August 15th Meeting - quevedor2/schramek_wiki GitHub Wiki

In attendance:

  • Samah, Rene, Ellen, Daniel

Goal: Initial meeting to get a better understanding of the project and introduce Samah to Daniel to discuss the possibility of a collaboration.

Samples that Schramek group have:

  • Scrambled control
  • Epigenetic regulators (i.e. Kdm6a, MLL3, MLL4, Asxl2, Setd2, ...)
  • p53 and APC as control groups
  • MCF10A with KO of PIK3CA and epigenetic regulators

ATAC-seq is 50bp single-end

  • 150bp PE would be good for footprinting and determining mutations, but out of budget and scope for this project
  • mouse tumours don't acquire mutations
  • Samah to do: differential accessibility between Scrambled (control) and other epigenetic regulators
  • Check peaks size for potential super-enhancers
  • Any interesting hits would need validation with H3K27ac and H3K4me3

Daniel is interested in looking at Kdm6a

  • Enough cells for Cut&Run, collaboration with Michael Wilson lab
  • For cut&run, methylation works most of the time, acetylation not as much

Samah can do open ATAC differential peaks

  • Targeted-seq dataset from her own cohort covers only 2 of the epigenetic regulators discussed
  • Could always probe more in her 90+ breast cancer cohort

Todo:

  • Compare ATAC-seq between the epigenetic regulators
  • Cistrome prediction from the mouse cell lines to examine enhancers related to genes
  • Examine gene expression of identified target genes
  • Ellen to transfer bam's from OICR cluster
  • Mutual exclusivity test of long-tail TCGA breast cancer genes
  • Ellen ran GeneFu and METABRIC on her own samples
  • Check clustering for the RNAseq profiles, talk with Arvind to discuss clustering between mouse and human transcriptomes