Alistair's Lab Notebook

9:30 am – 11:45 pm

Chromatin manuscript

• revising text
• settled on final sentence
• discussed eq. globule
• settled on examples for fig 1
• polishing methods
• polishing main text
• XZ will give focused read tonight.

Fly experiments

• flip fly plates.

11:20 am – 11:20 pm
(lab volleyball practice, 9:15 am – 11:00 am)

Chromatin manuscript

• change 95% CI to standard error for fit quality everywhere
• figure out parabolic definition of uncertainty range around linear fits for the shaded patch.
• update all figures with new uncertainty patch (not obviously visibly different, parabolic region is a bit tighter around the middle).
• update all figures and text with new SE notation.

Figure adjustments

• additional small tweak XZ requested to all figures (some italics, some spacing, adjustments to the 3D-view angle).

More text revisions

• sent 3 versions of final sentence with 3 explanation paragraphs to XZ as requested.

10:00 am – 7:00 pm, 9:30 pm – 12:30 am (remotely)

Chromatin manuscript

Discussing Equilibrium Globule

• Definitions in literature
  • Erez 2009 Hi-C paper: ““equilibrium globule”: a compact, densely knotted configuration originally used to describe a poly- mer in a poor solvent at equilibrium (26, 27).”
  • Mirny 2011: “the density of monomers is independent of the polymer length and is uniform inside the globule. This uniform-density contrasts with that of an ideal chain”
  • Mirny 2011 adds R(s) ~ s^(1/2) for s< N^(2/3) and const for s > N^(2/3) in the definition, to distinguish from fractal (crumpled globule), R(s) ~ s^(1/3).
  • presumably “being at equilibrium” is part of the definition implied by the name.

data organizing

• moved Hi-C data to dropbox. Fixed up PlotHiC function to change filepaths better (should add filepath to varargin optional inputs).
• moved van Steensel color data to dropbox. Fixed PlotSmoothDamID to accept a filepath argument to work from multiple computers/ directories.
• moved raw fasta files for probe data to dropbox

manuscript revisions

• discuss and address equilibrium globule comparison
• tune a few things in the methods — add expanded discussion of pairing.
• devising alternative final sentence versions
• sent to JM
• BB fixing up figures and updated in dropbox.

10:00 am – 3:10 am

Meetings

• lab meeting (see protected notes)

paper to do

• revised alternate version of ED Fig 2
• rotate conv image for Fig 1
• new contrasted images for fig 1
• JM comments for last paragraph
• sentence about cell selection and pairing for methods
• update timestep (adaptive timestep) in methods

10:00 am – 12:15 am

Chromatin manuscript

• minor figure revisions

10:00 am – 1:00 am

Chromatin manuscript

To do

• citation revisions as discussed
• expand citations as suggested

New opening reviews

• Bickmore 2013
• Levine … Tjian 2014
• Killian … Wang 2012
• Kornberg 1999
• Dekker 2013
• Cremer 2010

Draft

• completed sent back to XZ

10:00 am – 2:45 am

To do

• Length / count correlation across chromatin types. Same accessibility? (done)
• Finish write-up of super-resolution chromatin papers (done)
• Reviews for nucleosome position mapping (started)
• restore track changes from 8-4. (done)
• reply to Mirny’s comments. (started)
• write to XZ about Frey, DR + Patent, (not done)

Manuscript discussions

• have comments now from all co-authors.
• see drafts and embedded notes.
• Violin plots
• box plots
  

9:25 am – 2:30 pm, 7:15 pm –

To do

• Flip fly stocks
• figure changes
• text changes
• get stamps

Tasks finished

• flipped Fly stocks

Contact XZ

• DR report patents
• Dale Frey Award application (due beginning of July)

Manuscript changes

• see drafts and git-pushes.

To read

• DNase Hi-C and lincRNA: http://www.ncbi.nlm.nih.gov/pubmed/25437436