Stem Cell Transcriptional Networks: Methods and Protocols

ISBN-13: 9781071603000 / Angielski / Twarda / 2020 / 308 str.

Benjamin Kidder

Spis treści

Part I: Next-generation Sequencing Technologies and Data Analysis

 

1. 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, E. Christopher Partridge, Eric M. Mendenhall, and Richard M. Myers

 

2. User-friendly and Interactive Analysis of ChIP-seq data using EaSeq

Mads Lerdrup and Klaus Hansen

 

3. Evaluation of 3D Chromatin Interactions using Hi-C

Gangqing Hu

 

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

Yusen Ye, Lin Gao, and Shihua Zhang

 

5. Creating 2D Occupancy Plots using plot2DO

Paula Beati and Răzvan V. Chereji

 

6. Detection of Epigenetic Field Defects Using a Weighted Epigenetic Distance-based Method

Ya Wang, Min Qian, Peifeng Ruan, Andrew E. Teschendorff, and Shuang Wang

 

Part II: Analysis and Visualization of Single-Cell and Bulk RNA-Seq Transcriptome Data

 

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

Chloé B. Steen, Chih Long Liu, Ash A. Alizadeh, and Aaron M. Newman

 

8. Visualization of Single Cell RNA-Seq Data using t-SNE in R

Bo Zhou and Wenfei Jin

 

9. Use of SuperCT for Enhanced Characterization of Single-cell Transcriptomic Profiles

Jianmei Zhong and Wei Lin

 

10. Interactive Alternative Splicing Analysis of Human Stem Cells using psichomics

Nuno Saraiva-Agostinho and Nuno Luís Barbosa-Morais

 

11. Gene Ontology Semantic Similarity Analysis using GOSemSim

Guangchuang Yu

 

Part II: Derivation of Stem Cells

 

12. Derivation of Maternogenic Epiblast Stem Cells from Haploid Embryos

Benjamin L. Kidder

 

13. Derivation of LIF-independent Embryonic Stem Cells using Inducible OCT4 Expression

Benjamin L. Kidder

 

14. Simultaneous Derivation of Embryonic and Trophoblast Stem Cells from Mouse Blastocysts

Benjamin L. Kidder

 

 

Part IV: Transcriptional Programs That Promote Reprogramming, Transdifferentiation, and Cancer Formation

 

15. Reprogramming Fibroblasts to Neural Stem Cells by Overexpression of the Transcription factor Ptf1a

Kangxin Jin, Min Zou, Dongchang Xiao, and Mengqing Xiang

 

16. Reprogramming of Fibroblasts to Neural Stem Cells by a Chemical Cocktail

Chuijin Wei, Shumin Xiong, and Lin Cheng

 

17. Efficient RNA-based Reprogramming of Disease-associated Primary Human Fibroblasts into Induced Pluripotent Stem Cells

Patrick S. McGrath, Shennea S. McGarvey, Igor Kogut, and Ganna Bilousova

 

18. Direct Reprogramming Of Mouse Embryonic Fibroblasts to Induced Trophoblast Stem (iTS) Cells

Benjamin L. Kidder

 

19. Characterization of Arsenic-induced Cancer Stem-like Cells

Qingshan Chang, Zhuoyue Bi, Yao Fu, M’Kya Anique Rice, Qian Zhang, Priya Wadgaonkar, Bandar Almutairy, Wenxian Zhang,  Yongju Lu, Liping Xu, Chitra Thukar, and Fei Chen

 

 

 

 

Blurb

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.