Item Details

Stem Cell Transcriptional Networks [electronic resource]: Methods and Protocols

edited by Benjamin L. Kidder, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
Format
EBook; Book; Online
Published
New York : Humana Press/Springer, [2014]
Language
English
Series
Methods in Molecular Biology
Springer Protocols
Methods in Molecular Biology (Clifton, N.J.)
Springer Protocols (Series)
ISBN
9781493905119 (alk. paper), 1493905112 (alk. paper), 9781493905126 (eBook), 1493905120 (eBook)
Abstract
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.
Contents
  • 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
  • 2. Analysis of next-generation sequencing data using Galaxy / Daniel Blankenberg and Jennifer Hillman-Jackson
  • 3. edgeR for differential RNA-seq and ChIP-seq analysis: an application to stem cell biology / Olgar Nikolayeva and Mark D. Robinson
  • 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
  • 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
  • 6. Identifying stem cell gene expression patterns and phenotypic networks with AutoSOME / Aaron M. Newmann and James B. Cooper
  • 7. Visualization and clustering of high-dimensional transcriptome data using GATE / Patrick S. Stumpf and Ben D. MacArthur
  • 8. Interpreting and visualizing ChIP-seq Data with the seqMINER software / Tao Ye, Sarina Ravens, Arnaud R. Krebs and Làszlò Tora
  • 9. A description of the molecular signatures database (MSigDB) web site / Arthur Liberzon
  • 10. Use of genome-wide RNAi screens to identify regulators of embryonic stem cell pluripotency and self-renewal / Xiaofeng Zheng and Guang Hu
  • 11. Correlating histone modification patterns with gene expression data during hematopoiesis / Gangqing Hu and Keji Zhao
  • 12. In vitro maturation and in vitro fertilization of mouse oocytes and preimplantation embryo culture / Benjamin L. Kidder
  • 13. Derivation and manipulation of trophoblast stem cells from mouse blastocysts / Benjamin L. Kidder
  • 14. Conversion of epiblast stem cells to embryonic stem cells using growth factors and small molecule inhibitors / Jyoti Rao and Boris Greber
  • 15. Generation of induced pluripotent stem cells using chemical inhibition and three transcription factors / Benjamin L. Kidder
  • 16. Transdifferentiation of mouse fibroblasts and hepatocytes to functional neurons / Samuele Marro and Nan Yang
  • 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
  • 18. Direct reprogramming of cardiac fibroblasts to cardiomyocytes using MicroRNAs / Tilanthi Jayawardena, Maria Mirotsou and Victor J. Dzau
  • 19. Reprogramming somatic cells into pluripotent stem cells using miRNAs / Frederick Anokye-Danso.
Description
Mode of access: World wide Web.
Notes
Includes bibliographical references and index.
Series Statement
Methods in molecular biology, 1064-3745 ; 1150
Springer protocols, 1949-2448
Methods in molecular biology (Clifton, N.J.) ; v. 1150. 1064-3745
Logo for Copyright Not EvaluatedCopyright Not Evaluated
Technical Details
  • Access in Virgo Classic

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    a| 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 -- 2. Analysis of next-generation sequencing data using Galaxy / Daniel Blankenberg and Jennifer Hillman-Jackson -- 3. edgeR for differential RNA-seq and ChIP-seq analysis: an application to stem cell biology / Olgar Nikolayeva and Mark D. Robinson -- 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 -- 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 -- 6. Identifying stem cell gene expression patterns and phenotypic networks with AutoSOME / Aaron M. Newmann and James B. Cooper -- 7. Visualization and clustering of high-dimensional transcriptome data using GATE / Patrick S. Stumpf and Ben D. MacArthur -- 8. Interpreting and visualizing ChIP-seq Data with the seqMINER software / Tao Ye, Sarina Ravens, Arnaud R. Krebs and Làszlò Tora -- 9. A description of the molecular signatures database (MSigDB) web site / Arthur Liberzon -- 10. Use of genome-wide RNAi screens to identify regulators of embryonic stem cell pluripotency and self-renewal / Xiaofeng Zheng and Guang Hu -- 11. Correlating histone modification patterns with gene expression data during hematopoiesis / Gangqing Hu and Keji Zhao -- 12. In vitro maturation and in vitro fertilization of mouse oocytes and preimplantation embryo culture / Benjamin L. Kidder -- 13. Derivation and manipulation of trophoblast stem cells from mouse blastocysts / Benjamin L. Kidder -- 14. Conversion of epiblast stem cells to embryonic stem cells using growth factors and small molecule inhibitors / Jyoti Rao and Boris Greber -- 15. Generation of induced pluripotent stem cells using chemical inhibition and three transcription factors / Benjamin L. Kidder -- 16. Transdifferentiation of mouse fibroblasts and hepatocytes to functional neurons / Samuele Marro and Nan Yang -- 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 -- 18. Direct reprogramming of cardiac fibroblasts to cardiomyocytes using MicroRNAs / Tilanthi Jayawardena, Maria Mirotsou and Victor J. Dzau -- 19. Reprogramming somatic cells into pluripotent stem cells using miRNAs / Frederick Anokye-Danso.
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