9:15a – 11:15p
Goals
- Call Dad, happy birthday
- Analyze Ph polymer simulations for meeting with Ting.
STORM
- Finish D07 on STORM2 (9 kb green, transcribed, RNaseA treated). Looks transcribed – variable spots, larger than expected for only 9 kb maybe?
- Start E02 on STORM2. (13 kb green (between R/Y)) These look better, pretty clear single spots.
- Scores of beads drifting through the field of view, none stuck. Damn it. I don’t have time to fix this this morning.
- Replaced beads, Adhered with EDAC. Now running E02 imaging O/N.
- Hot washes of RNA stains: D12, E08 and E10 RNA.
- STORM – no signal in D12 RNA. Not good, this worked last time. Maybe RNase contamination?
- no signal in E08 RNA either
- Attempting to image E10dna (previously imaged RNA). Can’t switch scopes easily — Steve-array offsets much easier to same system!
- Broke coverslip removing from STORM 4. Scored coverslips are more delicate, new tape was very strong and the objective was still in contact with the slide.
Meeting with Ting Wu
- not that excited about HiC comparisons
- very excited about showing flanking regions
- try secondary labeling techniques. Design primers for this tomorrow?
- need some genetic manipulation test. Maybe heat shock, maybe LPS. Or siRNA?
Analyzing dot data
- list2img not working given xc, yc, zc, and a data. No idea why. Suspect an imaxes problem. Now troubleshooting.
- Fixed list2img (bug with Z and bug with exclusive inequalities). Still need to test that it works correctly with with STORMrender still.