9:15 am – 5:05 pm,
Goals
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
STORM2
- 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
