Thursday 07/11/13

10:00 A – 7:00P, 8:30P-10:00P


  • Finish O/N run of PhM-flag-488, Ph-647
  • take bead images
  • transfer data to ProRAID
  • Set up analysis to run on Cajal

Embryo in situs

  • wash out probes
  • check staining: All embryos washed off!
  • 1 tiny section remaining on coverslip 1 (HCl treated, primary + secondary) No sections found on previously excellent coverslip 2. No engrailed expressing cell re-located.
  • complete and horrible failure yet again at En protein + DNA region doubles…


  • HoxD probe finding finally complete.
  • 30K probes (skipping the interval regions for the most centromeric loci, which are respectively 32.5K and 12K probesets)
  • All regions have over 100 probes (min size = 120 probes, median = 583).


  • Reviewing 2013 Hi-C literature
  • read Cavalli review and commentary
  • good general multiC review by Dekker in Nature Genetics.
  • several structural models out: only the simplest like binding sites in region cause like clusters looks reasonable. Infering 3D structures of what might be random polymers from interaction data is BS. What if within a domain, all individual contacts look different.
  • Several software pipelines available for analyzing Hi-C data, none seem to be easy to run and take raw read or paired-region data (raw data on Corces Hi-C paper is paired map locations, not yet mapped back).
  • Li/Corces online data claims it uses the Yaffe bias correction. Recent Harvard Stats code claims to accelerate Yaffe method >1000 times.
  • could request un-normalized data and for annotated ‘region boundaries’?

presentation prep

  • going through Hi-C data
  • added visualization of color regions with Hi-C data + indicator color tracks.

oligoPaint STORM

  • analyzing BX-C sample 1.
  • Nice bright dots, dense cells.
  • Not much switching after bleaching. recording 32K frames.
  • Beads didn’t stick except few clumps. Need to make new beads. Give beads longer to settle.
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