Cancer Biology

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    Protocols in Current Issue
    A CRISPR Competition Assay to Identify Cancer Genetic Dependencies
    Authors:  Vishruth Girish and Jason M. Sheltzer, date: 07/20/2020, view: 1170, Q&A: 0
    [Abstract] The CRISPR/Cas9 system is a powerful tool for genome editing, wherein the RNA-guided nuclease Cas9 can be directed to introduce double-stranded breaks (DSBs) at a targeted locus. In mammalian cells, these DSBs are typically repaired through error-prone processes, resulting in insertions or deletions (indels) at the targeted locus. Researchers can ...
    NMR waterLOGSY as An Assay in Drug Development Programmes for Detecting Protein-Ligand Interactions–NMR waterLOGSY
    Authors:  Carole J. R. Bataille, Terence H. Rabbitts and Timothy D. W. Claridge, date: 07/05/2020, view: 806, Q&A: 0
    [Abstract] In drug development programmes, multiple assays are needed for the determination of protein-compound interactions and evaluation of potential use in assays with protein-protein interactions. In this protocol we describe the waterLOGSY NMR method for confirming protein-ligand binding events.
    Isolation of Lipid Rafts from Cultured Mammalian Cells and Their Lipidomics Analysis
    Authors:  Nigora Mukhamedova, Kevin Huynh, Hann Low, Peter J. Meikle and Dmitri Sviridov, date: 07/05/2020, view: 834, Q&A: 0
    [Abstract] Lipid rafts are distinct liquid-ordered domains of plasma membranes of most eukaryotic cells providing platform for signaling pathways. Lipid composition of rafts is critical for their structural integrity and for regulation of signaling pathways originating from rafts. Here we provide a protocol to isolate lipid rafts from cultured human and ...
    In vivo Tumor Growth and Spontaneous Metastasis Assays Using A549 Lung Cancer Cells
    [Abstract] Metastasis accounts for the majority of cancer related deaths. The genetically engineered mouse (GEM) models and cell line-based subcutaneous and orthotopic mouse xenografts have been developed to study the metastatic process. By using lung cancer cell line A549 as an example, we present a modified protocol to establish the cell line-based ...
    Single-cell qPCR Assay with Massively Parallel Microfluidic System
    Authors:  Marta Prieto-Vila, Takahiro Ochiya and Yusuke Yamamoto, date: 03/20/2020, view: 1210, Q&A: 0
    [Abstract] The single-cell transcriptome is the set of messenger RNA molecules expressed in one cell. It is extremely variable and changes according to external, physical and biochemical conditions. Due to sensitivity shortages, most of genetic studies use bulk samples, providing only the average gene expression. Single-cell technologies have provided a ...
    Detection of Individual RNA in Fixed Cells and Tissues by Chromogenic ISH
    Authors:  Meng Jiang, Chen Lin and Rongqin Ke, date: 02/05/2020, view: 1229, Q&A: 0
    [Abstract] Visualization of RNA molecules in situ helps to better understand the functions of expressed genes. Currently, most conventional in situ hybridization methods for visualization of individual RNAs are based on fluorescence detection. Herein we present a chromogenic in situ hybridization protocol for visualization of ...
    Approaching RNA-seq for Cell Line Identification
    Authors:  Tabrez A. Mohammad and Yidong Chen, date: 02/05/2020, view: 1326, Q&A: 0
    [Abstract] Cancer cell lines serve as invaluable model systems for cancer biology research and help in evaluating the efficacy of new therapeutic agents. However, cell line contamination and misidentification have become one of the most pressing problems affecting biomedical research. Available methods of cell line authentication suffer from limited access, ...
    Automated Analysis of Cell Surface Ruffling: Ruffle Quantification Macro
    Authors:  Nicholas D. Condon, Jennifer L. Stow and Adam A. Wall, date: 01/20/2020, view: 1233, Q&A: 1
    [Abstract] Cell surface protrusions include F-actin rich, wave-like ruffles that are erected transiently in response to stimuli and during cell migration. Macrophages are innate immune cells that ruffle constitutively and more dramatically in cells activated by pathogens. Dorsal ruffles and their resulting macropinosomes are key sites for environmental ...
    Enhanced-ice-COLD-PCR for the Sensitive Detection of Rare DNA Methylation Patterns in Liquid Biopsies
    Authors:  Florence Mauger and Jörg Tost, date: 12/05/2019, view: 1684, Q&A: 0
    [Abstract] In the context of precision medicine, the identification of novel biomarkers for the diagnosis of disease, prognosis, predicting treatment outcome and monitoring of treatment success is of great importance. The analysis of methylated circulating-cell free DNA provides great promise to complement or replace genetic markers for these applications, ...
    An Optimized Method to Isolate Human Fibroblasts from Tissue for Ex Vivo Analysis
    [Abstract] Despite their involvement in many physiological and pathological processes, fibroblasts remain a poorly-characterized cell type. Analysis of primary fibroblasts while maintaining their in vivo phenotype is challenging: standard methods for fibroblast isolation require cell culture in vitro, which is known to alter phenotypes. ...



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