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Preview: Nature Protocols

Nature Protocols

Nature Protocols is an interactive online resource for laboratory protocols for bench researchers. The core content is high quality, peer-reviewed protocols that are presented in a 'recipe' style, providing step-by-step descriptions of procedures that use


Identification of RNA-binding domains of RNA-binding proteins in cultured cells on a system-wide scale with RBDmap


Here the authors provide an extension to their earlier RNA interactome capture protocol. This Protocol Extension describes RBDmap—a method to identify the regions of RNA-binding proteins engaged in native interactions with RNA, in a proteome-wide manner.

A high-throughput in vivo screening method in the mouse for identifying regulators of metastatic colonization


In this protocol, the authors present an experimental metastasis assay in which cancer cells are injected into the tail vein of a mouse, and the resulting secondary organ colonization is assessed, primarily in the lung, 10 d later.

Chromatin-state discovery and genome annotation with ChromHMM


This protocol describes how to use ChromHMM, a robust open-source software package that enables the learning of chromatin states, annotates their occurrences across the genome, and facilitates their biological interpretation.

Compartmentalized partnered replication for the directed evolution of genetic parts and circuits


This protocol describes the procedures for compartmentalized partnered replication (CPR), an emulsion-based directed evolution method for the generation of proteins, genetic elements, and genetic circuits with improved or altered function.

Production of knock-in mice in a single generation from embryonic stem cells


This protocol describes the generation of mice entirely derived from genome-edited embryonic stem cells, enabling the production of transgenic mice in a single generation.

Multimodal profiling of single-cell morphology, electrophysiology, and gene expression using Patch-seq


This protocol describes how to integrate whole-cell patch-clamp in single neurons from mouse brain tissue slices with single-cell RNA sequencing and morphological recovery.

Chemical synthesis of membrane proteins by the removable backbone modification method


This protocol describes how to chemically synthesize membrane proteins through the installation of solubilizing removable backbone modification tags into hydrophobic transmembrane peptides. The implementation of the protocol is demonstrated by the chemical synthesis of phosphorylated M2 (M2-pSer64), a 97-aa proton channel protein from the influenza A virus. The synthesis of M2-pSer64 at milligram scale takes ∼200 working hours (excluding the time for lyophilizations).

Langmuir–Blodgett nanotemplates for protein crystallography


Protein crystallization still presents a challenge for X-ray crystallography. This protocol describes the Langmuir–Blodgett nanotemplate method, in which 2D protein LB nanotemplates trigger formation of 3D protein crystals by hanging-drop vapor diffusion.

Visualizing endocytic recycling and trafficking in live neurons by subdiffractional tracking of internalized molecules


This protocol describes a pulse–chase approach to studying activity-dependent internalization of fluorescent ligands into endocytic compartments using subdiffractional single-particle tracking in live hippocampal neurons.

Preparation of viable adult ventricular myocardial slices from large and small mammals


This protocol describes how to obtain 100- to 400-μm-thick slices of a living myocardium from rodents, pigs, humans and dogs that retain the native multicellularity, architecture and physiology of the heart.

Deriving genotypes from RAD-seq short-read data using Stacks


In this protocol, the authors provide a strategy and set of methods to analyze restriction-site-associated DNA-sequencing (RAD-seq) data using Stacks, enabling the genome-wide discovery and genotyping of SNPs across a range of systems.