Monday 10/28/13

10:00a – 8:30p

Goals

reboot Tuck/Cajal
disconnect all external drives and power supplies. Clean-up all cables for Tuck/Cajal.
Check STORM4 run.
Work on Slides for Rowland Center Talk on Thursday.
Run genes for Hao

Lost focus somewhere. Looks like positions 24-27. Not too bad. Reset remotely this morning, still running
Dyes seem less bright than last night. not sure why. Should look at raw data and see if this difference is real.
STORM4 power progressions don’t use the levels set in the control window. Conventional images end up using Max 488 power and screwing up the image entirely (get’s bleached at the beginning of the z-frame).
power progression failure also starts bleaching the cy5 (with both max 647 and max 488). Seems in fact to be an issue in switching settings files.
STORM4 doesn’t always update settings files: I’ll switch to a new settings file and the run shutters will remain unchecked, but the system will in fact run shutters. Sometimes the display doesn’t update and remains showing the image of the last one.

see what happens with non-unique common names /entrez id but unique ucsc names
Absolutely NO matches to 20,000 ucsc gene names from 1,500 new candidate genes.
Take just first ucsc name for each gene, look up gene in complete Transcriptome.fasta, BLAST to uniqueTranscriptome.fasta
Discuss error calculations

for some reason the PhM is still clustering better than the wt. should be intefering more and move less than wildtype, not more.
did not have FlagM affecting binding between different chromatin clusters. Fixed and rerunning.
currently compute BindingPotential as Bound – Mutant. Binding happens as bimolecular reaction proportional to product of BindingPotential at each site.
need only large clusters to form inter-chromatin bonds. Probability of binding needs to be very small (multiplied by product of site occupancy makes it very large).
Should make the move condition bond breaking energy also related the number of contacts.
breaking should be min(bond1,bond2) not product.

cross-linked feducials: carboxyl-beads (as current) + EDAC (Invitrogen, see protocol) can crosslink to Lysines.
Will need to play with bead concentration and washes to figure out optimal density.

folder: J:\2013-10-04_G05\splitdax
savepath C:\Users\Alistair\Documents\Research\Projects\Chromatin\Data\2013-10-28_coloredRegions