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
