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Stem Cell Transcriptional Networks

Methods and Protocols

  • Book
  • © 2020

Overview

Editors:
  1. Benjamin L. Kidder

    1. Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, USA

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  • includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

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

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Table of contents (19 protocols)

  1. Front Matter

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

    1. Front Matter

      Pages 1-1
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    2. Epitope Tagging ChIP-Seq of DNA Binding Proteins Using CETCh-Seq

      • Sarah K. Meadows, Laurel A. Brandsmeier, Kimberly M. Newberry, Michael J. Betti, Amy S. Nesmith, Mark Mackiewicz et al.
      Pages 3-34

    3. User-Friendly and Interactive Analysis of ChIP-Seq Data Using EaSeq

      • Mads Lerdrup, Klaus Hansen
      Pages 35-63

    4. Evaluation of 3D Chromatin Interactions Using Hi-C

      • Gangqing Hu
      Pages 65-78

    5. MSTD for Detecting Topological Domains from 3D Genomic Maps

      • Yusen Ye, Lin Gao, Shihua Zhang
      Pages 79-92

    6. Creating 2D Occupancy Plots Using plot2DO

      • Paula Beati, Răzvan V. Chereji
      Pages 93-108

    7. Detection of Epigenetic Field Defects Using a Weighted Epigenetic Distance-Based Method

      • 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
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    2. Profiling Cell Type Abundance and Expression in Bulk Tissues with CIBERSORTx

      • Chloé B. Steen, Chih Long Liu, Ash A. Alizadeh, Aaron M. Newman
      Pages 135-157

    3. Visualization of Single Cell RNA-Seq Data Using t-SNE in R

      • Bo Zhou, Wenfei Jin
      Pages 159-167

    4. Use of SuperCT for Enhanced Characterization of Single-Cell Transcriptomic Profiles

      • Jianmei Zhong, Wei Lin
      Pages 169-177

    5. Interactive Alternative Splicing Analysis of Human Stem Cells Using psichomics

      • Nuno Saraiva-Agostinho, Nuno Luís Barbosa-Morais
      Pages 179-205

    6. Gene Ontology Semantic Similarity Analysis Using GOSemSim

      • Guangchuang Yu
      Pages 207-215

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

    1. Front Matter

      Pages 243-243
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    2. Reprogramming Fibroblasts to Neural Stem Cells by Overexpression of the Transcription Factor Ptf1a

      • Kangxin Jin, Min Zou, Dongchang Xiao, Mengqing Xiang
      Pages 245-263
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Keywords

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.

Editors and Affiliations

  • Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, 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/10.1007/978-1-0716-0301-7

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2020

  • Hardcover ISBN: 978-1-0716-0300-0Published: 21 January 2020

  • Softcover ISBN: 978-1-0716-0303-1Published: 21 January 2021

  • eBook ISBN: 978-1-0716-0301-7Published: 20 January 2020

  • 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

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