Saturday 03/24/12

10:15 A

  • Assemble draft protocol of embryo multiplex RNA-Protein STORM send to Stacie at Stowers.
  • 5 mL of culture in probably too much to get good aeration in small round-bottom tubes.  Try 2 mL next time.  use Zhuang shaker, it shakes faster.
  • Pellet cells, will continue mini-preps when I catch up on my paperwork stuff.
Genome work
  • Attempting to upload multiple mod-encode tracks to the UCSC browser.  Current obstacle is all tracks are have ‘BED format’ as the file name, and they just replace each other when you go to upload them.
  • Chromosome names also mismatched on many modenocde data sets, UCSC uses chr2L, chr3R etc, modencode some users use just 2L, 3R… on uncompressed wig, change “chrom=” to “chrom=chr”.  Can also change file name from ‘BED format’ to correct data descriptor, then upload tracks.  works!  Very strong global Psc / H3K27me3 correspondence.
Data Analysis
  • Processing oligo-STORM round 1 data (see post).
  • Saturated camera during bead calibration images = not usable for calibration.  Need to remember to check this.
  • Embedding HP1 samples and Bcd and en-locus samples.  In oven at 70C in pure resin at 7P.
  • 2nd Bcd y(i) sample stopped in EtOH at 4C.  Can embed later.
Data collection / Image acquisition
  • barely any vertical buffer on O/N 4x snail, try an 8 um offset difference next – 10 too much, 6 too few.
  • 3 hours seems to etch sufficiently the 500 nm sections of sample S6.  mounted but not imaged.


  • working on SDB abstract draft
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