Kun:LabNotes/MONOD/2013-11-22: Difference between revisions

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***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 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
***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.]]


===BSPP capture===
===BSPP capture===
===Data analysis===
===Data analysis===

Revision as of 03:35, 19 March 2014

MONOD round 1

Target identification

  • Data used:
    • Cancer data:
      • GBM: U87 (ENCODE RRBS Hudson Alpha; ENCODE 450k)
      • Pancreatic cancer: PANC1 (ENCODE RRBS UW & Hudson Alpha; ENCODE 450k)
    • Whole blood data: GSE30253 RRBS data; GSE31263 WGBS data
  • DMSs and DMS clusters identification:
    • I wrote a simple script that takes the average of all existing data for each CpG site, and reported the sites at which the methylation difference was greater than 0.8 between cancer and whole blood.
  ./find_DMS_MONOD_v1.pl > MONOD_v1_DMS.txt
    • These sites were then grouped into DMS clusters.
  ./extract_clusters.pl MONOD_v1_DMS.txt > MONOD_v1_DMS_clusters.txt

Probe design

BSPP capture

Data analysis