10:00a – 7:30p, 9:50p – 1:40a

Literature

• need an article for journal club in 2 weeks.
• Elife article on transcription imaging from Tijan lab.
• Feng Zhang lab optical control of transcription.
  • Optical control of transcription. Nature, this was published 7 months ago. Why on earth is the pdf STILL labeled ‘Not Final Version’?
• These might be a better bet:
  • HoxD switch paper
  • HoxA regulation paper: Clustering of tissue-specific subTADs

Ph project

Data analysis

• start analysis of PhM data on Cajal.
• getting images
• There’s got to be a better way than this
  • A.dax + B.ini/B.xml -> Alist.bin/Aalist.bin + Apars.txt
• To recover the ROI we do
  • Alist.bin -> Apars.txt -> B.ini/B.xml. Read ROI.

Working on manuscript revisions

Thoughts on manuscript organization

[Some thoughts on the side: Maybe this could be figure 1 by itself as something simple and short. It’s a less complicated experiment I think then some of the later stuff, but I think it’s also a clear and solid message, and one that really takes a direct debate in the field.
Maybe we could combine figures 5 and 7? They show the mutation affects chromatin binding (at some loci) and gene expression (at some genes). These are absolutely critical experiments, and I think the data is fully convincing. But it’s not really blow-you-away data, the reader anticipates these two effects, and the effects we find are convincing, but small (especially with the Fig 7). So maybe we don’t want to focus so much attention, especially on the expression data, as its own figure — as a final figure I think it’s not a strong punch. I think this is impart a consequence of the cell variability – a reasonable fraction of the total cells in several of the mutant transfections are expressing pretty low levels of the protein, and we systematically don’t pick these guys to image. But we have no way to systematically exclude them in transcriptome profiling (unless you can stain with flag and sort with FACS or something crazy, which I don’t recommend).
Or maybe make the S2 STORM fig 1, combine the multi-color STORM and the Ph-FLAG in fig2? I kinda want to try the DNA FISH immuno doubles (not sure our antibodies will work well, DNA FISH doesn’t play well with a number of antibodies/antigens), but I’m hoping the anti-FLAG at least will still work after FISH. I bet BXC and ANTC colocalize with small clusters of Ph when they are outside of the obvious PcG bodies.

Data collection

• start STORM imaging of WT-Ph-Flag + Psc-647 stain
• running O/N
• still need to image calibration beads

Chromatin Project

• Imaging new stains of ANTC in fresh cells, to correct for partial breakdown of sample.