Monday 09/02/13

8:30a – 6:00p, 8:00p – 11:10p

T7 plate reaction planning (?)

  • NEB Quick High Yield T7
  • template = 10 uL of T7 template (~30-120 ng/uL from spot check)
  • 10 uL NTP buffer mix + 1uL (1/2x) T7 polII mix + 10 uL template (~1 ug)
  • 820 uL NTP buffer mix + 82 uL T7 enzyme mix.
  • supplemental NTP buffer mix (400 ul) = 40 uL 25mM rNTPs + 40 uL RNasin + 80 uL 10x buffer + 240 uL ddH2O.
  • incubating at 37C, from 2:30P.

STORM analysis

  • insightM analysis giving weird results — loaded molecule lists back into STORMfinder don’t hit most of the molecules. The frame by frame finder does much better. I’ve seen this before and I can’t remember what causes the error.

Review writing

Review feedback

  • Why use Markov Models
  • How we are going to use Markov models: cartoon, equation, evaluate with computer algebra, interpret analytical solution
  • will be illustrated with examples from literature, examples should be clear enough to build on
  • Need to talk through how to build the Matrix
  • Don’t need extra algebra in the result
  • Mention briefly model approaches in intro.

Additional Goals

  • write paragraph on Thermodynamic gene reg models in development
  • write conclusion paragraph

New STORM buffer

  • made new glox
  • making aliquots of Cyclooctatetraene
  • molecular weight 104.15. 200 mM stock. 104 g in 1 L is 1M. 200 mg in 1 mL is 2M. 20 mg in 1 mL DMSO is 200 mM.
  • made 14 aliquots from 1 mL of 200 mM COT stock
  • sample 2 dots look good.
  • hal not talking to 405 laser, unable to do STORM

Things for discussion with XZ on Thursday

  • keeping feducials attached to sample. (check cross-linked beads tonight/tomorrow)


  • write to participants, final reminder / planning.
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