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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.
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.
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.
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.
Neural differentiation and self-organization of hPSCs are induced by culture in suspension. Neural spheroids are then differentiated into dorsal or ventral forebrain spheroids that can be combined to obtain functionally integrated human assembloids.
This protocol describes how to use a fully defined, synthetic hydrogel to support the in vitro generation and culture of human organoids derived from pluripotent stem cells and the in vivo delivery of hydrogel-encapsulated organoids into mouse colon.
This protocol describes focused ion beam–milling approaches for fabricating oriented single-nanocrystal atomic force microscopy probes, as well as how to measure direction-specific interaction forces between nanocrystals in solution and in vacuum.
This protocol describes TRACER, a 3D cell culture system that enables the assembly of heterogeneous model tumors or tissues that easily disassemble for rapid analysis of different cell populations from particular microenvironments.
Phage immunoprecipitation sequencing (PhIP-Seq) is a method for analyzing antibody-repertoire binding specificities. Phage-displayed oligonucleotide libraries encoding peptidomes are immunoprecipitated and analyzed by high-throughput DNA-Seq.
This protocol describes how to configure targeted spinal cord stimulation using electromyographic recordings and real-time processing of gait kinematics to enable voluntary control of specific leg movements in rats and nonhuman primates.
This protocol describes fit-free analysis of fluorescence lifetime imaging microscopy (FLIM) data using the phasor approach. Pixel-by-pixel decays are transformed to the phasor space, and then the clusters can be connected to the image by the reciprocity rules of the phasor plots.
This protocol describes the EasyPhos platform, a high-throughput and user-friendly workflow for reliable identification of phosphopeptides from small amounts (<200 μg) of sample.
Improved and robust procedures for a cyclodextrin-mediated preparation of asymmetric large unilamellar vesicles of diverse lipid compositions and the characterization of their degree of asymmetry and individual leaflet compositions with NMR and GC.