Alistair's Lab Notebook

10:00 am – 9:45 pm, 11:00 pm – 1:00 am

Project 2

• troubleshooting experiments — see post
• troubleshooting drive failure. NO! — see post
• team meeting, planning new experiments.
• paper draft requested by Monday

Chromatin Project

• sent draft to XZ through googledocs
• sent figures to XZ as PDFs
• requested to share through dropbox

Chromatin Supplemental Figures

• working on S2 layout.

9:50 am – 12:20 am

Chromatin Manuscript

Figure work

• save images of Black-black, blue-other, and black-blue interactions
• save figure of simulation entanglement results
• average examples of equilibrated BLUE simulations
• figures basically done
• updated all figure captions

A few final revisions to Fig 4

• Fix fit domain so that scaling fits for the “whole domain” plotted on the intact curves matches

Draft 1 basically complete, ready for Xiaowei

Fly request from Heng

• send hb-y flies. I think these are still alive(!)
• only MP02 is still alive. (distal removed)

To add

• MED31 and H3K4me2 as highly enriched in red, very low in Yellow

9:30 am – 1:15 am

Goals

• passage Kc cells
• working on figures
• project 2 experiments for Jeff to Image

Cell culture

• passaged Kc cells
• density looks good, ready to start new experiments

Project 2

• see post

Finalize figures!

• moving more stuff into matlab
• have Bogdan look at simulation results

Launch new blue simulations

• not running effectively on Odyssey yet
• Odyssey still giving trouble
• running locally.
• this is going to be extremely slow.

10:00 am – 9:30 pm

Project 2

• IMR90s, plated and in incubator
• new L7E1 scratch staining since Thursday night at 37C.
• stained L8E1 scratch and L7E1 normal in 4C
• scratch the 2000K density plates Today (11/08)

Chromatin Project Data to Process

Black internal domains

• 2014-08-15_L4E1
• 2014-08-16_L4E2
• 2014-09-17_D08
• 2014-09-18_D08

Black-Black junctions

• one of these may already be analyzed. Some of these probably failed
• 2014-08-17_L4E2-6_E1-7
• 2014-09-06_D10-6_D11-7
• 2014-09-09_D10-6_D11-7
• 2014-09-12_D11-6_D12-7

Yellow-Yellow junctions

• 2014-09-12_E05-6_E04-7
• 2014-09-13_E08-6_E07-7

Chromatin Project Figure making

• Making S3 as a single figure

9:45 am – 7:00 pm

Goals

• send Fly Meeting draft abstract to XZ (due Mon)
• images of small yellow domains for Ting
• work on manuscript

Oligo secondaries revision planning

• sent example images of small yellow regions
• see smallDomainImates_141106.m in OligoSecondaries code

Manuscript revisions

• re-writing introduction with Bogdan
• revising body text to account for modifications to figure layout.

Fig 4, modeling: rearrangements

• combine multiple simulations for black ‘intact’ domains

9:30 am – 9:50 pm

Goals

• write abstract for fly meeting
• project 2 experiments with Hao
• meeting with XZ and Ting
  • discuss Brian’s PAINT experiments
  • discuss revision experiments
• project 2 team meeting
• revise figures
• 2 color image for Ting
• start up cell culture

server troubleshooting

• Morgan requires users to be Members of “Remote Desktop Users” (or Domain Admins) in order to log in remotely.
• now fixed for all users

revising figures

• finished converting entanglement to bar graph
• finished splitting fraction overlap by boundary type

Figure 1

• writing code to visualize domains for figure 1

Chromatin Manuscript

• Revising text
• started new google Doc: Super-resolution Imaging of Chromatin Nanostructure
• writing new intro according to yesterdays outline.

Chromatin experiments

• start new Kc cell in culture