Tuesday 05/12/15

Chromatin Paper

  • updated PlotGenes to fix issues with arrowheads. Much nicer now.
    • applied in Extended Data Fig 3. Others still need updating.
  • Working on Extended Data Fig 6: illustrating differences between active domains of similar size.

Paper To Do list


  • For the abstract and mostly intro: don’t over-emphasize epigenetic structure. We study structure at the relevant length scales for gene regulation / genome functions. Epingenetic domains are one of the indicators that this length scale is important, and it turns out a strong predictor of structure.
  • With respect to Blue internal scaling, can’t say most models — invites question of other models. Move to discussion of models, not in data. Discuss the equilibrium globule model. Say no model fits all the data for Blue.
  • Need to discuss off-trend points in model section
  • be sure word “loop” does not appear in text
  • need to write Cover Letter.

Main Figures

  • add scalebars to Fig 1a
  • need multiple examples of different contrast /saturation options for Fig 2a and b
    • contrast / saturation for Repressed domains is a bit strong.
    • images are a little blury — plot with different Gaussian widths

Extended Data Figure

  • New Fig
    • histograms of volume and radius of gyration distributions for all domains.
    • similar histograms for FG model data?
  • ED2 ‘internal scaling of repressed regions’
    • reorder panels. BX-C vol, ANTC chip, ANTC rg, ANTC vol
    • All int data plots: solid lines for int-data, dashed for old data
  • Tracing fig
    • no backbone
    • 15 spots
    • green-green junctions linked by green lines. magenta by magenta lines. Black lines between interjunctions
    • also in data follow junction code.
  • New example stats
    • select regions similar length
    • show existing stats
    • also show cell-cell variation
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