Monday 12/02/13

9:00a – 12:20a


  • work on data analysis / slides for meeting with Ting tomorrow
  • new round of yellow chromatin RNA DNA double stains. Include attempt restain E10rna. Still needs RNase.
  • 3D z-calibration [POSTPONED]
  • Start statistical analysis of Blue Polymer simulations [POSTPONED]
  • Work on figures for Ph project [POSTPONED]

Chromatin Colors

Cell Staining

  • stained new RNA: D12 E08, E10
  • RNase treated E10rna sample.
  • new DNA stain for E10rna cells, attempt sequential imaging tomorrow.

STORM Imaging

  • Finish O/N STORM run of F08 on STORM2
  • Transfer data from STORM2 to Monet

Polymer Simulations

  • All simulations on Odyssey O/N ended in NODE-FAIL

Data Analysis

F11 (ANTC left, 180 kb) Observations

  • Highly variable


  • Generally very large. Could use more spots.

F09 Observations:

  • F09 dots are way too big.
  • possible cross contamination?




follow up on cross-talk in F09

  • Check cross contamination using M matrix. Looks pretty substantial (see above)
  • But previous analysis suggests most of these contaminates are not (nearly) full length.
  • Working on new pipeline to look at purity.
  • Looking at off target sequences that have 25 bp of sequence.
  • G02 and F09 have 3′ primer overlap! Need to screen this out! how was this missed by BLAST?

Some dots look much more G2 like. Others maybe more


Basic Data Processing

  • Ran chromatic analysis for 13-11-24_D10 beads. Substantial offset (25+ pixels!) needed to register colors
  • Reran / troubleshot chromatic analysis for 13-11-01_F07 Beads
  • Ran chromatic analysis for 13-11-25_D08 beads.


  • Could use more robust matchmols function. When multiple molecules are within the match radius, chose the nearest.

Computer Stuff

  • Install updates and Reboot Tuck / Cajal
  • Install new 16Gb RAM (on Tuck?)
  • Tuck fails to boot with new ram. Despite the fact all modules are PC3-10600 4Gb DDR3 1333 MHz.
  • Ram is incompatible — needs to be ECC Registered ram.
  • Forgot to put fan cover back on Tuck before reboot. Will need to do this.
  • Install Matlab 2013b on Tuck, Cajal and Monet (requires all active versions of Matlab to be shut down).
  • downloaded 2013b directly from FAS website (download from mathworks site not enabled any more under current license).
  • OligoArrayAux / OligoArray2.1 now running on Tuck

Odyssey computing

  • all queue_Blue tasks ended with NODE_FAIL errors.
  • wrote to RC about repeated issues.
This entry was posted in Summaries and tagged , , . Bookmark the permalink.