Tuesday 10/29/13

9:30a – 10:00p

Other Goals

  • Spoke broke. Pick up repair between 4p-6p.

Presentation Prep

  • working on slides for Rowland Center Talk.


  • Finish O/N imaging of E08 (75kb R)
  • Set up imaging of E10 (100kb Y)

Mentoring HC

  • 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.

Mentoring BB

  • 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.

Ph Project

  • running simulations

Regions for detailed analysis:

Yellow series:

  • 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

Difficult probes

  • 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
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