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Stem Cell Transcriptional Networks

Methods and Protocols

  • Book
  • © 2014

Overview

Editors:
  1. Benjamin L. Kidder

    1. Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, USA

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  • Includes cutting-edge methods and protocols for the interrogation of stem cell transcriptional networks
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 1150)

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Table of contents (19 protocols)

  1. Front Matter

    Pages i-x
    Download chapter PDF

  2. Next-Generation Sequencing Library Preparation and Data Analysis

    1. Front Matter

      Pages 1-1
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    2. Efficient Library Preparation for Next-Generation Sequencing Analysis of Genome-Wide Epigenetic and Transcriptional Landscapes in Embryonic Stem Cells

      • Benjamin L. Kidder, Keji Zhao
      Pages 3-20

    3. Analysis of Next-Generation Sequencing Data Using Galaxy

      • Daniel Blankenberg, Jennifer Hillman-Jackson
      Pages 21-43

    4. edgeR for Differential RNA-seq and ChIP-seq Analysis: An Application to Stem Cell Biology

      • Olga Nikolayeva, Mark D. Robinson
      Pages 45-79

    5. Use Model-Based Analysis of ChIP-Seq (MACS) to Analyze Short Reads Generated by Sequencing Protein–DNA Interactions in Embryonic Stem Cells

      • Tao Liu
      Pages 81-95

    6. Spatial Clustering for Identification of ChIP-Enriched Regions (SICER) to Map Regions of Histone Methylation Patterns in Embryonic Stem Cells

      • Shiliyang Xu, Sean Grullon, Kai Ge, Weiqun Peng
      Pages 97-111

  3. Visual Analysis and Interpretation of Large-Scale Interaction Networks

    1. Front Matter

      Pages 113-113
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    2. Identifying Stem Cell Gene Expression Patterns and Phenotypic Networks with AutoSOME

      • Aaron M. Newman, James B. Cooper
      Pages 115-130

    3. Visualization and Clustering of High-Dimensional Transcriptome Data Using GATE

      • Patrick S. Stumpf, Ben D. MacArthur
      Pages 131-139

    4. Interpreting and Visualizing ChIP-seq Data with the seqMINER Software

      • Tao Ye, Sarina Ravens, Arnaud R. Krebs, Làszlò Tora
      Pages 141-152

    5. A Description of the Molecular Signatures Database (MSigDB) Web Site

      • Arthur Liberzon
      Pages 153-160

  4. Transcriptional Networks in Embryonic and Adult Stem Cell

    1. Front Matter

      Pages 161-161
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    2. Use of Genome-Wide RNAi Screens to Identify Regulators of Embryonic Stem Cell Pluripotency and Self-Renewal

      • Xiaofeng Zheng, Guang Hu
      Pages 163-173

    3. Correlating Histone Modification Patterns with Gene Expression Data During Hematopoiesis

      • Gangqing Hu, Keji Zhao
      Pages 175-187

  5. Embryo Culture and Derivation of Stem Cells

    1. Front Matter

      Pages 189-189
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    2. In Vitro Maturation and In Vitro Fertilization of Mouse Oocytes and Preimplantation Embryo Culture

      • Benjamin L. Kidder
      Pages 191-199

    3. Derivation and Manipulation of Trophoblast Stem Cells from Mouse Blastocysts

      • Benjamin L. Kidder
      Pages 201-212

  6. Transcriptional Programs that Promote Self-Renewal, Reprogramming, and Transdifferentiation

    1. Front Matter

      Pages 213-213
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    2. Conversion of Epiblast Stem Cells to Embryonic Stem Cells Using Growth Factors and Small Molecule Inhibitors

      • Jyoti Rao, Boris Greber
      Pages 215-226
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Keywords

About this book

Stem Cell Transcriptional Networks: Methods and Protocols collects techniques used to increase our understanding of the underlying transcriptional programs of stem cells that promote self-renewal and differentiation. The volume opens with a section on next-generation sequencing library preparation and data analysis. Continuing with a collection of protocols on visual analysis and interpretation of large-scale interaction networks, this detailed compilation features transcriptional networks in embryonic and adult stem cells, embryo culture and derivation of stem cells, as well as transcriptional programs that promote self-renewal, reprogramming, and transdifferentiation. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials, step-by-step, readily reproducible protocols and tips on troubleshooting and avoiding known pitfalls.

Authoritative and practical, Stem Cell Transcriptional Networks: Methods and Protocols aims to provide a key resource for biologists seeking to interrogate these vital networks.

Editors and Affiliations

  • Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, USA

    Benjamin L. Kidder

Bibliographic Information

  • Book Title: Stem Cell Transcriptional Networks

  • Book Subtitle: Methods and Protocols

  • Editors: Benjamin L. Kidder

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-0512-6

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2014

  • Hardcover ISBN: 978-1-4939-0511-9Published: 18 April 2014

  • Softcover ISBN: 978-1-4939-5406-3Published: 23 August 2016

  • eBook ISBN: 978-1-4939-0512-6Published: 17 April 2014

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: X, 286

  • Number of Illustrations: 8 b/w illustrations, 142 illustrations in colour

  • Topics: Cell Biology, Stem Cells

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