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Visualization of a cell-lineage reconstruction of early nervous system development in Drosophila. The reconstruction was performed with TGMM and CATMAID, using SiMView light-sheet microscopy images. Imaged cell nuclei are shown in grey (200 min after egg laying (AEL)). Tracks and endpoints of progenitor cells are shown as colored lines (purple to yellow: 170–320 min AEL) and green spheres, respectively. Taken from the protocol by Fernando Amat et al. DOI: 10.1038/nprot.2015.111. Cover design by Jamel Wooten.
In SHAPE-MaP, reverse transcriptase–induced mutations at SHAPE-modified RNA nucleotides are detected by high-throughput sequencing. ShapeMapper converts sequence data to mutational profiles (MaPs), which can be used by SuperFold for RNA structure modeling.
When an electric field is applied across a membrane containing nanopores, it induces an ion current that alters upon ligand binding. Single-walled carbon nanotubes form nanopores that can be used as sensors; specificity is a function of pore size.
Rat or human lung samples are enzymatically digested, and CD31-expressing cells are positively selected using magnetic-activated cell sorting before plating in endothelial-specific growth conditions.
This protocol describes how to perform CUBIC (Clear, Unobstructed Brain/Body Imaging Cocktails and Computational analysis), a simple and efficient method for organ clearing, imaging by light-sheet microscopy, and quantitative imaging analysis.
The micro-EROD assay is a high-throughput screening method used to assess the CYP1A-inducing potential of dioxins and dioxin-like chemicals in rat hepatoma cells.
Changes in the levels of cellular thiols (e.g., glutathione) are linked to many diseases. This protocol is for the synthesis of CPDSA, a fluorescent turn-on glutathione probe with near-infrared emission. In-cell and in vivo assays are also described.
This protocol describes a modular approach to modify existing genetically engineered mouse models (GEMMs) by re-derivation of embryonic stem cells (ESCs) and subsequent modification of these cells by recombinase-mediated transgene insertion.
Pu-seq (polymerase usage sequencing) is an approach for identifying ribonucleotides by high-throughput sequencing to allow the mapping of replicative polymerase usage genome wide. This has been used to define origin efficiencies and replication timing in yeast.
Here, the authors describe genetically engineering the Pseudomonas genome by two-step allelic exchange. Suicide vector-encoded alleles are used to generate mutations by homologous recombination at the single base pair level.
In this protocol, the authors describe methods for the direct delivery of ZFN, TALEN and Cas9 nuclease proteins into cells for efficient and targeted genome editing.
This protocol describes how to fix, embed, clear and stain excised organs or whole organisms to create optically transparent samples. This versatile protocol is able to process a wide range of sample types for high-resolution imaging.