Category Archives: Research Planning

Levine Progress Reports, planned experiments, research summary

observations on Insulator organization

Posted on October 16, 2012 by admin

CTCF sites are TF rich: (en locus) CTCF sites are TF rich ~HOT DNAs?  (though not as strong DNA-hypersensitive regions).  rich ~HOT DNAs?  (though not as strong DNA-hypersensitive regions). Do these insulators co-localize (most insulators HiC/3C together) Coerces 2012 MolCell chromatin domain boundaries … Continue reading →

Posted in Chromatin, Research Planning | Tagged , | Comments Off on observations on Insulator organization

Matlab Coding guidelines

Posted on October 14, 2012 by admin

  On writing readable matlab code [In development] Rule 1: The code you run and re-run on different stuff should be functions Functions can be shared / read used by others.  Scripts generally cannot.  Script with front-matter inputs = bad … Continue reading →

Posted in Research Planning | Tagged | Comments Off on Matlab Coding guidelines

Wednesday 10/10/12

Posted on October 10, 2012 by admin

10:00 A – 8:00P, 9:00P – 11:15P Collect virgins Working on presentation for meeting with Xiaowei (see notes below on data processing and analysis). Meeting with XZ.  Notes here. Processing STORM data 8/25/12 AbdA, no 750 movies analyzed yet in … Continue reading →

Posted in Research Planning, Summaries | Tagged , , | Comments Off on Wednesday 10/10/12

Friday 09/21/12

Posted on September 21, 2012 by admin

(Working remotely from Berkeley) Ideas: can I have the analysis script call Git bash and update the code with a ‘run to export images’ (check with Carl?) export a text file at the same time as it writes an image: … Continue reading →

Posted in Research Planning, Summaries | Tagged , | Comments Off on Friday 09/21/12

Coding projects to do:

Posted on September 11, 2012 by admin

mRNA counting package change fname to include slidedate folder as well as fileroot in all major scripts: Unsupervised_Dotfinding, Analyze_data, Plot_data scripts STORM analysis Matlab wrapper for multifit Daostorm (to run locally). Finished and running smoothly on Tuck, 09/16/12 Modify insightM … Continue reading →

Posted in Research Planning | Tagged | Comments Off on Coding projects to do:

Saturday 04/21/12

Posted on April 21, 2012 by admin

10:45 A – 7:45 P, 10:30P – 11:30 P Working on lab meeting presentation slide organization new analysis of Psc, H3K27, H3 localization differences HP1a doesn’t haven’t correct conventional level nuclear localization Samples to cut and image 4H  — K27me3-750, … Continue reading →

Posted in Research Planning, Summaries | Tagged , | Comments Off on Saturday 04/21/12

Protected: progress report

Posted on January 28, 2012 by admin

There is no excerpt because this is a protected post.

Posted in Research Planning | Tagged | Comments Off on Protected: progress report

STORM imaging progress update

Posted on January 14, 2012 by admin

Review of recent progress on multicolor STORM imaging of gene regulation. WGA labeling   membrane in 100 nm section.  little Hb detected (red stain mostly background). en-dig stains well with H3K27.  just need to cut it better. AbdA (red) and Ubx (green) … Continue reading →

Posted in Research Planning | Tagged , | Comments Off on STORM imaging progress update

chromatin regulation

Posted on November 30, 2011 by admin

Selected ubiquitous genes flanking Antp complex: Taf1 (left) and alphaTub84B (right).  Need to clone and make probes for these at some point. Look at maintenance of gene activation –how to keep a gene on. Does it require enhancer looping.  How … Continue reading →

Posted in Chromatin, Research Planning | Tagged , , | Comments Off on chromatin regulation

Protected: Chromatin dynamics project

Posted on November 19, 2011 by admin

There is no excerpt because this is a protected post.

Posted in Research Planning | Comments Off on Protected: Chromatin dynamics project