9:00 am – 11:00 pm
Working on U01
- drafting figure 1 describing paper results
- drafting figure 2 describing methods
Presentation for Kingston group
- went well, hope this strengthens our collaboration
- should touch base with Nicole about paper
- discussed MNase with Michael
- discussed HiC 5C and mouse hox genes with Patrick
Discussion with Mirny group
Notes
- remember to get google-hangouts or skype setup in advance of meeting and charge PC
- skype now supports multiple video chat (though I think hangouts will interface the slides better)
- action plans below
Geoff will handle
- images of the Hi-C data from all the domains, with the domains labeled (I gave them little names like L2D03, just the genome coordinates will also be fine).
- categorize the domains into “TAD” or “Linker” (or whatever breakdown you think might be interesting. Then I can pick out just these domains and see how they scale for radius of gyration and also compute eccentricities / gyration tensors and all that and look for patterns.
- label the different scaling trends you see in each chromatin type. It would be great to know which blue domains are the ones which show mostly short range contacts vs. more long range contacts. If you just label all the curves, or make a table of scaling coefficients from Hi-C for all domains, that would be very helpful.
- Bogdan and I were talking, and decided it would be nice to use the Hi-C data to look at interaction between neighboring domains. Maybe we could just sum the average number of normalized contacts per 10kb for 50 kb upstream and downstream of the boundary, and compare that the to global average contact frequency.
I will handle
- gyration tensor computations
- comparisons of gyration tensor eigenvalue ratios with Hi-C scaling groups
- comparisons of scaling coefficient fits with Hi-C scaling groups
- incorporation of Hi-C data into figure 3 and main text