Volume 15 Issue 4, April 2020

R-DeeP identifies, quantifies and analyzes RNA-dependent proteins using sucrose density gradient ultracentrifugation followed by western blotting for individual proteins or proteome-wide mass spectrometry and biostatistical analysis. RNase-treated samples are compared with controls to reveal differences in protein complex composition in the presence of RNA.

This protocol describes how to visualize and quantify translation of individual mRNAs in live cells by fluorescence microscopy. Example procedures for quantitative analysis of 3ʹ-UTR translation, nonsense-mediated mRNA decay, and translation start-site selection are provided.

Neuroimaging-based machine-learning models should be interpretable to neuroscientists and users in applied settings. This protocol describes how to assess the interpretability of models based on fMRI.

This protocol describes the generation and delivery of embedded viral barcode libraries to track single-cell clones. Barcodes are amplified from genomic DNA and quantified by high-throughput sequencing and bioinformatics analysis.

This protocol describes collection, storage and lysis of different types of mouse organs for monitoring gene expression on a whole-organism scale. Procedures for high-throughput RNA extraction and multiplexed RNA sequencing library preparation are included.

CellPhoneDB combines an interactive database and a statistical framework for the exploration of ligand–receptor interactions inferred from single-cell transcriptomics measurements.

This protocol discusses design principles for CARs responsive to soluble ligands and delineates steps for producing T cells expressing synthetic receptors. Functional assays for quantifying the ability of CAR T cells to sense and respond to soluble ligands are also presented.

Automation of new methods for ¹⁸F incorporation into unactivated (hetero)arenes for translation to the clinic has progressed slowly. This protocol describes a workflow leading to automated radiosynthesis of the PARP inhibitor [¹⁸F]olaparib.

In this operant model, rats press a lever to obtain addictive drugs or rewarding social interaction with a peer. The model can thus be used to study the role of operant social reward in addiction and addiction vulnerability in the context of choices.

This protocol describes how to differentiate human induced pluripotent stem cells into oogonia in vitro. It is suitable for investigating the mechanisms of human primordial germ cell specification and epigenetic reprogramming.