Friday 10/11/13

10:00a – 10:30p


  • send Ph modeling results to Ajaz
  • work on presentation
  • send reminder about racing Saturday

STORM analysis

  • 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

Ph analysis

  • 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.

Probe making

  • 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

Cell staining

  • 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).

Cell culture

  • Passaged cells, changed media


  • region 5 (last of the first 6 black regions) [Bogdan]
This entry was posted in Summaries and tagged , , , . Bookmark the permalink.