Wednesday 07/23/14

10:00 am – 12:15 am

Chromatin Project

snapped coverslip
tried mounting half on flow-system anyway
this leaks — not enough pressure seal in the gaskets (especially relative to pump pressure of manual syringe)
try manual hybes of second broken piece of coverglass
- hybe on glass slide at 47C 30 min
- wash in 50% formamide 2x SSCT at 37C 20 min
- This failed: coverslip upside down 🙁
try manual hybes with failed stain of the mounted (larger) half of the broken coverglass
- hybe on glass slide at 47C 30 min
- wash in 50% formamide 2x SSCT at 37C 20 min
- Still failed: very weak spots, not all cells have evident spots
- either 30 min is not enough time to hybe or this probe failed (which could explain why the flip failed).

Summary of S1 S3 toehold replacements

Goal: more troubleshooting / testing of sequential staining
L3E08-p1 + L3E09-p3 + S3-A647
L3E09-p1 + L3E08-p3
L3E08-p1 + L3E09-p3
L3E09-p1 + L3E08-p3
4 ul of each probe diluted into 120 uL hybe dilution buffer, split 2 ways (50-60 uL each)

ChromatinCropper Analysis today
- Finished ChromatinCropper analyzing BXC (last 2 cells)
- ChromatinCropper of F03F04 data — these spots are much smaller than I thought from the quick fit data.
- E06 (repeated for lower background)
renamed new BXC_data.mat file as BXC2_data.mat and moved to 2014-07-09_BlueInternalData
Analyzing G2toG4 data. Looks pretty good. Similar size as ANTC
launched analysis of E07toE09 data and E07 (rpt 3) data.
G05 automatic length extraction from name is incorrect — 40 bp, should be 64 !!
F4, G2, G3, G4 should be double-checked

RC now added openMM to python paths. should try again to see if we can get this to run at all.
no longer gives error on import simtk.openmm.openmm
now errors on import dumpOutput