High resolution mapping of 3D chromatin structure

Posted on 25 May 2013 by James Taylor

As part of a collaboration with Victor Corces’ and Job Dekker’s groups we have been working on methods for deriving sensitive high-resolution maps of 3D chromatin structure from 5C datasets. The first paper using these methods, “Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment” led by Jennifer Phillips-Cremins shows that 3D chromatin architecture changes at the sub-megabase scale during differentiation from mouse ES to NPC cells, and that CTCF, mediator, and cohesin are involved in organizing these interactions, but that different sets of proteins are involved in interactions at different length scales. Importantly, the increased resolution achieved with our 5C approach clearly shows that chromatin is organized in a hierarchical structure, with additional layers of domain organization below the level of “topological domains” as previously described.

Two articles on analysis of parasitoid wasp venomes

Posted on 23 May 2013 by James Taylor

Two new articles in collaboration with Todd Schlenke’s lab on wasp venoms were published this week. The first, “Integrative Approach Reveals Composition of Endoparasitoid Wasp Venoms” in PLoS ONE describes an approach for combining RNA-seq and mass spectrometry to identify peptides in dissected venom gland lumens, allowing the discovery of many new venom proteins in L. boulardi and L. heterotoma The second, “Parasitoid Wasp Venom SERCA Regulates Drosophila Calcium Levels and Inhibits Cellular Immunity” in PNAS uses this approach to describe the venoms of Ganaspis sp.1 (G1), a previously uncharacterized Drosophila parasitoid species. Using this characterization demonstrates plasmatocyte cytoplasmic calcium bursts as an important aspect of fly cellular immunity.

Galaxy For Interactive Visual Analysis

Posted on 20 November 2012 by Jeremy Goecks

Our latest publication on using Galaxy for interactive visual analysis is out in this month’s Nature Biotechnology.

This Galaxy Page includes the RNA-seq analyses described in the paper and visualizations that can used for visual analysis of Cufflinks transcript assemblies. In this paper, visual analysis was used to find good parameter settings.