© 2020

Stem Cell Transcriptional Networks

Methods and Protocols

  • Benjamin L. Kidder

Part of the Methods in Molecular Biology book series (MIMB, volume 2117)

Table of contents

  1. Front Matter
    Pages i-xi
  2. Next-Generation Sequencing Technologies and Data Analysis

    1. Front Matter
      Pages 1-1
    2. Sarah K. Meadows, Laurel A. Brandsmeier, Kimberly M. Newberry, Michael J. Betti, Amy S. Nesmith, Mark Mackiewicz et al.
      Pages 3-34
    3. Yusen Ye, Lin Gao, Shihua Zhang
      Pages 79-92
    4. Paula Beati, Răzvan V. Chereji
      Pages 93-108
    5. Ya Wang, Min Qian, Peifeng Ruan, Andrew E. Teschendorff, Shuang Wang
      Pages 109-131
  3. Analysis and Visualization of Single-Cell and Bulk RNA-Seq Transcriptome Data

    1. Front Matter
      Pages 133-133
    2. Chloé B. Steen, Chih Long Liu, Ash A. Alizadeh, Aaron M. Newman
      Pages 135-157
    3. Nuno Saraiva-Agostinho, Nuno Luís Barbosa-Morais
      Pages 179-205
  4. Derivation of Stem Cells

  5. Transcriptional Programs that Promote Reprogramming, Transdifferentiation, and Cancer Formation

    1. Front Matter
      Pages 243-243
    2. Kangxin Jin, Min Zou, Dongchang Xiao, Mengqing Xiang
      Pages 245-263

About this book


This second edition provides techniques used to study of the underlying transcriptional programs of stem cells that promote self-renewal and differentiation. Chapters detail next-generation sequencing technologies, data analysis, protocols on analysis and visualization of single-cell RNA-Seq data, analysis of 3D chromatin architecture, interpretation of large-scale interaction networks, transcriptional networks in embryonic and adult stem cells, derivation of stem cells, and transcriptional programs that promote reprogramming, transdifferentiation, and cancer formation. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

 Authoritative and cutting-edge, Stem Cell Transcriptional Network: Methods and Protocols, Second Edition aims to provide a key resource for biologists seeking to interrogate these vital networks.


RNA polymerase NET-Seq alternative splicing in stem cells RNA-Seq GOSemSim

Editors and affiliations

  • Benjamin L. Kidder
    • 1
  1. 1.Karmanos Cancer InstituteWayne State University School of MedicineDetroitUSA

Bibliographic information

  • Book Title Stem Cell Transcriptional Networks
  • Book Subtitle Methods and Protocols
  • Editors Benjamin L. Kidder
  • Series Title Methods in Molecular Biology
  • Series Abbreviated Title Methods Molecular Biology
  • DOI
  • Copyright Information Springer Science+Business Media, LLC, part of Springer Nature 2020
  • Publisher Name Humana, New York, NY
  • eBook Packages Springer Protocols
  • Hardcover ISBN 978-1-0716-0300-0
  • Softcover ISBN 978-1-0716-0303-1
  • eBook ISBN 978-1-0716-0301-7
  • Series ISSN 1064-3745
  • Series E-ISSN 1940-6029
  • Edition Number 2
  • Number of Pages XI, 308
  • Number of Illustrations 8 b/w illustrations, 67 illustrations in colour
  • Topics Stem Cells
  • Buy this book on publisher's site