Stem Cell Transcriptional Networks [electronic resource] : Methods and Protocols / edited by Benjamin L. Kidder.
- New York, NY : Springer New York : Imprint: Humana Press, 2014.
- Methods in Molecular Biology, Methods and Protocols, 1064-3745 ; 1150
Springer Protocols (Springer-12345)
Methods in Molecular Biology, Methods and Protocols, 1064-3745 ; 1150
1 online resource (X, 286 pages) : 150 illustrations, 142 illustrations in color.
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- 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.
- Kidder, Benjamin L. editor.
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- 10.1007/978-1-4939-0512-6 doi
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