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

From ZhangLabWiki
Jump to navigation Jump to search
Line 13: Line 13:


===Probe design===
===Probe design===
*I designed two sets of probes, one with ~150bp gap size and the other with ~400bp gap size.
*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.
**Target file: [[Media:targetFile_MONOD_v1.txt|targetFile_MONOD_v1.txt]]
*I modified get_probes.pl, and filtered out any candidate capturing arm that has over 6 A/T/G/Cs.
**ppDesigner output
*I repeated the probe design.
***150bp probes: [[Media:ppDesigner_out_150bp_MONOD_v1.txt|ppDesigner_out_150bp_MONOD_v1.txt]]
**PANC_GBM_DMS: [[Media:targetFile_PANC_GBM_DMS.txt|Target list]]
***400bp probes: [[Media:ppDesigner_out_150bp_MONOD_v1.txt|ppDesigner_out_150bp_MONOD_v1.txt]]
***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


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

Revision as of 03:32, 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