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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.
In this Protocol Extension, the authors extend their original Protocol used to generate a genome-scale metabolic model for a single strain to enable multi-strain models to be made, which can be used to study pan-metabolic capabilities and strain-specific differences across a species.
Circulating cell-free DNA (cfDNA) is shed in the bloodstream by normal and tumor cells and is a valuable liquid biopsy tool. This protocol describes a low-input approach to enrich methylated DNA fragments from cfDNA and prepare sequencing libraries.
Selective ribosome profiling (SeRP) reveals nascent chain length–resolved binding profiles of a co-translationally acting factor and relies on selective enrichment of factor-engaged monosomes. This protocol describes how to perform the procedure in yeast.
This Protocol Extension describes procedures used to identify cell-type-specific transcriptomes in mice without sorting cells. The approach combines cell-specific RNA labeling and chemical modifications to introduce T>C conversions in the labeled RNA.
This protocol describes the analysis of stable isotope (13C and 15N) incorporation into polar metabolites in central carbon metabolic pathways using HILIC separation and selected reaction monitoring with a hybrid triple quadrupole mass spectrometer.
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.
In this protocol extension, the authors detail an in-cell version of their previous in vitro SHAPE-MaP protocol, enabling RNA structure to be probed in living cells.
This protocol describes production and bioinformatics analysis pipelines for E/L Repli-seq, an extension of the earlier Repli-chip protocol, allowing rapid genome-wide replication-timing analysis by next-generation sequencing.
This protocol extension describes DNA-free genome editing of bread wheat by delivering in vitro transcripts (IVTs) or ribonucleoprotein complexes (RNPs) of CRISPR/Cas9 by particle bombardment. The authors' previously published protocol for genome editing of wheat used CRISPR/Cas9 plasmids.
Here the authors provide an extension to their earlier RNA interactome capture protocol. This Protocol Extension describes RBDmap—a method to identify the regions of RNA-binding proteins engaged in native interactions with RNA, in a proteome-wide manner.
This protocol extension describes how to obtain functionally mature oocytes from embryonic or induced pluripotent stem cells. These oocytes can be used to produce live mouse offspring.
Here the authors provide an extension of their original FLOTAC protocol, describing the Mini-FLOTAC technique, optimized to perform diagnosis of helminth and protozoan infections in humans and animals where centrifugation may not be practical.