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===Agilent probes, V3 (Feb. 2009)=== *Targets **16,379 T-DMRs identified by Irizarry et al. Nature Genetics 41:178-86, 2009 **SwitchGear TSS that overlap with CCDS first exons (-400bp to 200bp relative to TSS). Only 775 targets on chrX were included. **179 known or predicted imprinted genes *Degenerate probes: [http://genome-tech.ucsd.edu/LabNotes/upload/large_files/CpgProbes_Jan-chrX_Feb_09_combined-H1H2.xlsx Probe Information] [[Media:probe2padlockCpgLibFeb09.txt | probe2padlockCpgLibFeb09.pl]] [[Media:Amplifiable_MIP_design_KZ_v11.doc|Probe prep schema]]. **69,263 were designed. **Divided into four subsets based on dG: **Set I: dG <= -20; 461 (19 are too long) => 1147 non-degenerate probes **Set II: -20 < dG <= -8; 15,871 (1212 are too long) => 24,322 non-degenerate probes **Set III: -8 < dG < 0; 53,033 (1892 are too long) => 70,294 non-degenerate probes (IIIa: top 15,294 probes; IIIb: bottom 55,000 probes) **Set IV: dG > 0; 1,122 (32 are too long)=> 1,313 non-degenerate probes **The total number of non-degenerated probes is 97,076, which capture 67,332 targets. **The top 55,000 oligos (-8<dG<-2) are in CpgProbes_Jan_55kA; **The remaining 42,076 oligos are in CpgProbes_Jan_55kB. ***9136 Exome-March-09 non-unique probes (amplified with the V4 primers) were also included in this library. ***The remaining spaces were filled by all probes in Set I and some in Set II. **103nt, MW=34kD
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