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Circulating cell-free DNA (cfDNA) is shed in the bloodstream by normal and tumor cells and is a valuable liquid biopsy tool. This protocol describes a low-input approach to enrich methylated DNA fragments from cfDNA and prepare sequencing libraries.
This protocol describes the fabrication of nitrogen-vacancy diamond chips, construction of a ‘quantum diamond spectrometer’, and applications for nuclear magnetic resonance (NMR) and electron spin resonance (ESR) spectroscopy in nanoscale volumes.
Here, the authors describe a marker-independent, unbiased lineage-tracing method to quantitatively assess stem cell function and tumor growth dynamics in unperturbed tumor tissue.
This protocol describes how to assemble and characterize 2D plasmonic nanoparticle superlattice sheets. The freestanding nanosheets can be assembled from different nanoparticle building blocks to achieve tailored properties.
This protocol describes a quantitative 31P NMR spectroscopy approach for the analysis and determination of hydroxyl groups on biorefinery resources such as lignins and tannins.
Here, the authors detail how to fabricate a micrometer-thickness nanoparticulate TiO2-filmed Au ultramicroelectrode and use it for real-time detection of the intrinsic photoelectrochemical behaviors of each individual dye-tagged oxide semiconductor nanoparticle collision associated with a single-entity photoelectrochemical reaction.
An important feature of biochemical labeling strategies is their inherent biocompatibility. This protocol enables systematic evaluation of the reaction biocompatibility of (new) synthetic methodologies via bio-additive-based screening.
Whole-cell extracts are analyzed by gas chromatography–mass spectrometry to monitor interactions among all enzymes of distal cholesterol biosynthesis in a single experiment for inhibitor screening.
This protocol describes procedures for generating genome-edited mouse models by injecting CRISPR reagents into oviducts of pregnant females and subsequently electroporating the reagents into zygotes in situ, thus bypassing cumbersome ex vivo handling of embryos.
Here, the authors describe rhTCRseq, RNase H–dependent PCR-enabled TCR sequencing, for repertoire analysis from bulk RNA samples or single-cell profiling.
Selective ribosome profiling (SeRP) reveals nascent chain length–resolved binding profiles of a co-translationally acting factor and relies on selective enrichment of factor-engaged monosomes. This protocol describes how to perform the procedure in yeast.
This protocol describes how to create functional chromosome fusions in yeast through sequential rounds of CRISPR–Cas9-guided homologous recombination. Each round of pairwise chromosome end-to-end fusion deletes two telomeres and one centromere.
This protocol details labeling of bacterial outer-membrane proteins with spin labels to study conformational changes and their interaction with ligands and substrates in situ, using pulsed electron–electron double resonance (PELDOR or DEER) spectroscopy.
A protocol for the design, construction, and operation of an intelligent image-activated cell sorting (iIACS) machine that performs real-time image-based sorting of single cells from heterogeneous populations with high throughput and intelligence.
Cross-linking with mass spectrometry (XL-MS) can reveal the topology of protein complexes. This protocol describes how to synthesize a cleavable cross-linker and use it to map protein structures and interactions within intact cells and animal tissues.
This protocol describes the design of a paper-based analytical device with printed electrodes where the reagents are incorporated into the paper. Such a device can be used in conjunction with a portable detector connected to a PC or smartphone.
DNA origami can be used to create a wide diversity of 3D structures. This protocol describes a DNA origami silicification (DOS) approach for generating complex silica composite nanomaterials with tailored structural properties.
The transmembrane domains of many type I/II membrane proteins oligomerize in the lipid bilayer, mediating protein assembly and clustering that are critical to their function. The authors provide a general protocol for determining the structures of these domains in a near–lipid bilayer environment.
This Protocol Extension describes procedures used to identify cell-type-specific transcriptomes in mice without sorting cells. The approach combines cell-specific RNA labeling and chemical modifications to introduce T>C conversions in the labeled RNA.
A protocol for the assembly and use of the optoPlate-96, a platform for high-throughput three-color optogenetics experiments in microwell plates. With the provided design files, users can assemble the optoPlate-96 from 3D-printed and laser-cut components.