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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


Multiparametric characterization of rare HIV-infected cells using an RNA-flow FISH technique


This protocol describes flow cytometric identification of viral translation-competent reservoirs, based on concurrent detection of cellular HIV Gagpol mRNA by in situ RNA hybridization combined with antibody staining for the HIV Gag protein.

Preparation of biogenic gas vesicle nanostructures for use as contrast agents for ultrasound and MRI


This protocol describes the isolation of gas-filled protein nanostructures, called gas vesicles, their functionalization with moieties for targeting and fluorescence, and how to use them as contrast agents for ultrasound and MRI.

Live-cell confocal microscopy and quantitative 4D image analysis of anchor-cell invasion through the basement membrane in Caenorhabditis elegans


This protocol describes how to use multichannel time-lapse confocal imaging of anchor-cell invasion in live Caenorhabditis elegans to monitor cell invasion through basement membranes.

Use of a neonatal rat system as a bioincubator to generate adult-like mature cardiomyocytes from human and mouse pluripotent stem cells


This protocol describes how to generate mature adult-like cardiomyocytes by culturing mouse or human PSCs in vitro initially and then transferring to neonatal rats for further cell maturation.

Rapid curation of gene disruption collections using Knockout Sudoku


Knockout Sudoku allows construction of whole-genome knockout collections for a wide range of microorganisms at a lower cost and increased speed, using combinatorial pooling, next-generation sequencing, and a Bayesian inference algorithm to process and annotate extremely large progenitor transposon insertion mutant collections.

Lab-scale production of anhydrous diazomethane using membrane separation technology


Diazomethane is useful for inserting methyl or methylene groups in organic synthesis. Unfortunately, it is explosive. A tube-in-flask reactor where the Teflon AF-2400 tube allows only the diazomethane produced to enter the flask can be used to prepare it safely.

Genetically encoded releasable photo-cross-linking strategies for studying protein–protein interactions in living cells


This protocol describes strategies for the characterization of transient protein–protein interactions and their interaction interfaces via genetically encoded releasable photo-cross-linkers.

Generation and use of a humanized bone-marrow-ossicle niche for hematopoietic xenotransplantation into mice


Humanized bone-marrow-ossicle niches are formed in mice via in situ differentiation of bone-marrow-derived mesenchymal stromal cells and can be used for transplantation of normal and malignant human hematopoietic cells.

Synthesis of a HyCoSuL peptide substrate library to dissect protease substrate specificity


This protocol describes HyCoSuL, an approach that uses tetrapeptides containing natural and >100 unnatural amino acids to screen for protease substrate specificity and to engineer highly active and selective substrates and activity-based probes.