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This protocol describes the synthesis of magnetic resonance tuning (MRET) sensors. The sensors consist of two magnetic components separated by a linker and can be modularly designed for targets such as enzymes, nucleic acid sequences, and pH values.
This protocol provides a procedure by which Drosophila ovarioles are dissected with or without the epithelial sheath and placed in a closed chamber that mimics physiological conditions for imaging.
This protocol describes CIRCLE-seq (circularization for in vitro reporting of cleavage effects by sequencing), a sensitive and unbiased method for defining the on-target and off-target activity of CRISPR–Cas9 nucleases genome-wide.
Hydroxyl-radical footprinting provides a wealth of data on the structure of nucleic acid–protein complexes. HYDROID is a software tool used to quantify footprinting data from gel electrophoresis images and integrate them with structural models.
Here, the authors describe how to use BasePlayer, an interactive and user-friendly software that facilitates the identification of causative mutations from next-generation sequencing data.
This protocol update describes silica-based approaches for purification of DNA from ancient bone, tooth and sediment samples. The optimized buffers yield short DNA fragments compatible with high-throughput sequencing library preparation.
The immunoassay multiplexing capacity of single-cell mass cytometry relies on monoclonal antibodies labeled with stable heavy-metal isotopes. Nolan et al. describe procedures for conjugating monoclonal IgG antibodies with 48 heavy-metal isotopes.
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 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 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 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 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.
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.
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 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.
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.