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This protocol describes the design and implementation of an in vitro platform for highly multiplexed profiling of antibody reactivity using custom DNA-barcoded peptide libraries and deep sequencing.
Cryogenic electron microscopy is well suited to uncovering structural heterogeneity in protein complexes, but analyses of such heterogeneous datasets are challenging. CryoDRGN is a machine learning approach to reconstructing heterogeneous ensembles of cryogenic electron microscopy density maps.
This protocol provides analysis steps for the extraction of high-quality metagenome-assembled genomes from microbiomes and their subsequent analysis using the U.S. Department of Energy Systems Biology Knowledgebase (KBase) platform (http://www.kbase.us/).
This protocol describes how to design, implement and analyze the data from a forced desynchrony protocol to assess endogenous circadian rhythmicity and to separate circadian from evoked components of daily rhythms in physiology and behavior.
Targeted liquid chromatography–tandem mass spectrometry-based metabolomics using in vitro (organoids) and in vivo (gnotobiotic mice colonized with mono- or multi-species bacterial cultures) systems examines the role of specific microbially driven pathways of the mammalian gut–brain axis.
This protocol describes the procedure for the fabrication of electrochemical liquid cells for in situ liquid cell transmission electron microscopy. This allows direct visualization of complex electrochemical reactions at the nano scale in real time.
Ubiquitination and downstream reactions are dynamic, reversible processes with functionally transient intermediates. This protocol describes the preparation of stable mimics that can be used for structural and functional studies.
StarMap is a software package that increases the accuracy of macromolecular structures by refining models using state-of-the-art Rosetta algorithms. StarMap’s graphical user interface is fully integrated into UCSF ChimeraX.
This protocol details the preparation of selective organ-targeting lipid nanoparticles by several methods, their physical characterization, and in vitro/in vivo mRNA delivery evaluation.
Many applications of metal–organic frameworks relate to their nanometer-sized pores. This protocol describes three postsynthetic methods for making metal–organic frameworks with multiple levels of pores: Soxhlet washing, linker hydrolysis and linker thermolysis.
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 at different scales using the four green synthetic methods described in this protocol.
Hi-C-coupled multi-marker analysis of genomic annotation extends the widely used multi-marker analysis of genomic annotation tool for assigning genetic variants to their target genes by incorporating chromatin conformation data that allow discovery of genes associated with noncoding variants.
In HT-smFISH, multiple RNA probes are generated by parallel in vitro transcription from a large pool of unlabeled oligonucleotides. This reduces costs per targeted RNA compared with many smFISH methods and is easily scalable and flexible in design.
This Protocol Extension describes the fabrication and implantation of 3D-printed neural probes for tethered or wireless optogenetics in freely moving rodents.
This protocol presents an optimized version of the single-cell combinatorial indexing RNA sequencing protocol that is faster, less expensive and suitable for profiling tissues rich in RNases, as well as a ‘Tiny-Sci’ protocol for limited input samples.
The Braille Display valving platform described in this protocol can be used to generate droplets (each with 100 cells), assay reagents and a variety of drug combinations or to sort droplets on the basis of fluorescence signals.
This protocol combines microfluidic cell sorting with the CEPT small-molecule cocktail to minimize cellular stress and enable the robust single-cell cloning of human pluripotent stem cells in a high-throughput fashion.
The authors present a protocol for bioengineering human intestinal mucosal grafts. This includes the isolation, expansion and biobanking of patient-derived intestinal organoids and fibroblasts and the decellularization and recellularization of human intestinal scaffolds.
This protocol comprises two Agrobacterium-based methods (direct delivery and fast-treated Agrobacterium co-culture) that use developmental regulators to induce de novo meristems to create genetic modifications on either sterilely grown or soil-grown Nicotiana benthamiana plants.
Stem cell models for the trophoblast lineage have been lacking. This protocol describes the reprogramming of human fibroblasts into induced trophoblast stem cells, alongside steps for their molecular and functional characterization.