Stem cell transcriptional networks
Subtitle: methods and protocols
By: edited by Benjamin L. Kidder, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
Series: Methods in molecular biology -- 1150; Springer protocols; Methods in molecular biology (Clifton, N.J.) -- v. 1150.; Springer protocols (Series)
Publisher: Humana Press/Springer
Published: 2014
Place of publication: New York
Language: eng
Number of pages: 286
ISBN-13: 9781493905119; 9781493905126
Copyright date: 2014
Subjects: Stem Cells; Stem cells; Genetic Transcription; Gene Regulatory Networks; Laboratory Manuals; Research
Description: 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.
Notes: Includes bibliographical references and index.
Table of contents: title: Efficient library preparation for next-generation sequencing analysis of genome-wide epigenetic and transcriptional landscapes in embryonic stem cells / Benjamin L. Kinder and Keji Zhao; title: 2. Analysis of next-generation sequencing data using Galaxy / Daniel Blankenberg and Jennifer Hillman-Jackson; title: 3. edgeR for differential RNA-seq and ChIP-seq analysis: an application to stem cell biology / Olgar Nikolayeva and Mark D. Robinson; title: 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; title: 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; title: 6. Identifying stem cell gene expression patterns and phenotypic networks with AutoSOME / Aaron M. Newmann and James B. Cooper; title: 7. Visualization and clustering of high-dimensional transcriptome data using GATE / Patrick S. Stumpf and Ben D. MacArthur; title: 8. Interpreting and visualizing ChIP-seq Data with the seqMINER software / Tao Ye, Sarina Ravens, Arnaud R. Krebs and Làszlò Tora; title: 9. A description of the molecular signatures database (MSigDB) web site / Arthur Liberzon; title: 10. Use of genome-wide RNAi screens to identify regulators of embryonic stem cell pluripotency and self-renewal / Xiaofeng Zheng and Guang Hu; title: 11. Correlating histone modification patterns with gene expression data during hematopoiesis / Gangqing Hu and Keji Zhao; title: 12. In vitro maturation and in vitro fertilization of mouse oocytes and preimplantation embryo culture / Benjamin L. Kidder; title: 13. Derivation and manipulation of trophoblast stem cells from mouse blastocysts / Benjamin L. Kidder; title: 14. Conversion of epiblast stem cells to embryonic stem cells using growth factors and small molecule inhibitors / Jyoti Rao and Boris Greber; title: 15. Generation of induced pluripotent stem cells using chemical inhibition and three transcription factors / Benjamin L. Kidder; title: 16. Transdifferentiation of mouse fibroblasts and hepatocytes to functional neurons / Samuele Marro and Nan Yang; title: 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; title: 18. Direct reprogramming of cardiac fibroblasts to cardiomyocytes using MicroRNAs / Tilanthi Jayawardena, Maria Mirotsou and Victor J. Dzau; title: 19. Reprogramming somatic cells into pluripotent stem cells using miRNAs / Frederick Anokye-Danso.