Monday 12/30/13

9:20a -7:00p


  • Analyze 2-color STORM data
  • test out new image-writers for hal

Getting started

  • Monet windows explorer froze and got killed. Requires restart.
  • Finish up notes from yesterday, add gel images to notebook.


  • attempted software update to do bead-averaging on-the-fly. Failed.
  • STORM2 software several updates behind, frame objects have been substantially redefined.
  • More consultation with Hazen, updates will require some substantial reconfiguring. Needs to wait until Colenso’s data collection is finished.
  • github not yet set up on STORM2, let’s just try this manually for now.

Analyzing F11-F12 STORM data

  • Starting with image _0_0, 647 channel having trouble being well resolved in STORM images. Not sure why?
    • observation 1, 647 hardly visible in conventional image. I know this slide had good labeling, clear conventional dots. Not sure what’s up.
  • trimming down the number of frames seems to improve the quality in some cases. I think some images exhausted the low level labeling in the first three or five thousand frames and spend the rest of the movie accumulating background
  • background is legitimately quite high in theses movies.

coding matlab-storm

  • working on building a demo-data set
  • don’t really have impressive multi-color STORM images that I’m ready to share openly with the public.
  • building a demo data from down-sampled confocal data of Drosophila embyro — this should illustrate most of the points.




  • Continue reading Kieffer-Kwon et al Cell 2013.
  • still, a very nice data set. Best display of ChIA-PET data I’ve seen, the chip-seq tracks with the red lines linking peaks works well. The promoter enhancer culstering graphs and the complete array organized by complexity are also very nicely done.
  • Types of PolII groups — extragenic – tethering promoters to distal enhancers; intragenic, connecting promoters to gene bodies — (don’t you think these are intronic enhancers? they are rather clear peaks from intronic sequence more than general spread across the gene body) + promoter-promoter and enhancer + enhancer.
  • Though on closer examination I see that they see a clear, though subtle increase throughout the gene body as well of transcribed genes, so maybe this is what is referred to. In which case I think it is very likely enzyme accessibility.
  • how much of this is open chromatin driven? Maybe open chromatin is the biological basis of selection?
  • okay, also later on they do refer examples of an intronic enhancers. So you could call it 5 classes and be clearer, or not define enhancer contacts as necessarily ‘extragenic’.
  • 90% of enhancers linked to a single promoter, less than 2% linked to more than 2, max = 7. (what do you expect by chance as a function of local density of open chromatin regions?)
  • I wonder how many of these promoter promoter contacts are promoter proximal enhancer elements?
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