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OCTAD is a software pipeline for finding drugs that alter gene expression in such a way that they are likely to reverse the expression pattern of the disease. This protocol describes how to use both the web portal and the desktop version of OCTAD.
This protocol describes how to follow the behavior of immune cells by imaging ex vivo cultured human or mouse skin biopsies following labeling with antibody or nanobody reagents against specific cell surface markers.
This protocol describes a genome-wide approach for ultrasensitive and quantitative detection of DNA double-strand breaks (DSBs) that relies on encapsulating cells in agarose beads and labeling breaks with biotinylated adapters.
This protocol provides a detailed guide for the design and assembly of membrane-spanning DNA nanopores and includes assays for characterizing channel function.
A neonatal mouse model of pressure overload by transverse aortic constriction (nTAC) is described. Mice fully adapt following nTAC on postnatal day 1, but if nTAC is applied on day 7, a maladaptive response occurs that is similar to that seen in adult mice following TAC.
This protocol describes how to assemble a 4Pi single-molecule switching super-resolution microscope. Detailed instructions for beam-path alignment, testing, application to cellular samples and troubleshooting are provided.
This protocol describes a workflow that combines laser-capture microdissection with low-input genome sequencing, while circumventing the use of whole-genome amplification, for accurate detection of somatic mutations in non-neoplastic tissues.
This protocol describes the construction of spinning microfluidics platforms for facile production of perfusable hydrogel microtubes of various sizes and shapes. The microtubes can be loaded with cells to create biomimetic vascular channels.
This protocol describes how to implement high-speed single-point edge-excitation sub-diffraction (SPEED) microscopy in combination with 2D-to-3D transformation to obtain 3D sub-diffraction-limited information about rotational symmetric structures.
Malanchi and colleagues describe how to generate cancer cells with the ability to label their neighboring cells (within the tumor niche) by transferring a liposoluble fluorescent protein.
Human pluripotent stem cells are seeded in a microfluidic device to establish a model that resembles the progressive development of the early post-implantation human embryo.
This protocol describes a microfluidic platform for high-throughput sorting of individual cells from microbial communities. Metabolically active cells are labeled using D2O or 13C, selected by Raman imaging, and sorted on-chip with optical tweezers.
This protocol describes a set of tools and procedures for (1) intravital labeling for the identification of mural cells, (2) in vivo calcium imaging of pericytes and vSMCs, and (3) single- and two-photon optogenetics to study blood flow control.
This protocol describes the fabrication of 3D collagen scaffolds used to culture human colonic crypts derived from primary intestinal epithelial cells.
This protocol provides ImageJ-based workflows for the analysis of images obtained from colorimetric assays. New users can take advantage of a basic workflow; more experienced users can benefit from more advanced analysis procedures.
We report a new protocol for tracking endocytosis and cellular distribution of spherical nucleic acid nanoparticles of different clustering states by correlative imaging with dark-field microscopy, fluorescence microscopy and scanning electron microscopy.
Phosphatidylethanol (PEth) is a metabolite of ethanol that can be used as a stable, direct marker of alcohol usage. This protocol describes how to determine the concentration of PEth in dry blood spots via manual or automated extraction followed by LC-MS/MS.
Delivery of siRNAs to immune cells is challenging because of these cells’ sensitivity to standard transfection reagents. This protocol describes how to synthesize an amphiphilic dendrimer and apply it to transfect siRNAs in a variety of primary immune cells.