Volume 9 Issue 11, November 2014

From proteomics to networks, this protocol covers the processing, analysis and interpretation of AP-MS data. Sample data are pre-processed and scored using a variety of methods, and they are then imported into Cytoscape for network analysis and visualization.

Kumar et al. describe how to build a diSPIM from commercially available parts and use it to live-image cultured cells or worm embryogenesis. The inverted setup enables samples to be mounted directly on microscope slides, avoiding agarose embedding.

It can be difficult to express large amounts of membrane proteins for structural analysis. Using pEG BacMam it is possible to screen potential candidate proteins as well as to scale up expression in mammalian cells.

The high error rate of NGS methods has limited the ability to accurately detect ultra-low-frequency mutations. Duplex Sequencing reduces the error rate of NGS such that a single nucleotide mutation can be detected in >1×10⁷ wild-type nucleotides.

Palmitoylation plays a critical role in protein trafficking between membrane compartments. This Protocol provides directions on how to detect palmitoylation in a protein of interest in fixed single cells using fluorescence microscopy.

Dionicio Siegel et al. provide detailed instructions on implementing their facile, scalable, catalyst-free and functional group–tolerant approach to hydroxylating arenes.

Equipping an electron microscope with Zernike phase-contrast optics dramatically increases the contrast of the images. Dai et al. describe how to successfully apply this technology for the acquisition and analysis of electron tomograms.

A protocol for processing exome genotyping array data that proceeds by targeting the exome plus rare SNPs and provides a feasible, cheaper alternative to exome sequencing when analyzing data from large genome-wide association studies.

This protocol describes how to process samples potentially containing influenza A virus (IAV), amplify the samples in chicken eggs or mammalian cells and identify whether and which IAV is present.

Magnetic resonance colonography (MRC) can be used to monitor colonic tumors and mucosal inflammation. This protocol describes the use of a Fluorinert enema that distends the colon and forms a black homogeneous background in MRC images.

This protocol describes how to differentiate human pluripotent cells into ureteric bud progenitor–like cells, which then self-assemble into chimeric 3D structures in combination with embryonic mouse kidney cells.

Recurrent aggression occurs in many psychiatric and neurological disorders. This protocol describes how to set up a mouse model of repeated aggression.