TF meeting 2

  • TF -> gene interactions
  • Gene expression alone is challenging
  • ATAC can be used for Prior network
  • TRAC Loop is an alternative to ATAC
  • 20% of TF-gene interactions haven't been seen by the network

MAXATAC

  • can be used to predict TF binding from ATAC better than motif scanning.

Validation

  • ChIP-seq and TF KO RNA-seq is used as "gold standard"
  • results are variable based on type of gold standard.

14 CD4+ T cell populations

20 ChIP GS

VTR meeting

  • Do we need to redo the experiments
  • 81 samples in 4 groups
  • 10 HPV ChIP
  • 3 ATAC HPV

HPV

  • 4 strains
  • 2 high risk (16, 18)
  • 3 VTRs in each strains (E2, E6, E7)
  • RNA, ChIP, ATAC

MPRA

  • Combine VTRs
  • pull GWAS catalogue
  • lentivirus (chromatin context)

Can Skip QC

  • Matt Hass has passed them
  • Transient shows that tag does not affect physiological effect

HPV16 and 18 have fewer usable reads than desired

  • going to redo with existing chromatin