Methods Development


methods book



Table of Contents


Section I. Laboratory Essentials

1. The Stem Cell Laboratory: Design, Equipment, and Oversight
Robin L. Wesselschmidt and Philip H. Schwartz

2. Stem Cell Banks: Preserving Cell Lines, Maintaining Genetic Integrity, and Advancing Research
Lesley Young, Lyn Healy, and Glyn N. Stacey


Section II. Derivation

3. Embryonic Stem Cell Derivation from Human Embryos
Paul Lerou

 4. Derivation of Human Parthenogenetic Stem Cell Lines
Nikolay Turovets, Andrey Semechkin, Leonid Kuzmichev, Jeffrey Janus, Larissa Agapova, and Elena Revazova

 5. Generation of Induced Pluripotent Stem Cell Lines from Human Fibroblasts via Retroviral Gene Transfer
Justine D. Miller and Thorsten M. Schlaeger

 6. Derivation of Induced Pluripotent Stem Cells by Lentiviral Transduction
Hubert E. Nethercott, David J. Brick, and Philip H. Schwartz

7. Transgene-free Production of Pluripotent Stem Cells using PiggyBac Transposons
Knut Woltjen, Riikka Hämäläinen, Mark Kibschull, Maria Mileikovsky, and Andras Nagy


Section III. Growth, Maintenance and Expansion

 8. Traditional Human Embryonic Stem Cell Culture
Philip H. Schwartz, David J. Brick, Hubert E. Nethercott, and Alexander E. Stover

 9. Xeno-Free Culture of Human Pluripotent Stem Cells
Rosita Bergström, Susanne Ström, Frida Holm, Anis Feki, and Outi Hovatta

 10. Adaptation of Human Pluripotent Stem Cells to Feeder-Free Conditions in Chemically-Defined Medium with Enzymatic Single-Cell Passaging
Alexander E. Stover and Philip H. Schwartz

 11. GMP Scale-Up and Banking of Pluripotent Stem Cells for Cellular Therapy Applications
Lara J. Ausubel, Patricia M. Lopez, and Larry A. Couture

12. Culture of Human Pluripotent Stem Cells on Glass Slides for High-Resolution Imaging
Victoria Fox


Section IV. Characterization

13. Classical Cytogenetics: Karyotyping Techniques
Steven E. Bates

14. FISH Analysis of Human Pluripotent Stem Cells
Suzanne E. Peterson, Jerold Chun, and Jeanne Loring

 15. Immunocyhemical Analysis of Human Pluripotent Stem Cells
Hubert E. Nethercott, David J. Brick, and Philip H. Schwartz

16. Flow Cytometric Analysis of Human Pluripotent Stem Cells
Mirabelle SH. Ho, Andrew Fryga, and Andrew L. Laslett

 17. The Teratoma Assay: An In vivo Assessment of Pluripotency
Robin L. Wesselschmidt

 18. Detection of Copy Number Variation using SNP Genotyping
Gregory M. Cooper and Heather C. Mefford

 19. Genome-wide Epigenetic Analysis of Human Pluripotent Stem Cells by ChIP and ChIP-Seq
Michael J. Hitchler and Judd C. Rice

 20. Basic Approaches to Gene Expression Analysis of Stem Cells by Microarrays
Bernhard Schuldt, Qiong Lin, Franz-Josef Müller, and Jeanne F. Loring

 21. Development of High Content Screening Approaches and Analysis for Human Pluripotent Stem Cells
Sean P. Sherman, Jackelyn A. Alva, Kaushali Thakore-Shah, and April D. Pyle

 22. Quantitative Proteome and Phosphoproteome Analysis of Human Pluripotent Stem Cells
Javier Muñoz and Albert J. R. Heck


Section V. Genetic Manipulation (Gene Modulation)

 23. Lentivirus-mediated Modification of Pluripotent Stem Cells
Ruchi Bajpai

 24. Nucleofection of Human Embryonic Stem Cells
Helen Fong, K. A. Hohenstein Elliott, Leslie F. Lock, and Peter J. Donovan

25. Non-viral Gene Delivery in Neural Progenitors Derived from Human Pluripotent Stem Cells
Sujoy K. Dhara, Anirban Majumder, Mahesh C. Dodla, and Steven L. Stice

 26. Gene Targeting in Human Pluripotent Stem Cells
Ying Liu and Mahendra Rao

27. Episomal Transgene Expression in Pluripotent Stem Cells
Michele M.P. Lufino, Anna R. Popplestone, Sally A. Cowley, Pauline A.H. Edser, William S. James, and Richard Wade-Martins


Section VI: Differentiation

28. The Generation of Embryoid Bodies from Feeder-based or Feeder-free Human Pluripotent Stem Cell Cultures
Alexander E. Stover and Philip H. Schwartz

 29. Derivation of Oligodendrocyte Progenitor Cells from Human Embryonic Stem Cells
Jason Sharp, Maya Hatch, Gabriel Nistor, and Hans Keirstead

 30. Directed Differentiation of Dopamine Neurons From Human Pluripotent Stem Cells
Lixiang Ma, Yan Liu, and Su-Chun Zhang

 31. Methods for the Derivation and Use of Cardiomyocytes from Human Pluripotent Stem Cells
Wei-Zhong Zhu, Benjamin Van Biber, and Michael A. Laflamme

 32. In Vivo Evaluation of Putative Hematopoietic Stem Cells Derived from Human Pluripotent Stem Cells
Melinda K. Hexum, Xinghui Tian, and Dan S. Kaufman

 33. Differentiation of Dendritic Cells from Human Embryonic Stem Cells
Kathryn M. Silk, Su-Yi Tseng, Kevin P. Nishimoto, Jane S. Lebkowski, Anita Reddy, and Paul J. Fairchild




Other Works by Dr. Schwartz in Methods Development



Table of Contents

Foreword by James Battey

Foreword by Jeannie Fontana



Part I: Basic methods: Maintenance of stem cell cultures
1.Human Embryonic Stem Cell Culture

2.Feeder layers and feeder-free culture

3.Mouse Embryonic Fibroblast Feeder Cells

4.Cryopreservation of hESC


Part II: Basic methods: Characterization of stem cells

5.Classical Cytogenetics: Karyotyping

6.Spectral Karyotyping and Fluorescent in situ Hybridization

7.Using SNP Genotyping to Identify Cell Lines, Determine Genomic Abnormalities and Monitor DNA Methylation Patterns

8.FACS/Cell sorting

9.Fluorescence Immunocytochemical Analysis of Stem Cells

10.Characterization of Stem Cells Using RT-PCR

11.Gene Expression Profiling of Stem Cells by Microarray

12.Teratomas produced from Human Embryonic Stem Cells Xenografted into Immunodeficient Mice

13.Generation of HESC-Derived Teratomas


Part III: Differentiation of stem cells

14.“Embryoid Body” Formation and Neuroepithelia Differentiation

15.Motor Neuron and Dopamine Neuron Differentiation

16.Oligodendrocyte Differentiation from hESC




Part IV: Genetic manipulation of stem cells

19.Genetic Manipulation of hESC: Lentivirus Vectors

20.Methods developed for mouse ES cells


Part V: Advanced methods

21.Derivation of human ES cells

22.Neural Stem Cell Culture

23.Transplantation of stem cells

24.In vitro fertilization

25.Functional characterization-neural cells


Part VI: Practical issues in establishing a human ES cell laboratory
26.Setting Up a Facility for hESC Research


Part VII: Essays on stem cell biology

27.Intellectual Property: Owning the Stem Cell

28.Ethical Concerns for Stem Cell Research

29.Guidelines for hESC Research Oversight (ESCRO) Committees