9:30 A – 12:15 A
Meeting with Ajaz
- oops it’s daylight savings day!
- Ajaz will induce and fix cells, bring over fixed cells on coverglass
- label with m-anti-Flag + A647-A405-dk a-m secondary and STORM. Compare clusters.
STORM
- Finished O/N imaging of fab7 2xcy5+405 on STORM3
- cleared up failed O/N imaging of fab7 2xCy5 on STORM2
- previous crashes of Hal on STORM2 seem to have been caused by having two sequential conventional images with the same save name.
- set up fab7 3x cy5 for imaging (slide #4)
- cell density and staining is excellent
- dye response to 405 is minimal as expected. Strong 405 makes visible difference in global background
- Setup 22 hrs of data collection saving on to Alistarir10.
- Mounted slide #2: 2x cy5 fab7 for imaging on STORM2.
- Move 3xCy5 sample downstairs to STORM3 for O/N imaging.
- STORM3 power: 85 mW
- STORM2: O/N acquisition of 2xCy5 (this one has dots!)
- STORM3: O/N acquisition of 3xCy5 (def still 405 responsive)
Chromatin
- Design and order sequences
- Discussing library and probe design with Jeff (see post)
- Probe recovery efficiency: from 100 nmol of primer “expected yield” is 1 nmol
- My en probe: .691 cy5 peak. .691/1.7E5 = 4.06E-6 [M] = 4.06 nmoles/mL. .8 nmol yield in 200 uL.
- (yield on 500 kbp is about 40% less).
Writing
- Simplify promoter model
- fix error in previous model of promoter enhancer coupling. Generalize as a function of all enhancer states, not just the fully bound.
- Attempting to make Markov
