Thursday 10/03/13

10:00a – 7:00p, 10:00p – 11:50p

Goals today

  • prep slides for meeting with XZ
  • 10 cycle PCR with 2 uL of product to add on NEB adapters
  • STORM of more black regions
  • reply to Nicole and Ajaz about Ph


  • “single-cell Hi-C” article
  • Claims:
    1. similar structure on Mb scale (already claimed by previous Hi-C),
    2. cells display heterogeniety on the larger scale (the first Hi-C couldn’t even measure smaller than megabase scale with millions of cells, so it is impressive they even see ‘megabase’ scale. Though claims of resolution in Hi-C seem poorly standardized. However the contact distribution of big chromosome territories was also already known/measurable from chromosome paints).
    3. gene regions on periphery of cell (already claimed by chromosome paints).
  • Ph SAM clustering article
  • Claims
    1. SAM domain functions in recruitment / capture of PRC1 molecules through SAM-SAM interactions (supported by ChIP for Ph and other PRC1 components in SAM mutant)
    2. Promotes clustering of PRC1 components (and Ph) in nucleus through SAM-SAM interactions
    3. promotes looping/condensation of distant PcG bound chromatin regions though K27-PRC1-SAM-SAM-PRC1-K27 bridges

Data analysis

  • G4 round 1 region never got splitdax. Running now. Unfortunately very slow when there’s a lot of other traffic through my USB3.0
  • Analyzing G10 region STORM images on Tuck (Cajal is pending reboot). Currently data transfer limited.
  • Processing BXC and ANTC sub-domains for progress report.
  • Aborted G4 round 1, I have lots of cells in G4 round2, though the localization could look better.

Meeting Prep

  • working on slides for XZ meeting
  • meeting postponed till Monday, need to research physics stories.

Research for XZ AAAS

  • 3p – 6p, looking up / writing up stories of impact of physics on biology.
  • sent to XZ (see email).

Discussions with Thomas and Max

  • 7p-9:30p


  • E2 region (13 kb green)
  • many small spots per cell (2-8 range)
  • STORM going pretty well
  • some feducials vibrate — need to exclude this. Maybe we want ROI correlation based analysis. Or correlation based analysis on maximum density ROIs (some of those bits of junk that don’t turn off can be useful. But when averaged with all the noise it falls apart).
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