Kun:LabNotes/ASE: Difference between revisions
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**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. | ||
**[[Media:snp2RefGene.txt | Codes for getting SNP flanking sequences]] | **[[Media:snp2RefGene.txt | Codes for getting SNP flanking sequences]] | ||
**[[Media:circPlex_bigGaps. | **[[Media:circPlex_bigGaps.txt | Codes for generating capturing sequences]] | ||
**Amplification adaptors: Version 4, same as eSNP84k. | **Amplification adaptors: Version 4, same as eSNP84k. | ||
**Linker: Version 6, same as CES22k. | **Linker: Version 6, same as CES22k. |
Revision as of 02:57, 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 getting SNP flanking sequences
- 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