Nature Protocols, Published online: 08 October 2025; doi:10.1038/s41596-025-01269-yThe complex spatiotemporal signaling of human neural tube development is successfully engineered in a device using microfluidic gradients, creating a high-fidelity model of the developing human central nervous system.

Nature Protocols, Published online: 08 October 2025; doi:10.1038/s41596-025-01252-7CRISPR screens are widely used to identify essential genes and potential drug targets, but typical setups were designed for the study of highly proliferative cancer cell lines. Now, a protocol, using inducible Cas9, enables screens of non-proliferative cell states including senescence, quiescence and terminal differentiation, thereby expanding the applicability of CRISPR screens.

Nature Protocols, Published online: 08 October 2025; doi:10.1038/s41596-025-01251-8Here, the authors provide a platform for inducible CRISPR–Cas9 screening to interrogate non-proliferative cellular states.

Nature Protocols, Published online: 08 October 2025; doi:10.1038/s41596-025-01266-1Protocol for generating spatially patterned, human neural tube- and forebrain-like structures, by using a microfluidic device to impose orthogonal and independent chemical gradients on human pluripotent stem cells.

Nature Protocols, Published online: 08 October 2025; doi:10.1038/s41596-025-01250-9The simultaneous recording of fast-scan cyclic voltammetry and functional magnetic resonance imaging signals enable the coupling of local tissue oxygen and neurotransmitter dynamics for measuring changes in the brain

Nature Protocols - MOF-303 is a promising water-harvesting sorbent that can take up water at low relative humidity and release it under mild heating. This metal–organic framework can be made...

Nature Protocols, Published online: 06 October 2025; doi:10.1038/s41596-025-01280-3Addendum: Visualizing plant salt stress with a NaCl-responsive fluorescent probe

Nature Protocols, Published online: 03 October 2025; doi:10.1038/s41596-025-01259-0An expert recommendation is presented for the design and evaluation of research studies using transcranial electrical stimulation, resulting in the selection of a 66-point checklist aimed at improving the quality of transcranial electrical stimulation studies.

Nature Protocols, Published online: 03 October 2025; doi:10.1038/s41596-025-01263-4The synthesis of complex carbohydrates requires multiple steps, one of which is 1,2-cis-selective glycosylation. This protocol describes an iron-catalyzed, general approach to formation of rather challenging 1,2-cis-aminoglycosidic linkages.

The procedure for nextPYP facilitates the end-to-end processing of cryoelectron tomography data for high-resolution structure determination and conformational variability analysis.

Nature Protocols, Published online: 02 October 2025; doi:10.1038/s41596-025-01254-5To understand enzymatic redox reaction mechanisms, it is important to investigate the redox behavior at the metal centers. This Protocol describes metalloenzyme attachment to electrodes and how to perform X-ray absorption spectroelectrochemistry.

Nature Protocols, Published online: 02 October 2025; doi:10.1038/s41596-025-01262-5Optoelectronic devices based on two-dimensional layered thin film semiconductors can be tuned to directly sense and process spatial and temporal information, making them suitable to use as in-sensor computing devices.

Nature Protocols, Published online: 01 October 2025; doi:10.1038/s41596-025-01270-5NanoVar is a structural variant caller for low-depth long-read sequencing data, allowing repeat element annotation of non-reference insertion variants. This is a comprehensive guide, from quality assessment of raw data to downstream analysis.

Background Blood proteome analysis is becoming increasingly popular in veterinary research because many animal models have been used to study a range of human diseases. Most of the commercial high-abundance protein (HAP) depletion kits are optimized for human serum, whereas proteins in animal serum may not be present in human serum or may be present at different abundances. There are no previous studies investigating the efficacy of using various HAP kits for proteome analysis of animal serums. Method We used three commercial serum abundant protein depletion (SAPD) kits (i.e., ion exchange-based Norgen kit (ProteoSpin™), antibody-based Thermo Albumin Depletion Kit (Pierce™), solubility-based kit (Minute™), and a cost-effective method (i.e., perchloric acid (PerCA) HAP precipitation) to assess their effectiveness to process serums from five different species (i.e., mouse, chicken, dog, goat, and guinea pig). Protocols of the commercial kits were adopted from manufacturers’ guidelines with minor modifications for optimized performance. Following HAP depletion, proteins from all species were digested using a Trypsin/Lys-C enzyme mix, desalted, and subjected to label-free quantitative bottom-up proteomics analysis via liquid chromatography-tandem mass spectrometry (LC-MS/MS). The raw data were processed using the Andromeda search engine integrated into MaxQuant, and peptide identification was performed by searching against the UniProt-reviewed protein database. Advanced bioinformatics tools were employed to facilitate data analysis and visualization, ensuring comprehensive interpretation of the depletion efficiency and comparative performance of the methods across species. Result We determined their capabilities of protein identification (Norgen kit > Minute kit > PerCA precipitation > Thermo kit), depletion efficiencies of HAPs (Minute kit > Norgen kit > PerCA precipitation > Thermo kit), and cost-effectiveness (PerCA precipitation > Minute kit > Norgen kit > Thermo kit). Our results show that the PerCA precipitation method, which is > 20 times cheaper than commercial kits, outperforms other methods in depleting HAPs, especially in mouse serum. While Norgen kit excels in mouse and goat serum, the PerCA precipitation method offers broader applicability and reveals unique low abundant proteins. Protein pathway analysis highlights distinct biological processes affected by different depletion methods. Discussion Overall, our studies provide valuable insights into protein depletion techniques, with the PerCA depletion method emerging as a cost-effective and versatile option for proteomics research across various serums.

Nature Protocols, Published online: 30 September 2025; doi:10.1038/s41596-025-01248-3This protocol for imaging-based highly multiplexed in situ profiling of the spatial transcriptome uses three methods: antibody-based protein comapping with STARmap PLUS, ribosome-bound mRNA mapping with RIBOmap and spatiotemporal transcriptome mapping with TEMPOmap.

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Nature Protocols, Published online: 24 September 2025; doi:10.1038/s41596-025-01246-5A technique for ultrasound-induced luminescence imaging, which uses a dual-stage energy conversion mechanism to enhance the performance of luminescence.

Generative AI has made it trivial to generate fake microscopy images that are indistinguishable from real images, even for experts. As researchers in nanoscience, it is time for us to face this reality and discuss strategies to conserve the integrity of our discipline.

Nature Protocols, Published online: 22 September 2025; doi:10.1038/s41596-025-01242-9In the virus-encoded CRISPR-based direct readout system, single-guide RNA libraries are expressed directly from the genomes of viruses so that single-guide RNA abundance at distinct stages of the viral infection cycle provides direct and quantitative readout of gene-perturbation effects on viral propagation.

Nature Protocols, Published online: 22 September 2025; doi:10.1038/s41596-025-01241-wMehl and colleagues present a protocol for selecting aminoacyl-tRNA synthetase (RS)/tRNA pairs from a publicly available MaPylRS active site mutant library for specific and efficient incorporation of noncanonical amino acids into proteins.

Nature Protocols, Published online: 19 September 2025; doi:10.1038/s41596-025-01240-xAspiration-assisted bioprinting is a versatile biofabrication technique that enables the precise and selective patterning of biologics, such as tissue spheroids and organoids, addressing the limitations of conventional bioprinting techniques.

Nature Protocols, Published online: 17 September 2025; doi:10.1038/s41596-025-01261-6This Protocol provides detailed instructions for performing NAP-seq, an RNA sequencing technique for profiling full-length sequences of noncapped RNAs with various terminal modifications at single-nucleotide resolution.

Nature Protocols, Published online: 12 September 2025; doi:10.1038/s41596-025-01247-4This protocol describes a versatile strategy to generate structurally and functionally programmable hydrogels by using biological membranes as cross-linkers. This enables properties of tissues like muscle and skin to be mimicked.