9:30a – 11:50p

Chromatin project

Planning

• write up summary of yesterday’s meeting with XZ
  • (see post)
• work on improving metrics for comparison of chromatin regions
  • (see post)
• writing up plans for new ChromatinCropper to implement revised analysis
  • (see post)
• plans for sequencing validation
  • up to 12 lanes per library can be fully double indexed and distinguished (and 96 total lanes run in parallel on MiSeq)
  • 3 finalized probes, 2 fully independent replicates. (up to 6)
  • 2 independent PCRs of all 40 Drosophila loci (can run one 1 plate).
  • 2 limited cycle PCRs of 2 loci, (run on QPCR machine)

STORM

• imaging G05. I still think these domains are too large. It will be very interesting to see how they compare to the rest of ANTC.
• Analyzing ANTC data. Forgot to use my nice new daxwriter bead integration. Going to have to fit the beads separately.

Secondary Projects

Project 2

• revise writeup for Hao / XZ.

Ph Project

• image / test all new antibody stains. Find which 750 range dye looks the best
• m Alexa-750 #46 gives the best stains. I’m suspicious the bright dots one per cell here due to the secondary. But the rest of nuclear staining looks good. We’ll see if these dots cluster etc.
• Some of these dyes give no staining at all. Or maybe some cytoplasmic background but no