10:00a – 10:30p
- send Ph modeling results to Ajaz
- work on presentation
- send reminder about racing Saturday
- Copying F11 data to ProBox2. Delete data from Storm2
- Running splitdax on no405Primary, E07fail, F09, and F01v2 (latter 2 including 488 channel)
- This may be a problem for datasets that don’t have 488? Let’s check the source code. I think I coded this correctly so that it only affects channels out. Hopefully if the channel doesn’t exist it won’t attempt to export. Will need to watch and confirm.
- Run splitdax on other black chromatin data
- Running simulations for different concentrations of PhM-flag
- Meeting with Ajaz, see notes.
- Working on speeding up model. Need to replace loop over all collisions.
- Testing model where association rate depends on PhWt to PhM ratio.
- All in vitro transcription reactions failed: 20-100 ng/uL in 40 uL, expected 2,000-4,000
- Possibly RNA purification failure? Followed the 5 minute incubation recommended in the header rather than the 20 minute incubation previously used.
- RNase contamination? Run test gel to see if sample smears?
- Too much glycerol from T7 enzyme + RNase inhibitor?
- Unable to make conclusion on .25x vs .75x buffer (.75x is recommended concentration)
more samples for Bogdan PCR
- G01, ANTC left extreme
- F02, BXC_Y_left (15 kb)
- F03, Ubx_through_bxd
- F04, AbdA_through_iab4
- F05, iab5_through_AbdB
- F06, BXC_Y_right (50%Y 40%R 10% K) 140kb
- rinse out O/N hybe of F2, F12, G3/G4, G4/G3, F9/G3
- 60C heat oven in use, trying hot bath
- 10 min rinse 1 in 2x SSCT
- forgot samples in hot bath and extra ~40 minutes (instead of second 10 minute incubation).
- Passaged cells, changed media
- region 5 (last of the first 6 black regions) [Bogdan]