Thursday 01/02/2014

9:30a – 9:00p

Ph project

  • Finish O/N STORM run
  • Take IR bead images (slide is also getting clumpy. Maybe we need to stick these down with EDAC. I think making slides for long term storage with Glox is also a bad idea, brighter to start with but shorter shelf-life).
  • start copying data
  • PhM data still fitting
  • Psc Ph data finished analyzing (72 hrs).
  • start re-running Ph folding sims with revised correction of clustering based on unbound fraction.

Variable density of Ph staining (all cy7-Ph-flag staining in Ph Wt background):


More drift analysis

Installed inpaint_nans.m from matlab file exchange to interpolate through NaNs (frames in which beads were not detected). This is required for the cross-correlation to work properly.

Averaging 20 frames (5 Hz), and then smoothing 20 frames, cross-correlation between beads on small time frame is mostly correlated

Auto-correlation is shown on the left, cross-correlation to other beads is shown on the right.




Determining ideal down-sampling

  • comparing 20 frame averaging to 400 frame averaging
  • 20 frame averaging + 20 frame smoothing filter looks better, let’s see how this compares to 400 frame averaging.

Library3 Prep

  • choose black subregions form a solid black TAD (from chr2L)
  • choosing TAD regions



New cell staining

  • G1-P1 (positive control)
  • F3-P1 test
  • F4 P1 test
  • used 12/14 fixed and prepped cells.
  • No RNase treatment (these are all fully silent regions).
  • .5 uL secondary, 2 uL primary each. Used previously successful secondary aliquot (I had doubts about some of the aliquots, switching aliquots earlier correlated with success / failure of staining). Used hybe dilution mix.
  • pre-hybed about 5 min at 47C prior to adding probe, then about 1 hour at 47C after adding probe while heat block was stabilizing for denaturation.
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