9:45a – 6:15p
STORM imaging – multi-color chromatin
- O/N imaging of F5 F6 lost focus very early in night.
- O/N imaging buffer also did not survive well
Re-imaging F11 F12
- new freshly made Glox
- 2.5 uL BME + 5 uL COT
- 750 still nice and bright in these samples
- 750 imaging looks great at 60 Hz. Should totally drop the 30 hz approach
- Added fresh beads. beads still bleaching rapidly.
- trying to match z-offset better. Currently shooting for 100 nm offset (according to Hal’s measurements, not sure about the calibration quality on this system at present)
Re-imaging G1 G2
- getting new images with hopefully better signal in both channels
- 750 conventionals look kinda weak, but the STORM seems to be working out pretty well.
- 2.5 uL BME + 5 uL COT, 60 Hz.
- some issues with Hal freezing. Might be me trying to copy data
STORM analysis
- analyzing new F11 F12 data locally on Monet (just 3 positions)
- serious issues getting the beads to be bright. But I’d rather have bright dyes than bright beads.
- start analysis of Bx-C data on Cajal.
Library Design
errors in sublibrary 59:
Start 59__Disco_region_highly-interacting_TAD_(Y[G[K)__chrXC16481008-16544222_pt52
Running Blast (-e 0.0)... For sequence 59__Disco_region_highly-interacting_TAD_(Y[G[K)__chrXC16481008-16544222_pt52, the following exception was caugth: java.lang.StringIndexOutOfBoundsException: String index out of range: -2
Seems to stem from overly long file name. Shortened name, looks like its running now.
Pruning list, remove BX-C pieces (looks like I got the pieces from Lib2 working, will still be nice to have the whole thing available as a single shot as well). Remove some of the very low represented genes.