Volume 13 Issue 10, October 2018

This protocol describes Trim-Away, an approach for rapid protein depletion in different cell types. TRIM21–mediated proteasomal degradation is induced by microinjection or electroporation of an antibody into the protein of interest.

This protocol describes the co-culture of cells from multiple species and, after RNA-seq, the separation of reads by species via the Sargasso bioinformatics pipeline to elucidate the effects of one cell type on the transcriptome of the others.

This protocol describes a dynamic atomic force microscopy (dAFM) approach for high-speed and high-resolution mapping of the viscoelastic properties of live cells. The procedure describes sample preparation, AFM calibration, and data analysis.

In this protocol, the authors explain a new, more precise genetic-lineage-tracing system based on a dual-recombinase strategy. DeaLT enables specific fate mapping of resident stem cells by using both the Cre–loxP and Dre–rox systems.

In this protocol, a ligature is placed between mouse teeth. This induces gingival tissue inflammation and alveolar bone loss, resulting in a mouse model of periodontitis.

This protocol describes how to use a re-engineered MS2 system to image single mRNAs in Saccharomyces cerevisiae. The procedure describes tagging of endogenous genes with MBSV6, two-color smFISH, and how to quantify single mRNAs by live cell imaging.

This protocol describes an approach for pulse labeling of ventricular zone progenitors and their neuronal progeny in the developing brain. Labeled cells can be isolated and highlighted by FACS or immunohistochemistry.

This protocol describes how to design and assemble two-dimensional reconfigurable DNA arrays that can be used for long-range information relay. The procedure describes the design principles and AFM- and TEM-based imaging of the structures.

This protocol describes a method for direct fluorine-18 labeling of heat-sensitive proteins for PET imaging. After conjugation to RESCA chelators, proteins of interest can be radiolabeled with Al¹⁸F at room temperature in an aqueous medium.

This protocol describes the one-pot chemical synthesis and applications of BClO, an ultrasensitive fluorescent probe for detecting hypochlorous acid (HOCl) in live cells.

This protocol describes how to combine up to four genetically encoded fluorescent sensors to image redox landscapes. The procedure describes applications in live imaging and flow cytometry of cultured cells, and in vivo imaging in zebrafish larvae.

This protocol qualitatively and quantitatively assesses the involvement of factors in the nucleolar structure. After siRNA-mediated depletion of factors of interest, dedicated software is used to analyze images of nucleoli to determine an index of nucleolar disruption, the iNo score.

Faridani and colleagues describe Small-seq, a protocol for generating sequencing libraries of small RNAs from single cells.