Friday 03/28/14

9:45a – 11:50p


  • Record bead fields.
  • check isoforms differences and consequences for probes selected (do our probes still hit the most popular isoform of imr90s?)

Cell Staining

  • washout stains for new multi-color samples. Need to wait until oven is free.

Imaging samples

  • F03-p3 2 uL, F02-p1 7 uL — F02-P1-A647 actually works (first time!) should image this. F03-P3-cy7 is detectable but very dim. I have gotten much brighter A750 stains before. Background is also high.
  • F05 P3 1.5 uL, F06-P1 6 uL — F05 probe synthesis failed. F06-P1 looks strong and clear at thic concentration.
  • F06 P3 2.5 uL, F07-P1 6 uL — F06-P3-cy7 failed ? High background. F07-P1-A647 looks fine. Not clear why F06 works with P1 and not with P3.

New Stains

  1. F3-6, F1-7 6 uL, 6 uL
  2. G6-6, G8-7
  3. G8-6, G6-7
  4. F7-6, F6-7
  5. F6-6, F7-7
  6. G2-6, G3-7 1.5 uL, 1.5 uL (~1100 ng/uL)

New Probes

  • E01-E08
    1. chr3R:19929199-20187132__YELLOW_250kb_silent_flanks
    2. chrX:1907754-2083414__YELLOW_175kb_silent_flanks
    3. chr3R:19929199-20029199__YELLOW_250pt1_100kb
    4. chrX:1907754-1977754__YELLOW_175pt1_70kb
    5. chrX:1977754-2047754__YELLOW_175pt2_70kb
    6. chr2R:19726615-19787585__YELLOW_D12a
    7. chr2R:19809874-19888410__YELLOW_D12b
    8. chr2R:19906491-19976552__YELLOW_D12c
    9. Neg control, E01fwd, E07rev
  • ran PCRs
  • started T7 reactions


Not sure why E06 and E07 failed, and E08 looks weird. Maybe press on with just E01-E05.

Research Organization

  • moved ChromatinCropper into matlab-functions
  • moved commonly used mature functions out of Beta into appropriate matlab-functions folder (e.g. normhistall is now in Plotting).
  • moved storm-analysis and storm-control into Software.
  • moved Scratch into Software
  • moved GeneralSTORM scope images onto Data and archived code into Archive2014 on D drive
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