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Kun:LabNotes/ExonomeSeq/2007-11-15
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==Design of padlock probes for the first proof-of-principle chip== *I received two sets of PCR primers targeting 200bp and 400bp amplicons. *I will design padlock probes for both sets, then select a subset of 55k for the first chip. I will include both 200bp and 400bp probes for the genes in the [http://www.sanger.ac.uk/perl/genetics/CGP/cosmic?action=gene_list Cosmic database]. The remaining space on the chip will be used for the 200bp probes in chromosome 22, 21, 20, ... until the chip is full. *I will use the [[Media:CircPlex_design_V7.doc|CircPlexV7]] design for padlock probes. It is a modified version from V6. The only difference is that I added another Mme I site so that I can remove the linker sequences after exon capture if necessary. I've checked the secondary structure of the padlock probe with this new site, and found no major difference. *The way to convert PCR primers to padlock probe is: padlock probe = AP1 + revcomp(RP) + linker + LP + AP2 AP1 = TTGGGTCATATCGGTCACTGTT AP2 = GATCAGGATACACACTACCCGTG Linker = GTTGGAGGCTCATCGTTCCTATTCAGCTGCAGATGTTATCGAGGTCCGAC *Here is the perl code for generating probes.
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