- 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.
- 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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