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In this protocol, the authors describe an approach for PCA-based 3D reconstruction of hollow sphere–shaped tissues and organs from single-cell gene expression data.
Lee et al. provide their protocol for fluorescent in situ sequencing (FISSEQ) of RNA. This technique allows spatial and quantitative information about mRNA expression to be obtained simultaneously.
Targeted proteomics by SRM/MRM or SWATH MS relies on reference assay libraries for peptide identification. This protocol is for building extensive, high-quality reference libraries starting with data acquired by discovery proteomics.
This protocol describes how in-solution protein FTIR can be used to obtain information about the relative contributions of α-helices, β-sheets, β-turn, and random coil structures to a protein's secondary structure.
Functional CFTR-expressing airway epithelial cells are generated via differentiation firstly into progenitors and then into mature epithelia with apical CFTR activity.
This protocol describes how to achieve optogenetics- and imaging-aided physiological analysis of synaptic interconnections among 4–30 simultaneously and sequentially recorded neurons.
This protocol describes how to direct differentiation of human pluripotent stem cells into developmental lung progenitors, and subsequently into predominantly distal lung epithelial cells, by following four stages that recapitulate lung development.
This Protocol from the Misteli lab describes how to determine the cell cycle stage of each individual cell in a population by using fluorescence microscopy and automated image analysis software.
UbiCRest is a simple PAGE-based method that leverages the varying specificities of deubiquitinating enzymes (DUBs) to generate information about the composition and architecture of ubiquitin chains.
This protocol describes how to use mass-tag cell barcoding to label individual cell samples with unique combinatorial barcodes. The samples can then be pooled for processing and measurement on a mass cytometer.
This protocol uses retrograde pronase-collagenase perfusion of the liver and subsequent density-gradient centrifugation and optional flow-cytometric sorting to isolate hepatic stellate cells.
This article provides guidelines on how to perform a voxel-based gray matter asymmetry analysis, taking structural brain images from the initial data pre-processing through statistical analyses and the final interpretation of the significance maps.
Protein SUMOylation, which has a crucial role in the regulation of important cellular processes, is difficult to replicate using living systems in the lab. Boll et al. describe here the chemical synthesis of functional SUMO-peptide conjugates.
This protocol describes how to perform liver confocal intravital microscopy in mice, revealing the morphology and function of hepatocytes, endothelial cells and leukocytes in their native environment under physiological or pathological conditions.
Chemical compositional information can be extracted from Raman and infrared microscopic images by MCR-ALS. The algorithm finds the spectral profiles of compounds contributing to each image pixel and their relative concentrations.
Zuo and Morris describe an approach to catalytic hydrogenation of prochiral ketones and imines to produce enantioenriched alcohols and amines that uses a more environmentally friendly iron-based catalyst instead of conventional Ru-based catalysts.