Stem Cell Transcriptional Networks (e-book) (used book) | bookbook.eu

Description

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