Stem Cell Transcriptional 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.