Monday 08/03/15

9:15 am – 5:05 pm,


chromatin STORM

  • finish STORM session of L2F03 dat in Ph-KD condition
  • take bead movies, transfer data
  • start fitting movies after transfer completes
  • setup auto-transfer (?) for next time

Ph project

  • send Ph data on downsampling for Fig 1 graphs to NF an AW
  • analyze effects of down-sampling on fig 2 results


  • new pixel size for 1.5x slider and 60x objective = 0.192 um (or 0.195 um)

Chromatin Project To Do list

  • live imaging
    • analyze new live imaging data from confocal
    • PCP imaging of telomeres (in U2OS?)
  • RNAi experiments
    • set up new RNAi for Pc(v2) and Ph-p + Ph-d
    • prep for sequencing Ph KD cells and WT cells.
    • repeat qPCR experiments for Ph KD — need more robust replicates
  • centromeric chromatin imaging
    • Design library for green regions
    • assemble and process existing data on green regions
    • image AATAT centromeric region in Kc (should be good live imaging target too)
  • PRE analysis
    • re-analyze PRE-density as a function of volume using new PREs, see if its a primary effect.
    • also compare difference from trend line with PRE density, see if its a secondary effect.
  • Hi-C analysis
  • Active chromatin analysis
    • correlate TSS density and difference from trend line
    • correlate expression level and difference from trend line
    • correlate insulator protein density and difference from trend line

Chromatin Project work

  • ordered CycB antibody
  • analyzing mmaple3-dCas9 data on Morgan
    • no obvious signs of telomere labeling
    • not a sharply defined nucleolous border
  • working on analyzing confocal live imaging data: see post
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