Volume 14 Issue 5, May 2019

This protocol describes how to fabricate and apply silicon-based structures for optically controlled neuromodulation. The structures can be used for nongenetic neuronal excitation in cultured neurons, brain slices, and in vivo applications.

This protocol provides instructions for using sigQC to obtain a set of quality control metrics to aid in the evaluation of gene signatures across datasets.

This protocol describes the design, in vitro characterization, and imaging applications of iGluSnFR-based genetically encoded glutamate indicators (GEGIs) in tissue culture of rat hippocampus.

Cells are seeded into an extracellular matrix template and flow is applied to create microfabricated blood vessels.

Individual animals are cultivated in custom microfabricated multiwell substrates. This protocol describes how to design, produce, and image the plates, as well as analyze the resulting behavioral data.

RATaR (RNase A treatment and reconstitution) enables users to study the role of DNA damage response RNA (DDRNA) in the assembly of DNA damage response foci.

A new protocol for high-speed whole-brain fluorescence imaging using block-face serial microscopy tomography (FAST). The protocol contains procedures for hardware assembly, sample preparation, imaging and data processing.

¹⁸F labeling of non-activated arenes (e.g., 3-[¹⁸F]fluoro-5-[(pyridin-3-yl)ethynyl] benzonitrile ([¹⁸F]FPEB)) is an unmet need for PET imaging. This protocol uses a spirocyclic iodonium ylide method for one-step, regioselective radiofluorination.

The aim of this spectral standardization model is to expedite multicenter studies with large numbers of samples. The protocol covers sample preparation, acquisition of FTIR spectra, data preprocessing and model standardization.

This protocol describes optimized procedures for transcriptome-wide sequencing of native 5′ and 3′ ends of mRNAs captured from the same sample to assess the full diversity of processed transcripts that exist in human cells.

This protocol is used to detect RNA decay intermediates in human cultured cells. Reporter mRNAs can be detected and quantified with molecular biology (northern blot, qPCR) and single-molecule fluorescence microscopy (smFISH, live imaging) approaches.

Tubulin with controlled posttranslational modifications can be purified by cycles of polymerization and depolymerization from cultured cells or single mouse brains for use in in vitro reconstitution assays.

This protocol describes the steps in R-ChIP, a procedure based on chromatin immunoprecipitation (ChIP) of an exogenously expressed mutant RNASEH1 to capture the genome-wide distribution of R-loops.