Nature Protocols

Article	Citations
Author Correction: Z-REX: shepherding reactive electrophiles to specific proteins expressed tissue specifically or ubiquitously, and recording the resultant functional electrophile-induced redox respo	1185
Author Correction: cfSNV: a software tool for the sensitive detection of somatic mutations from cell-free DNA	602
Inducible CRISPR–Cas9 screening platform to interrogate non-proliferative cellular states	517
Isoform-specific RNA structure determination using Nano-DMS-MaP	455
Design and application of the transformer base editor in mammalian cells and mice	420
Routine culture and study of adult human brain cells from neurosurgical specimens	396
Spontaneous and experimental models of lymph node metastasis	370
Open thoracic surgical implantation of cardiac pacemakers in rats	297
Expansion of human pluripotent stem cell–induced nephron progenitor cells (iNPCs) and the generation of nephron organoids from iNPCs	272
ChromEMT: visualizing and reconstructing chromatin ultrastructure and 3D organization in situ	271
Reproducible strategy for excisional skin-wound-healing studies in mice	268
Purification and functional characterization of novel human skeletal stem cell lineages	261
Open-vessel polymerization of N-carboxyanhydride (NCA) for polypeptide synthesis	201
Visualization of metabolites and microbes at high spatial resolution using MALDI mass spectrometry imaging and in situ fluorescence labeling	195
GLORI for absolute quantification of transcriptome-wide m6A at single-base resolution	195
Generating human bone marrow organoids for disease modeling and drug discovery	195
Author Correction: Reliable detection of somatic mutations in solid tissues by laser-capture microdissection and low-input DNA sequencing	185
Head-mounted central venous access during optical recordings and manipulations of neural activity in mice	181
Author Correction: Chromatin integration labeling for mapping DNA-binding proteins and modifications with low input	179
Publisher Correction: Rapid reaction optimization by robust and economical quantitative benchtop 19F NMR spectroscopy	174
How to isolate channel-forming membrane proteins using the E. coli expression system	164
Preparation and biomedical applications of single-metal atom catalysts	163
Spatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue	145
Expansion and fluctuations-enhanced microscopy for nanoscale molecular profiling of cells and tissues	144
Publisher Correction: In vivo pulse labeling of isochronic cohorts of cells in the central nervous system using FlashTag	144

Quantitative molecular imaging using deep magnetic resonance fingerprinting	143
Sonicated inks and focused-ultrasound writing enable deep-penetration acoustic volumetric printing	140
Bioengineering human intestinal mucosal grafts using patient-derived organoids, fibroblasts and scaffolds	130
Metabolomics using anion-exchange chromatography mass spectrometry for the analysis of cells, tissues and biofluids	126
SubCellBarCode: integrated workflow for robust spatial proteomics by mass spectrometry	123
Small RNA structural biochemistry in a post-sequencing era	122
Three-dimensional human neural culture on a chip recapitulating neuroinflammation and neurodegeneration	120
High-throughput fabrication of antimicrobial phage microgels and example applications in food decontamination	115
Rapid reaction optimization by robust and economical quantitative benchtop 19F NMR spectroscopy	110
Precise tracking of nanoparticles in plant roots	109
Fabrication of electron tunneling probes for measuring single-protein conductance	106
Photoimmunotechnology as a powerful biological tool for molecular-based elimination of target cells and microbes, including bacteria, fungi and viruses	104
Generation and characterization of hair-bearing skin organoids from human pluripotent stem cells	103
Hyperosmolar blood–brain barrier opening using intra-arterial injection of hyperosmotic mannitol in mice under real-time MRI guidance	102
Chromatin accessibility profiling by ATAC-seq	101
Fabrication of thin-film electrodes and organic electrochemical transistors for neural implants	93
Large-scale growth of C. elegans and isolation of membrane protein complexes	92
Collections from Nature Protocols	92
A practical guide to identifying associations between tandem repeats and complex human traits using consensus genotypes from multiple tools	91
Expansion of human hepatocytes and their application in three-dimensional culture and genetic manipulation	90
Gene expression and chromatin state mapped in space	90
Sequential orthogonal assays for longitudinal and endpoint characterization of three-dimensional spheroids	84
Establishment of human induced trophoblast stem cells via reprogramming of fibroblasts	82
Scalable growth of vertical graphene nanosheets by thermal chemical vapor deposition	82
A ‘print–pause–print’ protocol for 3D printing microfluidics using multimaterial stereolithography	80
Preparation and quantitative analysis of multicenter luminescence materials for sensing function	80
Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility	78
Generation of iPSC-derived human forebrain organoids assembling bilateral eye primordia	78
Structural connectome construction using constrained spherical deconvolution in multi-shell diffusion-weighted magnetic resonance imaging	77
mRNA lipid nanoparticle formulation, characterization and evaluation	76
Generation and long-term culture of human cerebellar organoids from pluripotent stem cells	75
Honey bee functional genomics using symbiont-mediated RNAi	74
Unraveling cell–cell communication with NicheNet by inferring active ligands from transcriptomics data	74
Achieving transient and reversible optical transparency in live mice with tartrazine	74
Fibrous polyisocyanide hydrogels for 3D cell culture applications	73
Sonoafterglow nanoprobes for deep-tissue imaging of peroxynitrite	71
A versatile tissue-rolling technique for spatial-omics analyses of the entire murine gastrointestinal tract	69
Comprehensive synthesis of Ti3C2Tx from MAX phase to MXene	68
Preparation of selective organ-targeting (SORT) lipid nanoparticles (LNPs) using multiple technical methods for tissue-specific mRNA delivery	67
Publisher Correction: A reconstituted cell-free assay for the evaluation of the intrinsic activity of purified human ribosomes	67
Divergent synthesis of amino acid-linked O-GalNAc glycan core structures	66
Manufacturing synthetic viscoelastic antigen-presenting cells for immunotherapy	66
Identification of immunogenic commensal antigens using phage display	66
Web-based multi-omics integration using the Analyst software suite	63
Scalable tissue labeling and clearing of intact human organs	62
Integrating genome-wide CRISPR screens and in silico drug profiling for targeted antidote development	62
High-throughput single-cell transcriptomics of bacteria using combinatorial barcoding	62
A bifunctional molecule-assisted synthesis of mimics for use in probing the ubiquitination system	62
Plant sperm cell sequencing for genome phasing and determination of meiotic crossover points	60
CONIPHER: a computational framework for scalable phylogenetic reconstruction with error correction	59

All-optical interrogation of neural circuits in behaving mice	57
Surface nanocoating of bacteria as a versatile platform to develop living therapeutics	57
Electrochemical molecular intercalation and exfoliation of solution-processable two-dimensional crystals	57
Author Correction: Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture	56
Enhancing consistency in brain imaging research for population neuroimaging	56
Use of synthetic circular RNA spike-ins (SynCRS) for normalization of circular RNA sequencing data	56
Filter-aided expansion proteomics for the spatial analysis of single cells and organelles in FFPE tissue samples	55
In vitro reconstitution of COPII vesicles from Arabidopsis thaliana suspension-cultured cells	55
Integrating optical neuroscience tools into touchscreen operant systems	55
Sonication-assisted protein extraction improves proteomic detection of membrane-bound and DNA-binding proteins from tumor tissues	55
Genome-wide analysis of the biophysical properties of chromatin and nuclear proteins in living cells with Hi-D	54
A guide to precise measurements of isotope abundance by ESI-Orbitrap MS	53
Comprehensive microcrystal electron diffraction sample preparation for cryo-EM	53
GlYcoLISA: antigen-specific and subclass-specific IgG Fc glycosylation analysis based on an immunosorbent assay with an LC–MS readout	53
Easy and accurate protein structure prediction using ColabFold	52
Profiling native pulmonary basement membrane stiffness using atomic force microscopy	52
Seed amplification assay for the detection of pathologic alpha-synuclein aggregates in cerebrospinal fluid	52
Enzyme-free targeted DNA demethylation using CRISPR–dCas9-based steric hindrance to identify DNA methylation marks causal to altered gene expression	50
Identification and validation of microbial biomarkers from cross-cohort datasets using xMarkerFinder	50
A guide to building a low-cost centrifuge force microscope module for single-molecule force experiments	50
Design and simulation of DNA, RNA and hybrid protein–nucleic acid nanostructures with oxView	49
Accurate determination of protein:ligand standard binding free energies from molecular dynamics simulations	49
A scalable protocol for the radiosynthesis of clinical grade lutetium-177-labeled theranostic agents	49
A graphic and command line protocol for quick and accurate comparisons of protein and nucleic acid structures with US-align	48
Capturing acyl–enzyme intermediates with genetically encoded 2,3-diaminopropionic acid for hydrolase substrate identification	48
In vivo and ex vivo electrophysiological study of the mouse heart to characterize the cardiac conduction system, including atrial and ventricular vulnerability	48
High-confidence and high-throughput quantification of synapse engulfment by oligodendrocyte precursor cells	47
Purifying recombinant proteins from Nicotiana benthamiana for structural studies	47
Spatial analysis of tissue immunity and vascularity by light sheet fluorescence microscopy	46
Construction of complex bacteriogenic protocells from living material assembly	46
Directional conjugation of monoclonal antibodies to nanoparticles using metal-free click chemistry	44
An optimized culture system for efficient derivation of porcine expanded potential stem cells from preimplantation embryos and by reprogramming somatic cells	43
Droplet-based functional CRISPR screening of cell–cell interactions by SPEAC-seq	43
Annotating genetic variants to target genes using H-MAGMA	43
Preparation and use of wireless reprogrammable multilateral optogenetic devices for behavioral neuroscience	42
CellPhoneDB v5: inferring cell–cell communication from single-cell multiomics data	42
Outcome devaluation as a method for identifying goal-directed behaviors in rats	42
Analyzing somatic mutations by single-cell whole-genome sequencing	39
Constructing and interpreting volcano plots and activity maps to navigate homogeneous catalyst landscapes	39
Optimal 13C NMR investigation of intrinsically disordered proteins at 1.2 GHz	39
Applications of and considerations for using CRISPR–Cas9-mediated gene conversion systems in rodents	38
Circular Vectors as an efficient, fully synthetic, cell-free approach for preparing small circular DNA as a plasmid substitute for guide RNA expression in CRISPR–Cas9 genome editing	38
Author Correction: PepSeq: a fully in vitro platform for highly multiplexed serology using customizable DNA-barcoded peptide libraries	38
RNA sample optimization for cryo-EM analysis	38
CRISPR-Combo–mediated orthogonal genome editing and transcriptional activation for plant breeding	36
Microfluidic gradients create a stem cell model of the human central nervous system	36
Stabilization and structure determination of integral membrane proteins by termini restraining	36
Printed photonic crystal biochips for rapid and sensitive detection of biomarkers in various body fluids	36
Standardized production of hPSC-derived cardiomyocyte aggregates in stirred spinner flasks	35
Fabrication of liquid cell for in situ transmission electron microscopy of electrochemical processes	35
Physical dynamic double-network hydrogels as dressings to facilitate tissue repair	34
Surface photovoltage microscopy for mapping charge separation on photocatalyst particles	34
Preparation of near-infrared AIEgen-active fluorescent probes for mapping amyloid-β plaques in brain tissues and living mice	34
Author Correction: Production and use of antigen tetramers to study antigen-specific B cells	33
Mapping T cell dynamics to molecular profiles through behavior-guided transcriptomics	33
YCharOS protocol for antibody validation	33
Derivation, expansion and cryopreservation of primary fetal organoids from second and third trimester human amniotic fluid cells	33
Improving accuracy and reproducibility of mass spectrometry characterization of protein coronas on nanoparticles	33
High-resolution in situ structure determination by cryo-electron tomography and subtomogram averaging using emClarity	33
High-throughput multiplex voltage-clamp/current-clamp evaluation of acutely isolated neurons	33
Direct analysis of biotransformations with mass spectrometry—DiBT-MS	33
Co-fractionation–mass spectrometry to characterize native mitochondrial protein assemblies in mammalian neurons and brain	32
Spatially resolved genome-wide joint profiling of epigenome and transcriptome with spatial-ATAC-RNA-seq and spatial-CUT&Tag-RNA-seq	31
Multilevel characterization of genome editor nuclease activity with BreakTag	31
Synthesis of N-heterocycles through alcohol dehydrogenative coupling	31
Addendum: Micro-CT acquisition and image processing to track and characterize pulmonary nodules in mice	31
A multi-glycomic platform for the analysis of food carbohydrates	31
m6A-SAC-seq for quantitative whole transcriptome m6A profiling	30
Activation of mechanoluminescent nanotransducers by focused ultrasound enables light delivery to deep-seated tissue in vivo	30
Biomarker analysis from complex biofluids by an on-chip chemically modified light-controlled vertical nanopillar array device	30
DARLIN mouse for in vivo lineage tracing at high efficiency and clonal diversity	29
Protocols and risks: when less is more	29
Universal platform for the generation of thermostabilized GPCRs that crystallize in LCP	29
A clinically relevant model of focal embolic cerebral ischemia by thrombus and thrombolysis in rhesus monkeys	29
Nano3P-seq: charting the coding and noncoding transcriptome at single-molecule resolution	29
Visualizing epigenetic modifications and their spatial proximities in single cells using three DNA-encoded amplifying FISH imaging strategies: BEA-FISH, PPDA-FISH and Cell-TALKING	29
A detailed guide to assessing genome assembly based on long-read sequencing data using Inspector	29
Purification of mammalian telomeric DNA for single-molecule analysis	29
Tutorial: a guide to diffusion MRI and structural connectomics	29
A proposed framework to evaluate the quality and reliability of targeted metabolomics assays from the UK Consortium on Metabolic Phenotyping (MAP/UK)	28

Determining chromatin architecture with Micro Capture-C	28
Graphene–molecule–graphene single-molecule junctions to detect electronic reactions at the molecular scale	28
Luciferase- and HaloTag-based reporter assays to measure small-molecule-induced degradation pathway in living cells	28
A consensus platform for antibody characterization	28
Generation of ‘semi-guided’ cortical organoids with complex neural oscillations	28
Labeling, isolation and characterization of cell-type-specific exosomes derived from mouse skin tissue	27
Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R and GenePattern Notebook implementations of CoGAPS	27
Photothermal nanofiber-mediated photoporation for gentle and efficient intracellular delivery of macromolecules	27
Solution-based self-assembly synthesis of two-dimensional-ordered mesoporous conducting polymer nanosheets with versatile properties	27
Preparation, maintenance and propagation of synchronous cultures of photoactive Chlamydomonas cells	27
A new era begins at Nature Protocols	27
scGPT: end-to-end protocol for fine-tuned retinal cell type annotation	27
The HADDOCK2.4 web server for integrative modeling of biomolecular complexes	27
Patient-derived and mouse endo-ectocervical organoid generation, genetic manipulation and applications to model infection	27
Synthesis of ordered mesoporous metal oxides by solvent evaporation-induced cooperative assembly	27
NanoVar: a comprehensive workflow for structural variant detection to uncover the genome’s hidden patterns	27