10:00 A – 5:30 P
STORM
- Finish O/N STORM of S3 repeated (not sure why contrast was low on first round).
- computer maintenance: update software, reboot system, relaunch all aborted STORM analysis scripts
- ProRAID required switching off during second reboot in order to reconnect. Working smoothly now.
chormatin paints
- updating probe design parameters based on: http://www.pnas.org/content/106/7/2289.full. Runs of As especially weak binding. Runs of Cs strong off-target binding.
- Updated parameters in Exons2OligoArray_Lib2 and Exons2OligoArray_HoxD, but have not rerun yet. (I should rename the base file here since this is not particularly to exons anymore).
- paper also provides potential starting reference set from which to derive new orthogonal primer sets for mouse + Drosophila genomes.
- url from paper for code and primer list is no longer active. Wrote to senior author to request list and code.
- # design expanded set of orthoganol primers
Probe making
- PCR en-T7 probe template
- test-gel — bands look different
- test gel denaturing gel:
Review writing
- working out mathematical details of two state model, why strong binding is noisy
- having difficulty proving difference is strictly positive.