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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


Engineering a humanized bone organ model in mice to study bone metastases


This protocol describes how to design 3D-printed scaffolds via melt electrospinning writing for bone tissue engineering applications and how to engineer humanized bone for the study of cancer metastasis in vivo.

Simple multiplexed PCR-based barcoding of DNA for ultrasensitive mutation detection by next-generation sequencing


Ståhlberg et al. describe SiMSen-seq, a barcoding NGS library preparation approach to enable detection of rare variant alleles from as little as 5 ng of input DNA. The method also works for fragmented templates such as cell-free DNA.

Coordinated generation of multiple ocular-like cell lineages and fabrication of functional corneal epithelial cell sheets from human iPS cells


This protocol describes how to grow a functional and transplantable corneal epithelium and how to generate ocular-like cell lineages resembling neuroectoderm, neural crest, ocular-surface ectoderm, or surface ectoderm derived from human iPS cells.

Translation complex profile sequencing to study the in vivo dynamics of mRNA–ribosome interactions during translation initiation, elongation and termination


Translation complex profile sequencing (TCP-seq) is a major technological step forward for analysis of mRNA translation. Unlike ribosome profiling, TCP-seq can be used to study all stages of translation, from initiation through to ribosome recycling.

Decerebrate mouse model for studies of the spinal cord circuits


This protocol describes how to create a decerebrate mouse model for investigating sensory-motor integration and motor output from the spinal cord.

Optimized labeling of membrane proteins for applications to super-resolution imaging in confined cellular environments using monomeric streptavidin


This protocol describes how to express and purify a protein probe and subsequently conjugate the probe to dyes with different fluorescence properties. The probes have applications in super-resolution imaging.

Backbone assignment of perdeuterated proteins by solid-state NMR using proton detection and ultrafast magic-angle spinning


Solid-state NMR is useful for getting structural information for insoluble proteins. In this protocol, chemical shifts for backbone atoms are assigned using proton detection and ultrafast magic-angle spinning of perdeuterated proteins.

Dissection of mechanical force in living cells by super-resolved traction force microscopy


Many cellular processes rely on cells generating or responding to nanoscale mechanical forces. This protocol describes STED–traction force microscopy (STFM), which allows these forces to be measured with higher resolution and accuracy than standard TFM.

Metabolomics and lipidomics using traveling-wave ion mobility mass spectrometry


Ion-mobility spectrometry (IMS) separates molecules according to charge, shape and size. In this protocol, traveling-wave ion mobility mass spectrometry (TWIMS) is coupled with LC for metabolomics and lipidomics analysis.

Directed differentiation of human induced pluripotent stem cells into functional cholangiocyte-like cells


This protocol describes how to recapitulate biliary development by differentiation of hPSCs into endoderm, foregut progenitor cells, hepatoblasts, cholangiocyte progenitors and mature 3D cholangiocyte-like cell organoids.

Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening


This protocol from Feng Zhang's lab enables genome-scale knockout and transcriptional activation screening using the CRISPR-Cas9 system, as sgRNA libraries are constructed and packaged into lentiviral vectors for delivery into cells for screening.