Stem Cell Transcriptional Networks

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.

Efficient Library Preparation for Next-Generation Sequencing Analysis of Genome-Wide Epigenetic and Transcriptional Landscapes in Embryonic Stem Cells. - Analysis of Next-Generation Sequencing Data Using Galaxy. -
edgeR
for Differential RNA-seq and ChIP-seq Analysis: An Application to Stem Cell Biology. - Use Model-based Analysis of ChIP-Seq (MACS) to Analyze Short Reads Generated by Sequencing Protein-DNA Interactions in Embryonic Stem Cells. - Spatial Clustering for Identification of ChIP-Enriched Regions (SICER) to Map Regions of Histone Methylation Patterns in Embryonic Stem Cells. - Identifying Stem Cell Gene Expression Patterns and Phenotypic Networks with AutoSOME. - Visualization and Clustering of High-Dimensional Transcriptome Data Using GATE. - Interpreting and Visualizing ChIP-seq Data with the seqMINER Software. - A Description of the Molecular Signatures Database (MSigDB) Website. - Use of Genome-Wide RNAi Screens to Identify Regulators of Embryonic Stem Cell Self-Renewal and Pluripotency. - Correlating Histone Modification Patterns with Gene Expression Data During Hematopoiesis. - In Vitro Maturation and In Vitro Fertilization of Mouse Oocytes and Preimplantation Embryo Culture. - Derivation and Manipulation of Trophoblast Stem Cells from Mouse Blastocysts. - Conversion of Epiblast Stem Cells to Embryonic Stem Cells Using Growth Factors and Small Molecule Inhibitors. - Generation of Induced Pluripotent Stem Cells Using Chemical Inhibition and Three Transcription Factors. - Transdifferentiation of Mouse Fibroblasts and Hepatocytes to Functional Neurons. - Direct Lineage Conversion of Pancreatic Exocrine to Endocrine Beta-Cells In Vivo with Defined Factors. - Direct Reprogramming of Cardiac Fibroblasts to Cardiomyocytes Using MicroRNAs. - Reprogramming Somatic Cells into Pluripotent Stem Cells Using miRNAs.