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The Resource Stem cell transcriptional networks : methods and protocols, edited by Benjamin L. Kidder

Stem cell transcriptional networks : methods and protocols, edited by Benjamin L. Kidder

Label
Stem cell transcriptional networks : methods and protocols
Title
Stem cell transcriptional networks
Title remainder
methods and protocols
Statement of responsibility
edited by Benjamin L. Kidder
Contributor
Editor
Subject
Genre
Language
eng
Summary
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
Member of
Cataloging source
NLM
Dewey number
616.0
Illustrations
illustrations
Index
index present
LC call number
QH588.S83
LC item number
.S846 2014
Literary form
non fiction
Nature of contents
bibliography
NLM call number
  • W1
  • QU 25
NLM item number
ME9616J v.1150 2014
http://library.link/vocab/relatedWorkOrContributorName
Kidder, Benjamin L.
Series statement
  • Methods in molecular biology,
  • Springer protocols,
Series volume
1150
http://library.link/vocab/subjectName
  • Stem cells
  • Gene Regulatory Networks
  • Stem Cells
  • Transcription, Genetic
Label
Stem cell transcriptional networks : methods and protocols, edited by Benjamin L. Kidder
Instantiates
Publication
Copyright
Bibliography note
Includes bibliographical references and index
Carrier category
volume
Carrier category code
  • nc
Carrier MARC source
rdacarrier
Content category
text
Content type code
  • txt
Content type MARC source
rdacontent
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
Control code
867615426
Dimensions
26 cm
Extent
x, 286 pages
Isbn
9781493905119
Isbn Type
(alk. paper)
Lccn
2014936042
Media category
unmediated
Media MARC source
rdamedia
Media type code
  • n
Other physical details
illustrations (some color)
System control number
(OCoLC)867615426
Label
Stem cell transcriptional networks : methods and protocols, edited by Benjamin L. Kidder
Publication
Copyright
Bibliography note
Includes bibliographical references and index
Carrier category
volume
Carrier category code
  • nc
Carrier MARC source
rdacarrier
Content category
text
Content type code
  • txt
Content type MARC source
rdacontent
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
Control code
867615426
Dimensions
26 cm
Extent
x, 286 pages
Isbn
9781493905119
Isbn Type
(alk. paper)
Lccn
2014936042
Media category
unmediated
Media MARC source
rdamedia
Media type code
  • n
Other physical details
illustrations (some color)
System control number
(OCoLC)867615426

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