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

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===BSPP capture===
===BSPP capture===
*Alan performed the first experiment on five cancer cell lines and three whole blood samples. Note that Alan also called this probe set as GP1: [[AlanFung:LabNotes/Capturing/2013-12-23]]; [[AlanFung:LabNotes/Capturing/2014-1-14]]
*Alan performed the first experiment on five cancer cell lines and three whole blood samples. Note that Alan also called this probe set as GP1:  
**[[AlanFung:LabNotes/Capturing/2013-12-23]];  
**[[AlanFung:LabNotes/Capturing/2014-1-14]]


===Data analysis===
===Data analysis===

Revision as of 03:46, 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