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 totrue. - 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.