Kun:LabNotes/ASE: Difference between revisions
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==Design of the CES27K probe set== | ==Design of the CES27K probe set== | ||
*This is the probe set following the CES22k set. The major differences are: | *This is the probe set following the CES22k set. The major differences are: |
Revision as of 01:06, 6 April 2008
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 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