Volume 11 Issue 2, February 2016

This single nucleus-targeted sequencing approach incorporates multiplexing and targeted capture for efficient high-throughput detection of genome variants. The protocol will be particularly useful for studying rare cells and complex cell populations.

Nanocomposites are particles comprising multiple components. Those prepared in this protocol—made up of MRI agents or smart drugs—are wrapped in polymers (e.g., PEG or dextran) derivatized with hydrophobic, fluorescent pyrenyl groups.

Understanding the mechanism of amyloid formation (protein aggregation) is important for developing treatments for many neurodegenerative diseases. Amylofit is a program for determining mechanisms and rates from protein aggregation kinetics.

icSHAPE allows transcriptome-wide RNA structure profiling in living cells. It uses a clickable SHAPE reagent to enable biotin-based enrichment of SHAPE-modified RNA, reducing the necessary sequencing depth.

This protocol describes the use of F-box–UBA domain fusion proteins known as ligase traps to capture and enrich for ubiquitinated proteins. By following a two-step purification procedure, enriched substrates can be identified by mass spectrometry.

Nowak-Sliwinska et al. describe a protocol for optimizing drug combinations using Feedback System Control (FSC). Drug combinations are tested in a cell-based assay in which results are entered into the FSC pipeline to predict new combinations to be tested in vitro.

This protocol describes affinity purification of endogenous protein complexes for mass spectrometry analysis. Optimized to study formaldehyde-crosslinked proteins isolated by chromatin immunoprecipitation, it can be adapted to study other protein complexes.

This protocol describes how to genetically and phenotypically tag, select and maintain naive-like hPSCs to enable homogenous hPSC cultures to be derived, characterized and maintained over the long term.

This protocol describes a strategy for generating 3D prostate organoid cultures from healthy mouse and human prostate cells (either bulk or FAC-sorted single luminal and basal cells), metastatic prostate cancer lesions and circulating tumor cells.

5PSeq is a method for studying ribosome dynamics based on co-translational mRNA decay. Genome-wide sequencing and quantification of 5′ phosphorylated mRNA degradation products allows the positions of the last translating ribosomes to be determined.

Volatile organic compounds (VOCs) are by-products of human activity that are particularly difficult to detect in water. This protocol describes an infrared chemical sensing device for enriching and detecting VOCs via attenuated total reflection spectroscopy.

This is a mass spectrometry–based biochemical assay to identify the site of SUMOylation on recombinant proteins from in vitro reactions. SUMO site identification is achieved using mutant SUMOs that release five amino acid remnants upon tryptic cleavage.