Protocol Extension in 2020

In this Protocol Extension, Lancaster et al. describe a modified version of their original protocol (published in 2014) that can be used to reliably generate cerebral organoids of a telencephalic identity and maintain long-term viability for later stages of neural development, including axon outgrowth and neuronal maturation.

This extension of the original silicon fluoride acceptor (SiFA) protocol for ¹⁸F-labeling of peptides describes modifications required for the preparation of clinical-grade [¹⁸F]SiFAlin-TATE for diagnosis of neuroendocrine tumors via PET imaging.

This protocol extension describes an improved method for global profiling of poly(A) RNA-binding proteins (RBPs) and quantitative analysis of RBP dynamics in response to biological and pharmacological cues that uses UV crosslinking, capture with LNA-modified oligo-dT probes, and proteomics.

Flow cytometry is used to track dynamics in microbial communities and link these changes with ecological parameters. This protocol describes how to prepare a fixed microbial cytometric mock community to standardize results over large-scale studies.

NAD⁺ is one of the noncanonical nucleotides recently found to cap the 5′ end of RNAs. This Protocol Extension describes procedures for genome-wide analysis of NAD⁺-capped RNAs by direct RNA sequencing on an Oxford Nanopore platform.

This Protocol Extension describes how to perform formaldehyde-assisted isolation of regulatory elements (FAIRE) from Arabidopsis leaves. The FAIRE protocol is optimized for compatibility with downstream qPCR analysis and next-generation sequencing.

In this extension to their original protocol applying TAR cloning to mammalian genomes, the authors apply the technique to microbes and environmental DNA samples, by adding ARS-like elements not commonly found in microbial genomes to the TAR cloning vector.

This protocol describes a biomimetic smoking robot that can be used in combination with microfluidic organ chips to simulate disease biogenesis in vitro.