Book Volume 1400 2016

Transposons and Retrotransposons

Methods and Protocols

Editors:

ISBN: 978-1-4939-3370-9 (Print) 978-1-4939-3372-3 (Online)

Table of contents (26 protocols)

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  1. Front Matter

    Pages i-xii

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    Protocol

    Pages 1-19

    Study of Transposable Elements and Their Genomic Impact

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    Protocol

    Pages 21-32

    Bacterial Group II Introns: Identification and Mobility Assay

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    Protocol

    Pages 33-45

    In Silico Methods to Identify Exapted Transposable Element Families

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    Protocol

    Pages 47-77

    Retrotransposon Capture Sequencing (RC-Seq): A Targeted, High-Throughput Approach to Resolve Somatic L1 Retrotransposition in Humans

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    Protocol

    Pages 79-93

    Long Interspersed Element Sequencing (L1-Seq): A Method to Identify Somatic LINE-1 Insertions in the Human Genome

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    Protocol

    Pages 95-106

    Combining Amplification Typing of L1 Active Subfamilies (ATLAS) with High-Throughput Sequencing

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    Protocol

    Pages 107-116

    RNA-Seq Analysis to Measure the Expression of SINE Retroelements

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    Protocol

    Pages 117-130

    Qualitative and Quantitative Assays of Transposition and Homologous Recombination of the Retrotransposon Tf1 in Schizosaccharomyces pombe

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    Protocol

    Pages 131-137

    LINE Retrotransposition Assays in Saccharomyces cerevisiae

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    Protocol

    Pages 139-156

    LINE-1 Cultured Cell Retrotransposition Assay

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    Protocol

    Pages 157-163

    L1 Retrotransposition in Neural Progenitor Cells

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    Protocol

    Pages 165-182

    Characterization of Engineered L1 Retrotransposition Events: The Recovery Method

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    Protocol

    Pages 183-201

    SINE Retrotransposition: Evaluation of Alu Activity and Recovery of De Novo Inserts

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    Protocol

    Pages 203-222

    The Engineered SVA Trans-mobilization Assay

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    Protocol

    Pages 223-236

    Detection of LINE-1 RNAs by Northern Blot

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    Protocol

    Pages 237-259

    Monitoring Long Interspersed Nuclear Element 1 Expression During Mouse Embryonic Stem Cell Differentiation

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    Protocol

    Pages 261-280

    Immunodetection of Human LINE-1 Expression in Cultured Cells and Human Tissues

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    Protocol

    Pages 281-297

    Cellular Localization of Engineered Human LINE-1 RNA and Proteins

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    Protocol

    Pages 299-310

    Purification of L1-Ribonucleoprotein Particles (L1-RNPs) from Cultured Human Cells

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    Protocol

    Pages 311-338

    Characterization of L1-Ribonucleoprotein Particles

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