Kun:LabNotes/ASE: Difference between revisions

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**I decided to extend the gap size from 1bp to 10bp, which will allow the exclusion of some non-specific circularization products.
**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.
**The capturing arms are Tm normalized with the exception of some SNPs in regions with extreme GC content.
**Amplification adaptors and linker: Version 6, same as CES22k.
**[[Media:circPlex_bigGaps.pl | Codes for generating capturing sequences]]
**Amplification adaptors: Version 4, same as eSNP84k.
**Linker: Version 6, same as CES22k.
**[[Media:p2MIP_bigGaps.pl | Codes for assembling padlock probes]]
**[[Media:eSNP27kbg.txt | Probe sequences]]
**[[Media:eSNP27kbg_info.txt | Probe information]]

Revision as of 02:49, 18 December 2007

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

Design of the CES28K 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 generating capturing sequences
    • Amplification adaptors: Version 4, same as eSNP84k.
    • Linker: Version 6, same as CES22k.
    • Codes for assembling padlock probes
    • Probe sequences
    • Probe information