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This protocol describes procedures for speed-breeding approaches using growth cabinets and LED-supplemented glasshouses. The approaches can be used to accelerate crop research and are compatible with a wide variety of crops.
This protocol describes how to generate high-resolution maps of the elastic properties of biomolecules and polymers using bimodal AFM. The procedure covers sample preparation, bimodal AFM setup and calibration, and data acquisition and processing.
In this tutorial, the authors provide a comprehensive description of the considerations for designing single-cell transcriptomics studies, from sample preparation and single-cell RNA sequencing methodologies through data processing and analysis.
This protocol describes strategies for targeted genome modification in axolotls. Eggs are injected with a CAS9–gRNA ribonucleoprotein complex, which allows for efficient generation of knockout and knock-in animals and immediate phenotypic analysis.
Adult endothelial cells from mice are reprogrammed to hematopoietic stem cells without transitioning through a pluripotent state. The protocol also describes in vitro and in vivo assays to confirm that the resulting cells function as expected.
This protocol describes the differentiation of hiPSCs into cardiomyocytes and subsequent cytotoxicity and contractility assays needed to calculate the ‘cardiac safety index’, which models the likelihood that a drug is cardiotoxic.
This protocol provides approaches for applying the CRISPR–Cas9 system for genome editing in apple and grapevine plants, using both plasmid-mediated delivery of components and direct delivery of CRISPR–Cas9 ribonucleoproteins.
This computational protocol offers a framework to integrate high-dimensional -omics datasets. A three-pronged association study integrating intestinal microbiome and serum metabolome data with measures of human host physiology is used as an example.
Valuable structural information can be derived by chemical cross-linking of proteins followed by mass spectrometry of the products. Iacobucci et al. use MS-cleavable reagents, enrichment by strong-cation-exchange chromatography, and LC-MS/MS analysis.
Endothelial cells, pericytes and astrocytes are cocultured to generate organoids that reproduce many features of the blood–brain barrier. This protocol also describes how to analyze drug penetration into the organoids.
This protocol describes how to implement and apply an adaptive light-sheet microscopy framework (AutoPilot). The procedure can be used to introduce AutoPilot in an existing microscope or to set up a new adaptive multiview light-sheet microscope.
This protocol describes the synthesis, characterization, and calibration of a nanoscale fiber-optic force sensor. The sensor can be used to detect sub-piconewton forces and acoustic waves in biological environments by means of optical readouts.
This Protocol Extension describes how to prepare plant tissue to enable Spatial Transcriptomics profiling. Spatial Transcriptomics is achieved through the combination of histological staining of the plant tissue with spatially resolved RNA sequencing.
This protocol describes how to generate transgenic zebrafish expressing a barcode array that can be edited by CRISPR–Cas9 at multiple developmental stages. Single-cell RNA sequencing of edited barcodes and cellular transcriptomes allows reconstruction of lineage relationships.
This protocol describes how to produce cell-laden microfibers using capillary microfluidic devices. The devices enable spinning of increasingly complex microfibers, which can function as building blocks for 3D cell culture and tissue engineering.
This protocol addresses the need to define informative priors to apply ensemble modeling in systems biology. The protocol collects parameters, assesses their plausibility and creates log-normal probability distributions for use as informative priors.
Spatial Transcriptomics combines histological staining and spatially resolved RNA-sequencing data from tissue sections. This protocol describes how to implement this method with mammalian tissue.