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Functional Analysis of DNA and Chromatin

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Cover of 'Functional Analysis of DNA and Chromatin'

Table of Contents

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    Book Overview
  2. Altmetric Badge
    Chapter 1 Predictive Binding Geometry of Ligands to DNA Minor Groove: Isohelicity and Hydrogen-Bonding Pattern
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    Chapter 2 Using Microchip Gel Electrophoresis to Probe DNA–Drug Binding Interactions
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    Chapter 3 Identifying Different Types of Chromatin Using Giemsa Staining
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    Chapter 4 Analysis of DNA Damage and Repair by Comet Fluorescence In Situ Hybridization (Comet-FISH)
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    Chapter 5 Alkaline Nuclear Dispersion Assays for the Determination of DNA Damage at the Single Cell Level
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    Chapter 6 Polarization Microscopy of Extended Chromatin Fibers
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    Chapter 7 DNA Labeling In Vivo: Quantification of Epidermal Stem Cell Chromatin Content in Whole Mouse Hair Follicles Using Fiji Image Processing Software
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    Chapter 8 A Historical Overview of Bromo-Substituted DNA and Sister Chromatid Differentiation
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    Chapter 9 Image Analysis of Chromatin Remodelling
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    Chapter 10 FISH Methods in Cytogenetic Studies
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    Chapter 11 Ultrastructural and Immunofluorescent Methods for the Study of the XY Body as a Biomarker
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    Chapter 12 Atomic Force Microscopy for Analyzing Metaphase Chromosomes: Comparison of AFM Images with Fluorescence Labeling Images of Banding Patterns
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    Chapter 13 Selective Detection of Phagocytic Phase of Apoptosis in Fixed Tissue Sections
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    Chapter 14 Selective Transport of Cationized Fluorescent Topoisomerase into Nuclei of Live Cells for DNA Damage Studies
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    Chapter 15 Visualization and Interpretation of Eukaryotic DNA Replication Intermediates In Vivo by Electron Microscopy
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    Chapter 16 Combined Bidimensional Electrophoresis and Electron Microscopy to Study Specific Plasmid DNA Replication Intermediates in Human Cells
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    Chapter 17 Standard DNA Methylation Analysis in Mouse Epidermis: Bisulfite Sequencing, Methylation-Specific PCR, and 5-Methyl-Cytosine (5mC) Immunological Detection
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    Chapter 18 Methyl-Combing: Single-Molecule Analysis of DNA Methylation on Stretched DNA Fibers
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    Chapter 19 Investigating 5-Hydroxymethylcytosine (5hmC): The State of the Art
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    Chapter 20 Hydroxymethylated DNA Immunoprecipitation (hmeDIP)
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    Chapter 21 Microscale thermophoresis for the assessment of nuclear protein-binding affinities.
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    Chapter 22 Analysis of Histone Posttranslational Modifications from Nucleolus-Associated Chromatin by Mass Spectrometry
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    Chapter 23 Salt-urea, sulfopropyl-sepharose, and covalent chromatography methods for histone isolation and fractionation.
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    Chapter 24 Chromatin Immunoprecipitation
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    Chapter 25 Analysis of Chromatin Composition of Repetitive Sequences: The ChIP-Chop Assay
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    Chapter 26 Purification of Specific Chromatin Domains from Single-Copy Gene Loci in Saccharomyces cerevisiae
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    Chapter 27 Deep Sequencing of Small Chromatin-Associated RNA: Isolation and Library Preparation.
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    Chapter 28 Deep Sequencing of Small Chromatin-Associated RNA: Bioinformatic Analysis.
Attention for Chapter 27: Deep Sequencing of Small Chromatin-Associated RNA: Isolation and Library Preparation.
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Chapter title
Deep Sequencing of Small Chromatin-Associated RNA: Isolation and Library Preparation.
Chapter number 27
Book title
Functional Analysis of DNA and Chromatin
Published in
Methods in molecular biology, January 2014
DOI 10.1007/978-1-62703-706-8_27
Pubmed ID
Book ISBNs
978-1-62703-705-1, 978-1-62703-706-8
Authors

Sarah Daniela Diermeier, Thomas Schubert, Gernot Längst

Abstract

Chromatin-associated RNA (caRNA) is a newly identified class of RNA molecules stably associated with chromatin, maintaining the higher order structure of euchromatic regions in an accessible form (Schubert et al., Mol Cell, doi:10.1016/j.molcel.2012.08.021, 2012). This section provides a detailed protocol describing the isolation of small caRNA from Drosophila cells and preparation of libraries suited for stranded small (20-200 bp) RNA deep sequencing on the Illumina platform.

Twitter Demographics

The data shown below were collected from the profile of 1 tweeter who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 5 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 5 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 2 40%
Professor > Associate Professor 1 20%
Unknown 2 40%
Readers by discipline Count As %
Agricultural and Biological Sciences 3 60%
Unknown 2 40%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 29 October 2013.
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#2,901,548
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Outputs from Methods in molecular biology
#1,438
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#76,255
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Outputs of similar age from Methods in molecular biology
#20
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