Volume 13 Issue 5, May 2018

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.

Coupling fluorescence imaging with fMRI allows study of the molecular processes underlying physiological responses. This protocol shows how to use a fiber-optic implant to measure calcium signaling and blood oxygenation (BOLD fMRI) simultaneously.

This protocol describes an on-chip microfluidic approach for high-throughput production of cell-sized liposomes. Monodisperse and unilamellar liposomes are formed by hydrodynamic flow focusing and immediately purified for further experimentation.

This is a one-step protocol for reprogramming and CRISPR/Cas9 gene editing in human fibroblasts, enabling rapid and clonal derivation of multiple gene-targeted iPSC lines.

This protocol enables genome editing using the CRISPR–Cpf1 system, an alternative to CRISPR–Cas9. The authors detail the design and assessment of engineered components of the system, both crRNAs and Cpf1 mRNAs, and their use for effective genome editing.

PGS addresses the challenge of reconstructing 3D genomes from cells by applying population-based genome structure modeling. The software models the variability of 3D genome structures across cells, accommodating all observed chromatin interactions.

This protocol describes stable conversion of unexcitable cell lines and primary cells into electrically excitable and actively conducting tissues with customizable phenotypes for in vitro electrophysiological studies and in vivo cell therapy applications.

This protocol describes how to set up arrayed and pooled CRISPR genome-editing experiments. It describes the design of sgRNAs using CRISPOR, the wet-lab implementations, and analysis of the generated results by CRISPResso.

Position-selective incorporation of modified nucleotides is useful for RNA study. This protocol describes how to prepare site-specifically labeled RNA using PLOR, an interrupted in vitro transcription-based approach.

This protocol describes CUT&RUN, a genome-wide targeted epigenetic profiling method that allows the analysis of low cell numbers at high resolution.

This protocol describes the chemical synthesis of a fluorescent carbon monoxide (CO) probe, Nile Red–Pd and its applications for detecting CO in tissue culture cells, in mouse organs ex vivo, and in zebrafish embryos.

This protocol shows how to combine fluorescence imaging with single-cell Hi-C, to study genome architecture in single cells with high resolution.

This protocol describes the guidelines and best practices for characterizing metal-binding sites in proteins through X-ray crystallography.

This protocol describes three methods to measure and map solid stress in both excised and in situ tumors of murine and human origin.

This protocol describes a native mass-spectrometry-based approach for identifying the key lipids that interact with membrane proteins.

This protocol describes how to use near-infrared optogenetic tools for controlling gene transcription, subcellular protein targeting and spectral multiplexing with blue-light-controlled tools.

Chrom3D is a computational platform designed to simulate the spatial positioning of chromosome domains relative to each other and to the nuclear periphery, starting from, for example, chromosome conformation capture and lamin ChIP-sequencing data.

This protocol describes an approach to generate chemically modified aptamers using CuAAC click chemistry. Such aptamers possess extended interaction properties and can be identified by in vitro selection procedures using established SELEX strategies.