Friday, 12/27/13

9:30a – 9:50p

Goals

  • Test run of library 3 design. See how many probes we are up to.
  • Test last round of 2 color stains

STORM

  • STORM imaging of F12-647, G1-750. Both dyes nice and bright. Background a bit high in 647 channel this time. (Also pretty pronounced in A750. Could probably drop the concentrations. No idea why they failed the first time).
  • still experiencing buffer run-down.
  • something odd at positions 4 and 5 causes focus loss. Manually fixed for now.
  • Imaged conventional overview and STORM movies
  • need new tape for next time — attachment to stage getting rather loose.

Probe Design

  • created new function OligoArrayCmd.m for turning a few parameters into an executable, and companion program BatchRunOligoArray.m for running in batch.
  • Run time pretty slow on these large chromatin regions (first batch all get killed by the 30 min abort. Bumped this up to 4 hours but only one of the first 4 has finished after nearly 3, so might need longer.
  • Many sequences not finding BLAST hits in genome? despite being assembled from the same genome? (okay, almost the same literal genome file, in truth the one still with chromosomes as separate entries).
  • Running Cajal on the exact Dm_Genome used to select the sequences in the first place (batch of 12).
  • Need to remember: Cajal needs the system paths for OligoArray to be called — took an hour or so of troubleshooting to recall this problem.

Ph Project

  • get cells from Ajaz (now in small 4C fridge. This one needs serious re-organization. As does my drawer yet again. Too many samples).
  • Plan. Get imaging done (Ph, Pc and Psc, all with Ph-flag M and Wt). Build in situ probe library and work on expression in multiple cell lines after submission.

Cell Culture

  • passage cells
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