Monday 04/28/14

9:00a – 4:50p, 9:30-9:55p

STORM coding stuff

Code Organization

  • Moved WarpPoints.m and CorrAlign.m into ChromeWarps
  • Commited GitScripts, matlab-functions and matlab-storm

z-calibration issues

  • Jeff reports substantial differences between beads and single-molecules on the 10-15% scale
  • should still be valid for separating different color domains in 3D.
    • should be careful of chromatic differences. Test at least with single-molecules of A750 and A647 on glass coverslip.

ChromatinCropper

  • fixed bug in menu implementation of RunSplitDax (didn’t through .dax flag in dir command)

Data analysis

  • Analyzing C02 data (90kb black TAD near Disco) through
  • some substantial issues with drift / disagreement between conventional and STORM image alignment
  • no accurate chromatic-bead data (not important, there is no bead blead-through in these samples. It has been a useful cross-check to have the bead image (unaligned) super-imposed to see the number and pattern of the beads.)
  • accidently marked locus as blue.
  • C02 data — not fully analyzed through DaoSTORM. Running further analysis now
  • Analyzing C03 data. Looks good.
  • wrote new ViewCC data to combine available data.

Literature

  • paper on cryo-EM of 30nm fiber packing in Science (Song et al)

New stains

  • E04p3 + E05p1 2 clr
  • G08p3 + G06p1 2 clr
  • G02p1 G03p4 2 clr
  • E04 + E05 1 clr
  • E06 + E07 1 clr
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