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====cpgMIP30k probe set==== Two chromosomes enriched in genes differentially expressed between hES/iPS and fibroblasts. # probes total bps covered CGI covered %CGI covered Chromosome 12 15,998 973,377/924,553 799,818/767,129 82.1%/83.0% Chromosome 20 11,651 654,755/693,920 576,059/550,144 83.0%/84.0% Additional space for other targets: #Key genes in maintaining pluripotency or differentiation. 2000bp up/down-stream of the Transcription Start Sites (TSS, based on SwitchGear TSS), ES-Fib-diff: 780 probes #Genes suggested by the Hochedlinger lab (MEG3,SNRPN,CDX1,HAND1,PAX6,FGF7) KH: 293 probes. [[Kun:LabNotes/CpgSeq/Cpg30k_selected_genes_list|Gene list of #1 & #2.]] #ENCODE regions, Stanf promoters: ENm004: Chr22 151 probes chr22:30,133,954-31,833,953 ENm005: Chr21 271 probes chr21:32,668,237-34,364,221 ENm006: ChrX 307 probes chrX:152,767,492-154,063,081 ENm007: Chr19 276 probes chr19:59,023,585-60,024,460 ENm010: HOXA cluster 135 probes chr7:26,924,046-27,424,045 ENm011: 1GF2/H19 188 probes chr11:1,699,992-2,306,039 ENr123: Chr12 10 probes chr12:38,626,477-39,126,476 ENr333: Chr20 157 probes chr20:33,304,929-33,804,928 Added: ES-Fib-diff 776 (duplicate probes) Total 30,000 Split into three sets: merge chr12 and chr20 probes, sorted by H1/H2 specificity [[Media:cpgMIP30kV2.1b.txt|cpgMIP30kV2.1: low score]] [[Media:cpgMIP30kV2.2b.txt|cpgMIP30kV2.2: medium score]] [[Media:cpgMIP30kV2.3b.txt|cpgMIP30kV2.3: high score + other subsets]] [[Media:cpgMIP30k_probeInfo.txt|Probe information]] [[Media:cpgMIP30k_2008-06-12-read-counts.txt|Capturing Efficiencies based on end-sequencing.]]
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