Kun:LabNotes/MONOD/2014-3-18

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MONOD Round 3[edit]

Target identification[edit]

  • The specificity of the Round 2 probe set seemed to be very low. Dinh found that 42.5% of the captured targets overlap with repeats. This could explain many off-target reads.
  • In this re-design, I included the RRBS data (ENCODE, GSE52140) for the A549 and HTB56 lung cancer cell line for identifying cancer DMS. In addition, I also added ENCODE RRBS data from normal brain, lung and pancreas as the controls.
  ./find_DMS_PANC_GBM_LC_v3.pl > GBM_PC_LC_DMS_v3.txt
  ../extract_clusters.pl GBM_PC_LC_DMS_v3.txt > GBM_PC_LC_DMS_clusters.v3.txt

Probe design[edit]

  ../filter_probe.pl < GBM_PC_LC_DMS_probes_v3.txt > GBM_PC_LC_DMS_probes_v3_4cpg.txt
  • Dinh helped me to annotate the repeat content of these probes.
  • In the final 12k oligo pool, I included all 6466 non-repetitive probes in this set, plus additional 5534 non-repetitive fetal DMR v2 probes in chrs 13/18/21/X to fill up the space.