Dinh/Dinh 2012/NOTES/2012-4-6

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Meeting with Sergio[edit]

  • Our PNAS paper:
  • To do:
    • Thoroughly read related papers on comparing iPSC and stem cells, especially the Bock paper. Go through our manuscript and make sure that all related papers are cited and referenced correctly.
    • We need to perform BSPP on more hESC lines and more iPSC lines if possible.
    • We will need to re-sequence the original 14 samples from Sergio.
      • I went through my boxes and asked both Noi and Alice for the genomic DNA. I have only some converted gDNA which I've kept at -80C. Noi did not handle any of the original 14 samples. The 14 samples' gDNA were kept by Alice, but we don't have any gDNA for several of the samples.
    • We need to do a comparison of our sites with the Bock paper.
      • I downloaded the full RRBS dataset (wig files with methylation fraction for each CpG.)
      • Next I will make a methylation matrix from their sites and our sites together,
      • Can a comparison be made across different technologies? If so, this is a positive thing for our assay.
      • Additionally, can we also see iPS clustering separately from hESC at our aberrantly methylated sites? - If so, we can use their data as "validation" for ours.
    • We need to move the current Figure 1 and make a new Figure 1.
  • One of the major contribution of our paper is that we are using iPSCs from multiple somatic sources.