Dinh/Dinh 2014/NOTES/2014-9-26

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Meeting notes[edit]

460K[edit]

  • TO do:
    • Perform more experiments to optimize capture.
    • At the same time, work with Tifffany on the TAB-seq for MDS project & get more experience with Tet oxidation prior to starting my own project.

Mouse SCNT[edit]

  • TO do:
    • Verify our iPS versus SCNT DMRs - do they lie in regions of different nucleosomal occupancies in ESC versus somatic/iPS ?
    • Can we tell whether all of our iPS and all of the SCNT can form tetraploids?
    • Can we show that iPS is still a viable technology?

Methylation Haplotyping[edit]

  • TO do:
    • Repeat methylation plots with only the BC samples. (Although it is encouraging that the cancer cell lines more methylated, this may not be an accurate representation of cancer in-vivo.)
  • We now have two approaches:
    • Fishing - start with a comprehensive database of what is considered cancer and then look for anything that is cancer-like. This is the more specific approach. We can use our solid cancer data & extract cancer specific haplotypes to build our cancer database
    • Substraction - start with a picture of what is normal, and then pull out anything that look abnormal. This is the more sensitive approach. Go through the plasma data and look for methylated regions in unmethylated bins in normal tissues.