Thursday 12/05/13

9:30a – 12:20a


  • Restart analysis for project 2
  • Probe making: check PCRs, continue if good, restart if not.
  • launch STORM analysis for last few days of imaging

project 2

Chromatin Project

Probe Making

  • Test PCRs
  • Clean, reorganize, recover gel bench. Lots of empty tip boxes, empty buffers,
  • set up T7 reactions. Run overnight
  • PCR gel: (D12, F11, F12, G1, G2, G3, G5, G6)

STORM analysis

  • running D10 and D08 data on Monet.
  • New storm-analysis repository version not working on Tuck / Cajal.
  • wrote to Hazen for suggestions in getting storm-analysis to work correctly.
  • Need to modify .pth file inside Python27 folder. Except we don’t want everyone modifying this file to be different.
  • Fixed startup to add python paths for windows. SetPythonPaths =['set PYTHONPATH=%PYTHONPATH%;',stormAnalysisPath,'; && '];

STORM imaging plans

  • Bogdan will image tonight and Saturday night.
  • I will image Friday and Sunday night.
  • Change of plans, I will image on both STORM2 and STORM4 tonight.
  • confirm E05 fails. F12b also works quite well (have F12 already from last night).
  • E03 small probe set surprisingly seems to work. Setting up to image E03 on STORM2 overnight
  • image beads on STORM4, setting up to test D12rna on STORM4
  • running E11 analysis on Tuck and Cajal
  • Running F08 analysis on Cajal
  • D12rna, spots highly variable. Not totally convinced this worked, I thought I had a much higher frequency of spots per cell last time I did D12. Actually, I don’t appear to have recorded a D12 rna dataset yet. I have multiple E10s. And a D12rna negative control. Should do the E10 rna neg control and the D10 rna soon.
  • Background very high on D12 rna. 47C 1hr washout not sufficient. (Need the 60C oven). Try 60C washout tomorrow. Current background is borderline for imaging.


  • very provactive:
  • seems to me active regions
  • I don’t know about 9 nm separation distances of non-point source objects.
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