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===Probe design=== *Dinh went through one round of design using ppDesigner v1.1. However, upon close inspection, I found that some capturing arms contain long stretches of poly-Ts or poly-Gs. *I modified get_probes.pl, and filtered out any candidate capturing arm that has over 6 A/T/G/Cs. *I repeated the probe design. **PANC_GBM_DMS: [[Media:targetFile_PANC_GBM_DMS.txt|Target list]] ***Set I: gap size = 400-450bp, flanking len = 250bp; [[Media:PANC_GBM_DMS_400bp_out.txt|ppDesigner Output]] + [[Media:probe2padlockCpgLibNov13V6.txt|probe assembly script V6]] = [[Media:PANC_GBM_DMS_400bp_probes.txt|Probe sequences]]: 3,514 probes ***Set II: gap size = 125-175bp, flanking len = 125bp; [[Media:PANC_GBM_DMS_150bp_out.txt|ppDesigner Output]] + [[Media:probe2padlockCpgLibNov13V4.txt|probe assembly script V4]] = [[Media:PANC_GBM_DMS_1505bp_probes.txt|Probe sequences]]: 6,960 probes **CRC_DMS: [[Media:targetFile_CRC_DMS.txt| Target list]]. ***Set I: gap size = 400-450bp, flanking len = 300bp; [[Media:CRC_DMS_400bp_out.txt|ppDesigner Output]] + [[Media:probe2padlockCpgLibNov13V6.txt|probe assembly script V6]] = [[Media:CRC_DMS_400bp_probes.txt|Probe sequences]]: 148 probes ***Set II: gap size = 125-175bp, flanking len = 175bp; [[Media:CRC_150bp_out.txt|ppDesigner Output]] + [[Media:probe2padlockCpgLibNov13V4.txt|probe assembly script V4]] = [[Media:CRC_DMS_1505bp_probes.txt|Probe sequences]]: 149 probes *[[Media:MONOD_v1_oligos.txt|MONOD v1 oligo pool ordered from Custom Array.]]
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