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

Text

• 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