Nature Protocols

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Three CLIP-based protocols—irCLIP-RNP, irCLIPv2, and Re-CLIP—map RNA-dependent associated proteins and binding regions with improved precision versus conventional CLIP, resolving adjacent interactions.

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Persephone is a pipeline that personalizes and evaluates human whole-body metabolic models and community microbiome models, running on 100 metagenomic samples in several days to a week on a single computer.

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Blocking neuron-specific triglyceride lipase enlarges neuronal lipid droplets so they can be purified by sucrose-gradient flotation for lipidomic profiling in cultured primary neurons.

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Image-derived mean squared displacement (iMSD) quantifies spatiotemporal dynamics in living cells without tracking, extracting diffusion coefficients and confinement dimensions from fluorescence stacks.

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FEBID tips made with a benchtop SEM enable high-resolution, long-term stable HS-AFM imaging of annexin V and plasmid DNA, with eight tips fabricated in 1–2 h.

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An adaptive-optics assisted isoSTED (4Pi-STED) nanoscope can be built and aligned to deliver isotropic sub-50-nm 3D imaging in thick samples up to 35 µm.

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Geneformer enables context-aware gene network predictions from limited single-cell transcriptome data, using in silico perturbations to rank candidate therapeutic targets by embedding shifts.

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Yeast nuclei carrying intact synthetic megabase-scale human DNA were delivered into mouse early embryos with 100% microinjection delivery efficiency while maintaining a naive state.

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A pillar[5]arene-incorporated MOF “molecular catcher” enables rapid single-crystal X-ray structure determination of long-alkyl-chain compounds without growing guest single crystals, finishing within 10 d.

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A label-free interferometry protocol enables high-speed quantitative phase imaging of thousands of 3D-bioprinted tumor organoids per experiment at single-organoid resolution, including drug response profiling.

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A universal surfactant-monolayer-assisted interfacial synthesis platform produces large-area, highly crystalline two-dimensional polymer crystals with ~28 cm² lateral size and tunable ~1–200 nm thickness.

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A customizable fabrication pipeline enables optically transparent ultrasound transducers (TUTs) whose measured optical and acoustic performance matches simulation predictions.

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A beginner-focused tutorial shows how to detect and quantify fast neutrons with a single EJ-309 liquid organic scintillation detector using a benchtop deuterium-deuterium fusion reactor.

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RMMR-SPPS enables efficient solid-phase synthesis of peptides containing N-methylated and/or α,α-disubstituted amino acids, achieving crude purities up to 98% with improved yields.

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A visible-light photocatalytic protocol defluorinates PTFE under mild conditions, producing soluble fluoride salts and defluorinated amorphous carbon, with fluoride recoverable as potassium fluoride.

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TRISCO enables single-cell 3D RNA mapping in cleared mouse organs, including brain, lung, heart, kidney, and spinal cord, with whole-tissue homogeneous in situ hybridization signal retention.

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A 3D concentric, three-compartment human bone marrow-on-a-chip builds an immunocompetent vascularized niche in ~7 d, enabling patient-derived testing of leukemia therapies.

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Comprehensive LC–MS2 workflows enable precise BMP species profiling by distinguishing BMPs from phosphatidylglycerol using retention time and positive-mode MS2 fragmentation, including in CLN5 knockout cells.

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Patient fibroblasts reprogrammed into 3D cortical neurons show detectable AD neuropathology—Aβ deposition, tau dysregulation, and neuronal death—by 4 weeks.

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A solid-phase synthesis protocol produces tetra-divinylpyrimidine (tetraDVP) cysteine-reactive linkers that rebridge all four interchain disulfide bonds in native IgG1 and IgG4 with one molecule.

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Nanoparticles can be rationally designed to control intracellular trafficking and localization to specific organelles, enabling precise diagnostics and therapies across multiple disease contexts.

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Nonexhaustive solid-phase microextraction enables integrated sampling, extraction, cleanup, and enrichment with high analytical efficiency while minimizing solvent use.

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CVSP-AIE, an AI-driven structure-based virtual screening platform, hierarchically screens 100,000 compounds in 30–45 minutes while ranking molecules by predicted binding scores.

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An optimized, validated multi-technique analytical workflow fully quantifies the entire hydrocarbon population from polyolefin hydrogenolysis, including headspace gases and soluble/insoluble fractions, within 4 d.

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UNITE enables personalized functional circuit-guided neuromodulation target localization within 30 min on a local GPU workstation, using DeepPrep for a tenfold speedup and improved robustness.

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TAP-seq enables sensitive, cost-effective targeted Perturb-seq by measuring hundreds of selected transcripts per cell, yielding guide RNA assignments and differential expression of perturbation effects.

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A protocol enables in situ peptide self-assembly in living cells using stimuli-responsive unnatural amino acids, with glutathione- or sulfatase-triggered responsiveness and defined assembly conditions.