12:15 pm – 5:30 pm, 8:40 pm – 11:20 pm

Ph manuscript revisions

• went through and main text revisions, updated and replied
• went through supp text revisions, updated and replied
• updated Supp Figs (updated SF1, check with NF about SF11 and 12)
• went through response to reviewers, updated and replied
• sent all docs to XZ for comments
• approved. Sent all docs to NF.

Chromatin manuscript

Main text revisions

• start adding new sections in response to reviewers

More data!

• imaging more examples of C03 to get over 200 cells (on STORM2)
• switching pretty well, selected 57 regions, 60,000 frames, started imaging 11:15 pm

Starting on Figure changes for chromatin manuscript

• (noted below)

Figure changes to do

• Figure 1
  • Add Pc knockdown results to panels c and d (remove ED Fig d)
  • BB
• Figure 2, no change
• Figure 3
  • angle bar graph labels.
  • provide multiple examples for the new images (3?)
  • shrink panels in b to be same size as in Fig 2
  • Try to compress c and b and keep half page
  • STARTED. See draft on MORGAN as AI file (extra space for alternative images)
• Figure 4
  • remove panels a and d
  • compress g and h below the other panels
  • reduce figure to half column width
  • First pass done. Font sizes should drop dramatically to match typical nature — this can be reduced to 50% size probably without switching the font.
• ED Fig 1.
  • keep only images of cells fixed with our method (PFA)
  • Put all bar graphs on same plot
  • “standard” rendering of telomeres. These look like gaussian blurs, should be shaped blobs, should be able to see single molecule background.
  • provide multiple example images.
  • BB will do
• ED Fig 2: no change
• ED Fig 3:
  • switch a and b.
  • render b using examples from Fig 1.
  • contrast and color STORM images in b so they print as in Fig 1.
  • provide multiple examples of this panel to chose from.
• ED Fig 4: no change (unless it can split)
• ED Fig 5:
  • 3 panels only. relabel a, b, c (cut forth panel).
  • COMPLETED
• ED Fig 6:
  • added panels c and d belong in ED Fig 8 instead.
  • COMPLETED
• ED Fig 7:
  • delete this figure
  • (Will need to update numbers)
• ED Fig 8:
  • color controls, PcG targets genes, and Knockdown targets. Add separating lines. For both panels a and c.
  • panel b (RNAseq data) plot as bar-graph ratio as in a.
  • panel d gets cut (this data goes in Fig 1 c and d).
  • add panels c and d from Fig 6.
  • COMPLETED
• ED Fig 9
  • split off new panels as a new ED Fig
  • match sig figs above graphs with those in table.
• Letter Fig 1: Hi-C data
  • for Xiaowei, add all the Hi-C data comparisons shown previously
• Letter Fig 2:
  • keep current version just for Xiaowei’s reference
  • create new figure for the reviewer. Just images, no quantification.
  • 3 x 3 STORM panel of ~.5 Mb domains, ~100 kb domains, and 50 kb domains of Active, Repressed, and Centromeric.