Volume 18 Issue 1, January 2023

This Protocol Extension describes the fabrication and implantation of 3D-printed neural probes for tethered or wireless optogenetics in freely moving rodents.

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.

This protocol describes proximity biotinylation in cells without transfection or transduction using an off-the-shelf recombinant ProtA-TurboID enzyme consisting of a biotin ligase fused to an antibody-recognizing moiety, which, combined with a bait-protein-specific antibody, can be used to identify bait-proximal proteins.

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.

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.

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.

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.

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 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.

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/).

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.