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===Agilent probes, V1=== *Several considerations in this design include: **Degenerate bases: I allowed at most two degenerate bases per primer. To convert PCR primers to padlock probes, multiple probes will be designed for one primer pair in order to cover all combinations. **Gap size: The range of amplicon size is 225-275bp, so the gap size is approximately 185-225bp. **Amplification adaptors: Version 4; Linker sequences: Version 7 AP1: GTAGACTGGAAGAGCACTGTT V4 AP2: GATCGGATACGCATGAGGCTA V4 Linker: GTTGGAGGCTCATCGTTCCTATTCAGCTGCAGATGTTATCGAGGTCCGAC ------ ---- ------ Mme I Alu I Mme I *Here is the [[Media: getCpGPrimers.txt |perl code for primer design]]. The input file is cpgIslandExt.txt downloaded from UCSC GoldenPath database. *Conversion of PCR primers to padlock probes: AP1 + revcomp(FP) + linker + RP + AP2. [[Media:primer2padlockCpgLibV1.txt|codes]]. <u>Some statistics</u> Total probes: 210,498 Total CpG islands: 23,496 Total non-overlapping regions: 12,037,010 bps Total captured sequences: 13,291,608 bps ===CpgMIP28k set=== probes CpG islands Chr6: 9,875 3,028 (1103/1251, 559kb/940kb) Chr20: 6,197 1,930 (695/779, 358kb/613kb) Chr21: 2,619 809 Chr22: 5,358 1,664 (622/716, 310kb/562kb) Chr19: first 3,857 **[[Media:Cpg28kV1_probes.gz|Probe information file.]] **[[Media:Cpg28kV1.txt|Probe raw sequences.]] **[[Media:cpgMIP28k_2008-05-14-read-counts.txt|Capturing Efficiencies based on end-sequencing.]] **ssDNA probes: len=102nt, MW=31KDa.
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