Stem Cell Transcriptional Networks

Part I: Next-Generation Sequencing Library Preparation and Data Analysis1. Efficient Library Preparation for Next-Generation Sequencing Analysis of Genome-Wide Epigenetic and Transcriptional Landscapes in Embryonic Stem CellsBenjamin L. Kidder and Keji Zhao2. Analysis of Next-Generation Sequencing Data Using GalaxyDaniel Blankenberg and Jennifer Hillman-Jackson3. edgeR for Differential RNA-seq and ChIP-seq Analysis: An Application to Stem Cell BiologyOlga Nikolayeva and Mark D. Robinson4. Use Model-based Analysis of ChIP-Seq (MACS) to Analyze Short Reads Generated by Sequencing Protein-DNA Interactions in Embryonic Stem CellsTao Liu5. Spatial Clustering for Identification of ChIP-Enriched Regions (SICER) to Map Regions of Histone Methylation Patterns in Embryonic Stem CellsShiliyang Xu, Sean Grullon, Kai Ge, and Weiqun PengPart II: Visual Analysis and Interpretation of Large-Scale Interaction Networks6. Identifying Stem Cell Gene Expression Patterns and Phenotypic Networks with AutoSOMEAaron M. Newman and James B. Cooper7. Visualization and Clustering of High-Dimensional Transcriptome Data Using GATEPatrick S. Stumpf and Ben D. MacArthur8. Interpreting and Visualizing ChIP-seq Data with the seqMINER SoftwareTao Ye, Sarina Ravens, Arnaud R. Krebs, and Làszlò Tora9. A Description of the Molecular Signatures Database (MSigDB) WebsiteArthur LiberzonPart III: Transcriptional Networks in Embryonic and Adult Stem Cell10. Use of Genome-Wide RNAi Screens to Identify Regulators of Embryonic Stem Cell Self-Renewal and PluripotencyXiaofeng Zheng and Guang Hu11. Correlating Histone Modification Patterns with Gene Expression Data During HematopoiesisGangqing Hu and Keji ZhaoPart IV: Embryo Culture and Derivation of Stem Cells12. In Vitro Maturation and In Vitro Fertilization of Mouse Oocytes and Preimplantation Embryo CultureBenjamin L. Kidder13. Derivation and Manipulation of Trophoblast Stem Cells from Mouse BlastocystsBenjamin L. KidderPart V: Transcriptional Programs that Promote Self-Renewal, Reprogramming, and Transdifferentiation14. Conversion of Epiblast Stem Cells to Embryonic Stem Cells Using Growth Factors and Small Molecule InhibitorsJyoti Rao and Boris Greber15. Generation of Induced Pluripotent Stem Cells Using Chemical Inhibition and Three Transcription FactorsBenjamin L. Kidder16. Transdifferentiation of Mouse Fibroblasts and Hepatocytes to Functional NeuronsSamuele Marro and Nan Yang17. Direct Lineage Conversion of Pancreatic Exocrine to Endocrine Beta-Cells In Vivo with Defined FactorsClaudia Cavelti-Weder, Weida Li, Gordon C. Weir, and Qiao Zhou18. Direct Reprogramming of Cardiac Fibroblasts to Cardiomyocytes Using MicroRNAsTilanthi Jayawardena, Maria Mirotsou, and Victor J. Dzau19. Reprogramming Somatic Cells into Pluripotent Stem Cells Using miRNAsFrederick Anokye-Danso... Mehr