Friday 11/01/13

10:00a – 9:15p

Coding

ChromatinCropper

  • Current version not saving vlists! (molecule lists specific to ROI).
  • need more display images in analysis.
  • Data analysis: H:\2013-09-24_F6-405\splitdax
  • Savefolder: ‘C:\Users\Alistair\Documents\Research\Projects\Chromatin\Data\2013-11-01_coloredRegions’

SplitDax

  • System now checks filesize of the new daxfile. If expected size = actual size, original file will be deleted when the 'delete' flag is set to to true.
  • testing with blank delete command.

Ph Modeling

  • Does the mutation affect the stability of clusters (e.g. off-rate) or the availability of binding sites for new molecules to join the cluster (on-rate)?
  • Does association of PRC1 into clusters require Pc to bind chromatin as well or just Ph to bind other Ph?
  • If PRC1 monomers do not require chromatin contacts in order to associate through Ph-Ph interaction, then Ph cluster size is determined by the total number of available binding sites, interactions between these binding sites, the concentration of total Ph.
  • If PRC1 association into clusters requires both Ph-Ph contacts AND PRC1-chromatin contacts (e.g. Pc-H3K27me3 association, then cluster size should depend much more weakly on total Ph concentration.
  • code cluster limited version of model.
  • This looks great. Has predicted very weak sensitivity to total Ph concentration.

STORM

  • Finish O/N imaging of G9.
  • Help Bogdan set up imaging on STORM4
  • Teach bead calibration (first time, my demo)

Cell culture

  • cell media looks contaminated
  • May need to add P/S to culture.
  • New cell culture media
  • passage cells (move supernant to new flask, add new (fresh) media to other cells.
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