Monday 03/02/15

9:00 am – 12:30 am

Oligo Secondaries

Revising manuscript

  • More failures of microsoft word: MSO recommends I change my whole Windows Settings language for the bloody desktop just to get the MS word spell checker to work. Stupid program, I have multiple manuscripts some which need to be written in U.K. English and some which need to be in U.S. English and I don’t want to reboot my editor and change my windows configuration every time I want to switch between the too.
  • restarted revisions based on CW replies to XZ
  • finalized revisions, sent to CW

Revised Fig 2

  • changed panels for one with smaller FWHM
  • redid code to make things smoother
  • changed formatting to match Fig 3 a bit better

Ph Project

  • reviewed latest draft of manuscript.
  • Re-read all STORM main text and methods sections and all ChIP-seq 4C comparison main text and supplement / methods sections.
  • reviewed all figures
  • sent comments to NF.

Chromatin project

Meeting prep

  • discussed slides for both talks with Bogdan
  • discussed Hi-C data, reviewed new code.
  • working on slides!
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Friday 02/27/15

9:30 am – 7:00 pm

Fly Meeting presentation prep

Cis-regulation talk Outline


  • scales of regulatory code
  • local sequence / protein occupancy at the enhancer
  • next scale up: how do you get from Here to There
  • Two Mechanisms
    1. Random (Shadow enhancers). 10 – 100 kb scale.
    2. Structurally organized genome? 100-1000 kb scale

Local stochastically driven interactions

  • Organization matters

  • enhancer promoter specificity is not encoded in either sequence

  • proximity matters (not with-standing classical enhancer definition)

Chromatin Paper


  • drop formal colors e.g. ‘BLUE’. Use: repressed, silent, active

Fig 1

  • Domain selection (show genes? show ChIP?)
  • Classify domains – show ChIP (histones? multiple tracks?)
  • Show domain Hi-C (each domain is also a Hi-C domain might be easiest)
  • show quantification of domain properties
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Thursday 02/26/15

(12:00am – 5:30am), 11:30 am – 7:00 pm

Ph oligimerization

  • revise Ph analysis in BX-C, just include peaks changed >50%
  • revising cartoons
  • incorporating Ajaz’s cartoons into main figure
  • lost some effects — see email.

Embryo chromatin analysis

Rotation Mentoring

  • ask Georgia about STORM4 status
  • troubleshoot circuit breaker – fixed.
  • started new cell cultures (new Kc cells arrived). Supervised procedure.

Chromatin Cropper

  • CC is getting confused on auto-detection of multi-color. This should just be a user defined input.
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Wednesday 02/25/15

10:00 am – 5:30 am

Project 2

Finalize and submit

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Tuesday 02/24/15

10:00 am – 2:15 am

Fly stocks

  • all newly arrived stocks Dead on Arrival.
  • 2406 Scm mutants may survive — some live larvae moving
  • no movement in 2057 of 1728
  • Reordered stocks 2057 and 1728 (yw isogeneic and Pc)

Project 2

  • minor fixes to tables 2 and 4
  • reviewing structured abstract
  • reviewing supp figures, captions, and tables
  • reviewing response to reviewer
  • prep night 1 for submission

Oligo secondaries paper

  • finished requested edits to Fig2
  • sent revised fig 2 pdf and ai to Brian

Embryo image analysis / rotation mentoring

  • convert stv2mat for mosaics.
  • steve.bat shows more dramatic mismatch upon loading files than my viewer? Should work with Georgia to document this more clearly for Hazen.
  • position seed in SteveMosaicViewer is broken.

Ph-polymerization paper

  • fix figure 2
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Protected: Lab Meeting 02/23/15

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Monday, 02/23/15

9:30 am – 1:45 am


  • project 2 paper revisions
  • fix figures for paper with Ting (add more scalebars)

project 2

  • discuss revisions with Jeff.

revised protocol for coating coverglass

  • .5% gelatin
  • .05% chromium-potassium
  • passively whick the solution off the coverglass.
  • also updated in protocols — need to push to Github still.


  • launched analysis with Georgia for all new data movies and fiducials
  • reviewed computation of chromatic calibration / correction
  • reviewed computation of z-calibration
  • tomorrow: annotate cells from mosaics. Find some good way to document this annotation process as well.

Lab meeting

  • see protected notes

Project 2 revisions

  • see emails
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Friday 02/20/15

To Do

  • check mail for flies (not done)
  • project 2, see notes
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Thursday 02/19/15

To do today

  • reply to Ting
  • reply to Nicole
  • send response to reviewers back to Xiaowei

To do:

  • analyze z-section results
  • Fix Fig S4
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Protected: Wednesday 02/18/15

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