9:30a – 10:00p
- Spoke broke. Pick up repair between 4p-6p.
- working on slides for Rowland Center Talk.
- Finish O/N imaging of E08 (75kb R)
- Set up imaging of E10 (100kb Y)
- genes for Hao, froze at 316. Restarted at 318, running smoothly now.
- Parse final gene list and send to Hao.
- Run for 30mers low stringency.
- Run for 30mers high stringency.
- Run for 40mers high stringency.
- Current implementation of radius of gyration is incorrect. Need to be vector differences. Also need to compute per monte carlo step, not per successful move to sample correctly.
- SAW polymer with finite N on cubic lattice does not have simple analytic form for radius of gyration. Nicodemi et al just use the corresponding polymer (same length with no bonds) to compute normalization.
- Discuss applications of model
- Discuss new statistics to compute on model and data: compute contact probabilities by sampling.
- use contact probabilities to compute scaling law exponent for relationship of contact probability to linear separation distance.
- histogram the frequencies of the different intensities as a proxy for a histogram of density distributions.
- running simulations
Regions for detailed analysis:
- E06 Epc (12 kb YELLOW)
- G06 AlphaTubRegion (37 kb yellow)
- E10 YELLOW 98 kb pure region
- F06 BXC_Y_right (50%Y 40%R 10% K) 140kb
- D12 YELLOW 385kb region
Probes to make next
moderate size regions
- G09 BLUE near ANTC 76 kb
- G04 Antp
- F03 Ubx_through_bxd
- E11 50 kb GREEN scattered with repeats
- E05 BLACK/blue 54 kb region upstream of E(Pc)
- D10 RED 50kb (upstream ush, no gene)
- D08 50 kb green, next to red domain
- G07 AlphaTub84 (5 kb yellow)
- F12 Taf1_(17kb yellow/green)
- F08 RED 7 kb region next to black 1, tRNA locus
- E02 13 kb green (between R/Y)
- E03 BLUE 13 KB (no genes, good PC/Psc)
- E04 BLUE 10 Kb (flanked by strong PolII)
- D07 9 kb Green transcribed