Cancer Biology

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    Protocols in Current Issue
    A Flow Cytometry-Based Method for Analyzing DNA End Resection in G0- and G1-Phase Mammalian Cells
    Authors:  Bo-Ruei Chen, Jessica K. Tyler and Barry P. Sleckman, date: 05/20/2022, view: 978, Q&A: 0
    [Abstract]

    DNA double strand breaks (DSBs) constantly arise in cells during normal cellular processes or upon exposure to genotoxic agents, and are repaired mostly by homologous recombination (HR) and non-homologous end joining (NHEJ). One key determinant of DNA DSB repair pathway choice is the processing of broken DNA ends to generate single strand DNA

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    Conditional Human BRD4 Knock-In Transgenic Mouse Genotyping and Protein Isoform Detection
    Authors:  Michael Paul Lewis, Shwu-Yuan Wu and Cheng-Ming Chiang, date: 04/05/2022, view: 702, Q&A: 0
    [Abstract]

    Bromodomain-containing protein 4 (BRD4) is an acetyl-lysine reader protein and transcriptional regulator implicated in chromatin dynamics and cancer development. Several BRD4 isoforms have been detected in humans with the long isoform (BRD4-L, aa 1-1,362) playing a tumor-suppressive role and a major short isoform (BRD4-S, aa 1-722) having

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    Single-cell Damagenome Profiling by Linear Copying and Splitting based Whole Genome Amplification (LCS-WGA)
    Authors:  Yichi Niu, Qiangyuan Zhu and Chenghang Zong, date: 03/20/2022, view: 823, Q&A: 0
    [Abstract]

    Spontaneous DNA damage frequently occurs on the human genome, and it could alter gene expression by inducing mutagenesis or epigenetic changes. Therefore, it is highly desired to profile DNA damage distribution on the human genome and identify the genes that are prone to DNA damage. Here, we present a novel single-cell whole-genome amplification

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    Whole-genome Methylation Analysis of APOBEC Enzyme-converted DNA (~5 kb) by Nanopore Sequencing
    [Abstract]

    In recent years, DNA methylation research has been accelerated by the advent of nanopore sequencers. However, read length has been limited by the constraints of base conversion using the bisulfite method, making analysis of chromatin content difficult. The read length of the previous method combining bisulfite conversion and long-read sequencing

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    Measurement of DNA Damage Using the Neutral Comet Assay in Cultured Cells
    Authors:  Elena Clementi, Zuzana Garajova and Enni Markkanen, date: 11/20/2021, view: 1998, Q&A: 0
    [Abstract]

    Maintenance of DNA integrity is of pivotal importance for cells to circumvent detrimental processes that can ultimately lead to the development of various diseases. In the face of a plethora of endogenous and exogenous DNA damaging agents, cells have evolved a variety of DNA repair mechanisms that are responsible for safeguarding genetic

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    Measuring Real-time DNA/RNA Nuclease Activity through Fluorescence
    Authors:  Paulina Wyrzykowska, Sally Rogers and Richard Chahwan, date: 11/05/2021, view: 1945, Q&A: 0
    [Abstract]

    DNA and RNA nucleases are wide-ranging enzymes, taking part in broad cellular processes from DNA repair to immune response control. Growing interest in the mechanisms and activities of newly discovered nucleases inspired us to share the detailed protocol of our nuclease assay (Sheppard et al., 2019). This easy and inexpensive method can provide

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    Measuring DNA Damage Using the Alkaline Comet Assay in Cultured Cells
    Authors:  Elena Clementi, Zuzana Garajova and Enni Markkanen, date: 08/20/2021, view: 2387, Q&A: 0
    [Abstract]

    Maintenance of DNA integrity is of pivotal importance for cells to circumvent detrimental processes that can ultimately lead to the development of various diseases. In the face of a plethora of endogenous and exogenous DNA-damaging agents, cells have evolved a variety of DNA repair mechanisms that are responsible for safeguarding genetic

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    Neutral Comet Assay to Detect and Quantitate DNA Double-Strand Breaks in Hematopoietic Stem Cells
    Authors:  Irene Mariam Roy, Pon Sowbhagya Nadar and Satish Khurana, date: 08/20/2021, view: 1927, Q&A: 0
    [Abstract]

    In vertebrates, hematopoietic stem cells (HSCs) regulate the supply of blood cells throughout the lifetime and help to maintain homeostasis. Due to their long lifespan, genetic integrity is paramount for these cells, and accordingly, a number of stem cell-specific mechanisms are employed. However, HSCs tend to show more DNA damage with increasing

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    Fe-NTA Microcolumn Purification of Phosphopeptides from Immunoprecipitation (IP) Eluates for Mass Spectrometry Analysis
    Authors:  Ethan J. Sanford and Marcus B. Smolka, date: 08/05/2021, view: 1758, Q&A: 0
    [Abstract]

    Protein phosphorylation is a nearly universal signaling mechanism. To date, a number of proteomics tools have been developed to analyze phosphorylation. Phosphoproteome-wide analyses using whole cell extracts suffer from incomplete coverage, often missing phosphorylation events from low-abundance proteins. In order to increase coverage of

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    ATAC-Seq-based Identification of Extrachromosomal Circular DNA in Mammalian Cells and Its Validation Using Inverse PCR and FISH
    Authors:  Zhangli Su, Shekhar Saha, Teressa Paulsen, Pankaj Kumar and Anindya Dutta, date: 05/05/2021, view: 5611, Q&A: 2
    [Abstract]

    Recent studies from multiple labs including ours have demonstrated the importance of extrachromosomal circular DNA (eccDNA) from yeast to humans (Shibata et al., 2012; Dillon et al., 2015; Møller et al., 2016; Kumar et al., 2017; Turner et al., 2017; Kim et al., 2020). More recently, it has been found that cancer cells obtain a selective

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