10:30a – 8:00p, 10:00p-11:50p
literature
- continue reading Berlivet et al PLoS Genetics on HoxA
- ID 19 candidate enhancers by ChIP and 5C
- 8 of 10 tested LacZ transgenics show limb bud enhancer activity
TAD contacts in silent tissue
- Shh signalling blocks processing of Gli TF into its truncated repressor form. Consequently GliR only exists in the anterior domain of the limb-bud in wt. In Shh nulls, GliR is everywhere.
- In this condition enhancers with GliR binding sites (e.g. e5) are silenced (no longer drive LacZ transgene expression). 3C contacts are still detected, though not as strong as wt. (This could mean the true interaction frequency is unaltered, and the promoter, not being transcribed, forms fewer contacts. Or it could be the authors interpretation that interactions are preserved yet weaker).
- 5C analysis in Shh nulls recapitulates wt contact pattern.
coding matlab-storm: STORMrender
- switched to a STORMrenderBreakOut branch to export STORMrender functions
- Completely exported all subfunctions from STORMrender
guidatacommands run fine from external functions, just need to passhObjectas well- No need to return
handlesand callguidatawithin the main GUI function (though I do this a good bit at first) - Now I need to see if how many of these are ready to use as crafted by my CC GUI. Wasn’t thinking of using by multiple GUIs…
- In the short run the Break out should make the details of changes much easier to track. If Bogdan and I get up to sync this way with CC it will be much smoother. All going to take some more work though.
more coding goals: bead-data compression
- Really should get back to bead-data compression soon, running out of disk space quickly at present.
- I recommend recording the compression in the new info file, and checking the infofile for compression when reading in the dax. Otherwise we could record it in the list_pars file, but since it’s a dax modification it really should go in the dax header file, i.e. the .inf file.
Chromatin staining
- F3 sample finally stains! (there was no good reason this one should have failed twice in the first place, this is nice confirmation.
- Let’s get some more BX-C sub-cluster imaging.
- Should also plan to stain
- Should keep the experimental front busy until I can get back on the 750 for multi-color
- Sonicating new batch of 561 beads. Making new batch of Glox.
Chromatin analysis
- F12 stains pretty backgroundy in all images checked so far. Need to add more filters.
- G1 G2 looks more promising.