Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain
the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in
Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles
and JavaScript.
This protocol provides step-by-step instructions for using MetaNeighbor, a computational tool that allows quantification of cell-type replicability across single-cell transcriptomic datasets and identifies the gene sets that contribute to cell identity.
The authors provide a protocol for generating mouse–human chimeric embryos by injecting naive human pluripotent stem cells converted from the primed state.
The protocol describes a quantitative measurement that uses commercially available reagents to compare thrombogenic products against the World Health Organization standard for factor XIa procoagulant activity.
This protocol describes co-detection by indexing, a highly multiplexed imaging technology that uses DNA-conjugated antibodies to image up to 60 markers in formalin-fixed, paraffin-embedded and fresh-frozen tissues.
This protocol describes the setup and characterization of a supramolecular assembly of small precursors into colloids or fibers driven by carbodiimide fuels. When the fuel is spent, the reaction reverses to form the initial peptides or amino acids.
The protocol describes coculture of a primary human colon monolayer derived from cells growing in colon organoids with aerotolerant bacteria, such as strains of B. thetaiotaomicron genetically engineered to respond to different stimuli in colonic microenviroments.
This protocol provides a step-by-step workflow for prioritizing the cell types most responsive to an experimental perturbation in single-cell data and describes various applications of the pipeline in five case studies.
This protocol uses transient reporters for editing enrichment to facilitate highly efficient base editing of human pluripotent stem cells, enriching for cells edited by adenosine and cytosine base editors and enabling the generation of clonal isogenic human pluripotent stem cell lines.
This protocol describes FlowSOM, a clustering and visualization algorithm for unsupervised analysis of high-dimensional cytometry data. The protocol provides clearly annotated R code and an example dataset for inexperienced users.
This protocol sets up a bioluminescent repair reporter system using engineered Gaussia and Vargula luciferases for noninvasive tracking of homology-directed repair and nonhomologous end joining, respectively, induced by SceI meganuclease, SpCas9 or SpCas9 D10A nickase-mediated editing.
This protocol describes Deepometry, an open-source application for supervised and weakly supervised deep learning analysis of imaging flow cytometry datasets. The protocol provides runtime scripts for Python, MATLAB and a standalone application.
This approach leverages the rapid, bio-orthogonal inverse electron demand Diels–Alder reaction between a radiolabeled tetrazine and a trans-cyclooctene–bearing antibody to enable pretargeted positron emission tomography imaging and endoradiotherapy in a murine model of cancer.
The hydroperoxide l-tryptophan derivative cis-WOOH regulates vascular tone under inflammatory conditions via redox signaling. This protocol describes the preparation of cis-WOOH and related compounds for use as analytical standards and biochemical tools.
This protocol details how to use Raman spectroscopy for cancer cytopathology diagnosis. Detailed instructions are provided for sample preparation (cervical, oral and lung exfoliated cells), data acquisition, preprocessing and analysis.
This protocol describes how to identify direct protein targets of noncoding RNAs—Xist, TERRA and U1—and outlines modifications specific to each noncoding RNA and its partners.
This protocol describes the implantation of Neuropixels probes for chronic recording of neural activity in rats and mice using 3D-printed fixtures. The fixtures enable routine probe reuse, and single-, dual- and movable-probe variants are described.
This protocol describes how to perform 3D super-resolution imaging on a conventional confocal microscope using metal/graphene-induced energy transfer (MIET/GIET). The protocol covers substrate and sample preparation, imaging and data analysis.
Glycosphingolipids found on the cell membrane play significant roles in many biological processes. This protocol describes how to analyze GSL glycans from cultured cells using a lectin microarray with confirmation by mass spectrometry.
Cerebral blood volume dynamics in awake head-fixed mice are tracked via functional ultrasound imaging through a chronic cranial window, giving a high-resolution measure of brain-wide activity.
This protocol describes a computational pipeline for analyzing the single-nucleotide positions and genomic context of DNA-embedded ribonucleotides that have been mapped with any of the currently available ribonucleotide sequencing techniques.