9:00a – 4:50p, 9:30-9:55p
STORM coding stuff
Code Organization
- Moved
WarpPoints.m
andCorrAlign.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 indir
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