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Nature Protocols is an interactive online resource for all laboratory protocols relevant to biological and biomedical research. Nature Protocols includes a free-to-access community site, 'Protocols Network', containing protocols that are posted directly o


Turning single-molecule localization microscopy into a quantitative bioanalytical tool


In the last decade, super-resolution microscopy has enabled us to image cells with unprecedented detail. This Perspective discusses how the field can move beyond images to extract quantitative biological information from multidimensional SMLM data.

Synthesis of a highly Mg2+-selective fluorescent probe and its application to quantifying and imaging total intracellular magnesium


Specific and sensitive tools for quantifying intracellular magnesium cations are needed in biochemical research. This protocol describes the synthesis and use of a fluorescent Mg2+ probe based on diaza-18-crown-6-hydroxyquinoline.

Preparation of visible-light-activated metal complexes and their use in photoredox/nickel dual catalysis


This protocol describes the synthesis of two photoredox catalysts, [Ir{dF(CF3)2ppy}2(bpy)]PF6 and [Ru(bpy)3](PF6)2, that are activated by visible light. These single-electron transfer agents are used to facilitate diverse synthetic transformations.

Cu-catalyzed enantioselective allylic alkylation with organolithium reagents


Cu-catalyzed asymmetric allylic alkylation (AAA) is used in the synthesis of pharmaceuticals and natural products. This protocol uses organolithium reagents in the Cu-catalyzed AAA of allylic substrates with Taniaphos or phosphoramidites as ligands.

Using connectome-based predictive modeling to predict individual behavior from brain connectivity


This protocol describes how to develop linear models to predict individual behavior from brain connectivity data with proper cross-validation, and how to use an online tool to visualize the most predictive features of the models.

A modular approach to the design, fabrication, and characterization of muscle-powered biological machines


This protocol describes steps to design and generate biological machines. Ring-shaped skeletal muscle actuators are cultured and coupled to a 3D-printed skeleton. Contraction of muscle rings can be controlled by optical or electrical stimulation.

Genome-wide base-resolution mapping of DNA methylation in single cells using single-cell bisulfite sequencing (scBS-seq)


Single-cell bisulfite sequencing (scBS-seq) is a cost-effective method for surveying CpG methylation across genomes of single cells. It gives higher coverage than other methods, is automatable and is compatible with parallel RNA-seq from the same cell.

Detecting natural adaptation of the Streptococcus thermophilus CRISPR-Cas systems in research and classroom settings


The authors describe here a core protocol with three variants, in which S. thermophilus cells are challenged with phages to study the adaptive nature of this bacterial CRISPR system. In addition, they elaborate on the use of this protocol in undergraduate education.

Spatial transcriptomic analysis of cryosectioned tissue samples with Geo-seq


Geo-seq combines laser capture microdissection and single-cell RNA-seq technology to enable transcriptome analysis of small quantities of cells from defined geographical locations.

Genome editing using FACS enrichment of nuclease-expressing cells and indel detection by amplicon analysis


This protocol provides a pipeline for increasing and evaluating the efficiency of genome editing by ZFNs, TALENs or CRISPR–Cas9 that includes enrichment of nuclease-expressing cells by FACS, followed by Indel Detection by Amplicon Analysis (IDAA).