Volume 16 Issue 3, March 2021

In this extension to their NET-seq protocol, the authors combine isolation of 4sU-labeled chromatin-associated nascent RNA with long-read direct RNA sequencing on nanopores to profile the kinetics and patterns of co-transcriptional RNA processing.

This protocol describes how to use natural language processing software to analyze metabolomics data to prioritize metabolites for further study, identify candidates for unique disease biomarkers and elucidate their function on a pathway level.

This protocol describes how to successfully design and execute molecular brightness analysis of G-protein–coupled receptor oligomerization. Labeling strategies, controls and instructions for spatial and temporal brightness imaging and data analysis are provided.

This protocol enables the sensitive detection of norovirus from environmental water samples in situ using a custom-built smartphone-based fluorescence microscope to detect anti-norovirus antibody-conjugated fluorescent particles on a paper microfluidic chip.

This protocol describes strategies for making N-heterocyclic carbene gold(I) chloride complexes. These can be used as synthons to access various oxygen-, nitrogen- or carbon-bound gold complexes that are widely used as catalysts.

This protocol describes the generation, maintenance and applications of snake venom gland organoids. These organoids can be derived within days from embryonic or adult venom gland tissues from various snake species.

The high-throughput PAM determination assay (HT-PAMDA) described here enables scalable characterization of the PAM preferences of Cas proteins.

This protocol describes how to isolate up to six different subpopulations of extracellular vesicles (EVs) from tissues. The procedure includes detailed instructions for EV characterization using electron microscopy, RNA and protein analysis.

The authors describe a process for the mass production and cryopreservation of definitive endodermal cells derived from human pluripotent stem cells using a chemically defined, xeno-free suspension culture in stirred tank bioreactors or rotating Erlenmeyer flasks.

This protocol describes how to perform single-particle tracking photoactivated localization microscopy (sptPALM) of membrane proteins in living plant tissues. The procedure covers all stages, from sample preparation to data analysis.

This protocol describes procedures for isolation of nuclei of multiple cell populations (neurons, microglia, oligodendrocytes, and astrocytes) from resected or postmortem brain tissue that are compatible with downstream epigenomic or transcriptomic profiling.

The authors provide experimental and computational procedures, including details on building an automated fluidic exchange system, for high-resolution imaging of multiple transcripts and chromatin structure in fixed cells or cryosectioned tissue.

CRISPR-induced on-target effects (large deletions, large insertions, rearrangements or loss of heterozygosity) occur frequently at the edited site. This protocol describes how to identify these effects using quantitative genotyping PCR and SNP genotyping.

The authors present a protocol for producing cyclic peptide precursors in Pichia pastoris that undergo in vitro enzymatic maturation into cyclic peptides using recombinant asparaginyl endopeptidases. Assays for characterizing purified cyclic peptides are also described.

The authors describe a reverse genetic system that enables rapid synthesis of wild-type, mutant and reporter SARS-CoV-2 strains to study viral infection, transmission, pathogenesis, therapeutics and vaccines.