Stem Cell Transcriptional Networks: Methods and Protocols

ISBN-13: 9781493905119 / Angielski / Twarda / 2014 / 286 str.

Benjamin L. Kidder

Opis

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.

Spis treści

Part I: Next-Generation Sequencing Library Preparation and Data Analysis

 

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

            Benjamin L. Kidder and Keji Zhao

 

2. Analysis of Next-Generation Sequencing Data Using Galaxy

            Daniel Blankenberg and Jennifer Hillman-Jackson

 

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

            Olga Nikolayeva and Mark D. Robinson

 

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

            Tao Liu

 

5. 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, and Weiqun Peng

 

Part II: Visual Analysis and Interpretation of Large-Scale Interaction Networks

 

6. Identifying Stem Cell Gene Expression Patterns and Phenotypic Networks with AutoSOME

            Aaron M. Newman and James B. Cooper

 

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

            Patrick S. Stumpf and Ben D. MacArthur

 

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

            Tao Ye, Sarina Ravens, Arnaud R. Krebs, and Làszlò Tora

 

9. A Description of the Molecular Signatures Database (MSigDB) Website

            Arthur Liberzon

 

Part III: Transcriptional Networks in Embryonic and Adult Stem Cell

 

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

            Xiaofeng Zheng and Guang Hu

 

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

            Gangqing Hu and Keji Zhao

 

Part IV: Embryo Culture and Derivation of Stem Cells

 

12. In Vitro Maturation and In Vitro Fertilization of Mouse Oocytes and Preimplantation Embryo Culture

            Benjamin L. Kidder

 

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

            Benjamin L. Kidder

 

Part V: Transcriptional Programs that Promote Self-Renewal, Reprogramming, and Transdifferentiation

 

14. Conversion of Epiblast Stem Cells to Embryonic Stem Cells Using Growth Factors and Small Molecule Inhibitors

            Jyoti Rao and Boris Greber

 

15. Generation of Induced Pluripotent Stem Cells Using Chemical Inhibition and Three Transcription Factors

            Benjamin L. Kidder

 

16. Transdifferentiation of Mouse Fibroblasts and Hepatocytes to Functional Neurons

            Samuele Marro and Nan Yang

 

17. Direct Lineage Conversion of Pancreatic Exocrine to Endocrine Beta-Cells In Vivo with Defined Factors

            Claudia Cavelti-Weder, Weida Li, Gordon C. Weir, and Qiao Zhou

 

18. Direct Reprogramming of Cardiac Fibroblasts to Cardiomyocytes Using MicroRNAs

            Tilanthi Jayawardena, Maria Mirotsou, and Victor J. Dzau

 

19. Reprogramming Somatic Cells into Pluripotent Stem Cells Using miRNAs

            Frederick Anokye-Danso