10:00 A — 11:00 P
- Colenso’s lab meeting
- PureLink DNA extraction — visible pellet but no DNA detected on nano-drop. Poor resupension? tried vortex and extended incubation at 37C. No improvement in conc.
- Test digest, try to detect by gel? Doubt this will work. Fails.
- Design and order primers to test BACs and DNA purification.
- Try using 5 kb Neu3 probes — transform colonies.
- Stocks left to Levine lab seem to have gotten labels mixed up or contaminated. Sad.
- cloning sxl, neu3 and toll 5kb sections to test probes.
- Split top10 competent cells 6 ways (using 3 different sxl fragments 5kb, 3kb, and 1kb).
- No SOC medium for cell recovery. Recovering cells in LB for 1 hr, hopefully we still get enough colonies, but apparently this is still supposed to work according to this: Competent cell protocol
- Working on GPU code and verification.
- GPU script does get much better sample density, but seems to overfit–more molecules than real, probably due to different localizations. Could try to combine repeated localizations to refine fit. Wrote to Fang about applying this on the GPU. Could also use matlab image processing functions just to merge these and take the new centroid. Would prefer to sum the individual, raw, ccd pixel limited spots and do a Gaussian fit on that.
- Resin embedded the 647-laminin 555-tup(1A) 488-sog(ex) embryos
and the 647-laminin 555-sna, 488-tup(1A) embryos which were made into slides yesterday. Still need to check slides by confocal. Resin embedded embryos are not post-fixed. - H3K27me3 antibody arrived — store at -20 in -20 reagents box (in 30% glycerol). recommended to aliquot and freeze.
- H3K4me3 antibody arrived, store at -4C with antibodies. Recommended to aliquot and freeze. (in PBS).
- signed up for 6 hrs of ultratome tomorrow, overlapping with Colenso.