- Linker: Version 6, same as CES22k.
- Codes for assembling padlock probes
- Probe sequences
- Probe information