StemBook is an open access collection of invited, original, peer-reviewed chapters covering a range of topics related to stem cell biology written by top researchers in the field at the Harvard Stem Cell Institute and worldwide. StemBook is aimed at stem cell and non-specialist researchers.

In addition to the contributions of the editorial board and the stem cell research community, the project is being done in collaboration with several other enterprises including Harvard’s Initiative in Innovative Computing. The Initiative in Innovative Computing created the Scientific Collaboration Framework (SCF), the extensible software infrastructure used for the project. SCF and the StemBook project were funded, in part, by a generous grant from an anonymous foundation and also appreciates the input of WormBase's Textpresso team.

Contents

• About StemBook
• Cellular and nuclear reprogramming
  • Inducing pluripotency
    Kit T Rodolfa.
    Published September 30, 2008.
    • Introduction
    • Nuclear transfer
    • Cellular fusion
    • Cell explantation
    • Direct reprogramming
    • Conclusions and future prospects
    • Acknowledgements
    • References
  • Stem cells in animal models of regeneration
    Kyle A Gurley and Alejandro Sánchez Alvarado.
    Published December 31, 2008.
    • Introduction
    • Regeneration in Amphibians: Urodeles (salamanders, newts, axolotls)
    • Regeneration in Amphibians: Anurans (frogs, toads)
    • Regeneration in Zebrafish
    • Regeneration in planarians
    • Concluding remarks
    • References
  • Small RNAs – their biogenesis, regulation and function in embryonic stem cells
    Joshua E Babiarz and Robert Blelloch.
    Published May 31, 2009.
    • Introduction
    • The Biogenesis of miRNAs and related small RNAs
    • The role of small RNAs in embryonic stem cells
    • Transcriptional regulation of the miRNA content of a cell
    • Post-transcriptional regulation of the processing of miRNAs
    • miRNAs and induced pluripotency
    • Non-canonical miRNAs and endogenous siRNAs
    • Conclusions
    • References
• Ectoderm specification and differentiation
  • The cranial sensory nervous system: specification of sensory progenitors and placodes
    Andrea Streit.
    Published December 15, 2008.
    • Introduction
    • Sensory placodes and their derivatives
    • A unique territory of multipotent sensory progenitors
    • Six and Eya genes and their role in placode development
    • Induction of the placode territory through combinatorial signalling
    • Specification of individual placodes from common field
    • Conclusions
    • References
  • Tooth organogenesis and regeneration
    Irma Thesleff and Mark Tummers.
    Published January 31, 2009.
    • Morphogenesis and cell differentiation during tooth development
    • Cell and tissue interactions and signaling centers
    • Regulation and molecular basis of odontogenic competence
    • Regeneration capacity and stem cells in mammalian teeth
    • Mouse incisor stem cell niche
    • Molecular regulation of the stem cell niche
    • Future perspectives for stem cell – based tooth bioengineering
    • References
  • Melanocyte stem cells
    Masatake Osawa.
    Published June 30, 2009.
    • Introduction
    • Melanocyte biology
    • Melanocyte stem cells and regeneration of pigmentary system
    • Molecular basis of melanocyte stem cell regulation
    • Hair graying: loss of melanocyte stem cells
    • Melanocyte stem cells: a model for the study of stem cell specification
    • Concluding remarks
    • Acknowledgement
    • References
  • Limbal epithelial stem cells of the cornea
    Genevieve A Secker and Julie T Daniels.
    Published June 30, 2009.
    • Function and structure of the cornea
    • Corneal development
    • The stroma and endothelium
    • The corneal epithelium
    • Homeostasis in the corneal epithelium
    • Limbal epithelial stem cells
    • Evidence for stem cells in the corneal limbus
    • Summary
    • References
  • Neural crest-derived stem cells
    Olga Shakhova and Lukas Sommer.
    Published May 4, 2010.
    • Introduction
    • Embryonic neural crest
    • Postmigratory NCSCs
    • NCSCs and other cells with neural potential in the skin
    • Conclusive remarks and perspective
    • Acknowledgments
    • References
• Endoderm specification and differentiation
  • Pancreatic stem cells
    L Charles Murtaugh and Daniel Kopinke.
    Published July 11, 2008.
    • Introduction
    • The normal pancreas: embryonic development and adult homeostasis
    • Pancreatic regeneration: re-growth or re-differentiation?
    • The exception that proves the rule: pancreatic duct ligation
    • Duct-to-islet differentiation: in vitro veritas?
    • From embryonic stem cell to beta-cell
    • Conclusions
    • Acknowledgements
    • References
  • Specification and patterning of the respiratory system
    Wellington V Cardoso and Darrell N Kotton.
    Published July 16, 2008.
    • Introduction
    • Specification of respiratory progenitors in the foregut
    • Fgf signaling and induction of respiratory cell fate
    • Activation of Fgf10-Fgfr2b signaling in lung progenitors is critical for bud morphogenesis
    • Gene interactions in the prospective respiratory field control Fgf10 expression and patterning of the lung primordium
    • Retinoids in early lung development
    • Dorsal-ventral (D-V) patterning and tracheal-esophageal separation
    • Gata6 in lung development
    • Canonical Wnt signaling in lung cell fate decisions
    • Chromatin remodeling and development
    • Do residual lung epithelial stem/progenitor cells remain after lung development is complete?
    • Embryonic stem cells and lung epithelial differentiation
    • Concluding remarks and perspectives
    • References
  • Liver development
    Aaron M Zorn.
    Published October 31, 2008.
    • Introduction
    • Endoderm formation
    • Endoderm patterning: making the foregut
    • Hepatic induction by FGF and BMP
    • Liver bud morphogenesis
    • Liver bud growth
    • Differentiation of hepatocytes and biliary epithelial cells
    • Gall bladder and extrahepatic bile ducts
    • Liver stem cells
    • Conclusions
    • Acknowledgement
    • References
  • Endoderm specification
    Anne Grapin-Botton.
    Published November 30, 2008.
    • Introduction
    • Cellular aspects of endoderm emergence
    • Molecular control of definitive endoderm formation
    • Engineering endoderm
    • Endoderm regionalization and morphogenesis
    • Differentiation of extraembryonic endoderm lineages
    • Concluding remarks
    • Acknowledgements
    • References
• Epigenetics
  • Epigenetic Mechanisms Controlling Mesodermal Specification
    Maria Jose Barrero and Juan Carlos Izpisua Belmonte.
    Published December 10, 2012.
    • Introduction
    • The dynamic equilibrium of undifferentiated ES cells
    • Mesodermal specification in stem cells
    • The resolution of the bivalent domains; a crucial step for specification
    • Control of specification by microRNAs
    • Future directions
    • Acknowledgements
    • Bibliography
  • Imaging chromatin in embryonic stem cells
    Eran Meshorer.
    Published July 11, 2008.
    • Introduction
    • Chromatin structural changes in stem cell differentiation
    • In vivo imaging of chromatin
    • Photobleaching methods to follow nuclear dynamics
    • The hyperdynamic stem cell chromatin
    • Imaging chromatin-protein interactions
    • Chromatin motion
    • Future perspectives
    • Acknowledgements
    • References
  • Epigenetic silencing during early lineage commitment
    Howard Cedar and Yehudit Bergman.
    Published April 30, 2009.
    • Introduction
    • Establishment of DNA methylation patterns
    • Role of DNA methylation
    • Repression complexes
    • Post implantation gene repression
    • DNA replication timing and gene repression
    • Long-term silencing
    • References
  • The chromatin signature of pluripotent cells
    Ky Sha and Laurie A Boyer.
    Published May 31, 2009.
    • Introduction
    • The chromatin landscape of the pluripotent genome
    • Histone modifiers and chromatin remodelers shape the stem cell genome
    • Chromatin and reprogramming cell fate
    • Perspectives and Future Directions
    • Acknowledgements
    • References
  • Stem cells, cancer, and epigenetics
    Stephen B Baylin.
    Published October 31, 2009.
    • Introduction
    • Relationships bewteen promoter DNA hypermethylation, genes which regulate stem/progenitor cells, and initiation of human cancer
    • Mouse knockout studies of the gene, hypermethylated in cancer 1 (HIC1), indicate that stem/progenitor cell related, epigenetic abnormalities, can contribute to the initiation of cancer
    • Relationships between a regulatory chromatin pattern in embryonic cells, abnormal promoter DNA hypermethylation, and cell progression to cancer
    • Future directions
    • References
• Genomics and proteomics
  • Proteomic studies of stem cells
    Jianlong Wang, Jennifer J Trowbridge, Sridhar Rao, and Stuart H Orkin.
    Published July 14, 2008.
    • Introduction
    • Proteomic studies of embryonic stem cells (ESCs)
    • Proteomic studies of adult stem cells
    • Concluding remarks
    • Acknowledgements
    • References
  • Genome-wide transcription factor localization and function in stem cells
    Wai-Leong Tam and Bing Lim.
    Published September 15, 2008.
    • Introduction
    • Key regulators of pluripotency
    • The transcriptional landscape in ESCs
    • The transcriptional landscape in somatic stem cells
    • Reactivating pluripotency
    • Cell type-dependent regulation of distinct circuitries
    • The integration of microRNAs in transcription circuits
    • Perspectives
    • Acknowledgements
    • References
  • The pluripotent transcriptome
    Marica Grskovic and Miguel Ramalho-Santos.
    Published October 10, 2008.
    • Introduction
    • Molecular signature of pluripotent stem cells
    • Co-expression to co-regulation: regulatory pathways
    • Novel genes and splice variants
    • Is everything transcribed? In every ES cell?
    • Differences between mouse and human ES cells
    • Expression of the pluripotent transcriptome in cancer
    • In vivo transcriptomics – a germline connection?
    • Concluding remarks
    • Acknowledgements
    • References
• Germ cell and somatic stem cell biology in reproduction
  • Regulation of spermatogonia
    Qing Zhou and Michael D Griswold.
    Published July 14, 2008.
    • Introduction
    • Spermatogenesis: in general
    • Spermatogonia
    • Conclusions
    • Grant Support
    • References
  • piRNA function in germline development
    Jaspreet S Khurana and William E Theurkauf.
    Published July 30, 2008.
    • Introduction
    • Germline development in Drosophila
    • Germline development in Zebrafish
    • Germline development in mouse
    • Summary and perspective
    • References
  • The role of microRNAs in germline differentiation
    Steve Reynolds and Hannele Ruohola-Baker.
    Published September 15, 2008.
    • Introduction
    • Origin of the germline
    • microRNA biogenesis and function
    • The three ages of the germline
    • Summary
    • Acknowledgements
    • References
  • Germline stem cell niches
    Ting Xie.
    Published September 30, 2008.
    • The anatomically simplest GSC niche in C. elegans
    • The first structurally and functionally defined GSC niche in the Drosophila ovary
    • The structurally and mechanistically well-studied GSC niche in the Drosophila testis
    • The complex GSC niche yet to be defined structurally and functionally in the mouse testis
    • Commonalities and differences in different GSC niches
    • Conclusions and future directions
    • References
  • Uterine stem cells
    Jose Teixeira, Bo R Rueda, and James K Pru.
    Published September 30, 2008.
    • Introduction
    • Uterine development
    • Adult uterine stem cells
    • Endometrial cancer
    • Conclusion
    • Acknowledgments
    • References
  • Modeling germ cell differentiation
    Niels Geijsen and George Q Daley.
    Published November 30, 2008.
    • Germline differentiation of embryonic stem cells
    • Applications, practical and ethical challenges
    • References
  • Lineage analysis of stem cells
    DT Fox, LX Morris, T Nystul, and AC Spradling.
    Published January 31, 2009.
    • Introduction
    • Lineage tracing methods
    • Identifying stem cells
    • Analyzing stem cells
    • Conclusion
    • Acknowledgments
    • References
  • Somatic stem cells of the ovary and their relationship to human ovarian cancers
    Henry L Chang, David T MacLaughlin, and Patricia K Donahoe.
    Published April 30, 2009.
    • Introduction
    • Ovarian development
    • Granulosa and theca cells
    • Granulosa cell tumors and thecomas
    • Ovarian surface epithelium and related malignancies
    • Acknowledgements
    • References
  • Sex differentiation in mouse and man and subsequent development of the female reproductive organs
    Nelson A Arango, Ph.D. and Patricia K Donahoe, M.D.
    Published September 30, 2010.
    • Formation, proliferation, and migration of mouse primordial germ cells
    • Genital ridge formation
    • Testis development
    • Embryonic ovary development
    • Postnatal ovary development
    • Müllerian duct formation
    • Müllerian duct regression
    • Müllerian duct differentiation and uterine maturation
    • References
  • C. elegans germline stem cells and their niche
    Judith Kimble and Hannah Seidel.
    Published November 15, 2013.
    • Introduction
    • C. elegans germline stem cells and their niche
    • Molecular regulation of GSC self-renewal
    • Molecular regulation of GSC differentiation
    • Conclusions, perspectives and future challenges
    • Acknowledgments
    • References
• Manufacturing
  • Regulatory challenges for the manufacture and scale-out of autologous cell therapies
    Paul Hourd, Amit Chandra, Nick Medcalf, and David J Williams.
    Published March 31, 2014.
    • Introduction
    • Manufacturing and supply approaches
    • Clinical and industrial landscape
    • Regulatory pathway for autologous cell therapies
    • Regulatory challenges for the manufacture of MTMM autologous cell therapies
    • Future perspectives – the need for regulatory debate
    • Acknowledgements
    • References
  • From production to patient: challenges and approaches for delivering cell therapies
    Karen Coopman and Nick Medcalf.
    Published March 31, 2014.
    • Introduction
    • Possible delivery routes
    • Deciding which route is suitable for a product
    • Future perspectives
    • Acknowledgements
    • References
• Mesoderm specification and differentiation
  • Epigenetic Mechanisms Controlling Mesodermal Specification
    Maria Jose Barrero and Juan Carlos Izpisua Belmonte.
    Published December 10, 2012.
    • Introduction
    • The dynamic equilibrium of undifferentiated ES cells
    • Mesodermal specification in stem cells
    • The resolution of the bivalent domains; a crucial step for specification
    • Control of specification by microRNAs
    • Future directions
    • Acknowledgements
    • Bibliography
  • Mouse kidney development
    Alan J Davidson.
    Published January 15, 2009.
    • Overview of kidney structure and embryonic development
    • Structure and function of the nephron
    • The intermediate mesoderm
    • The pronephros and formation of the nephric duct
    • The Mesonephros
    • The Metanephros
    • Concluding remarks
    • Acknowledgments
    • References
  • Adipose
    April Cook and Chad Cowan.
    Published March 31, 2009.
    • Introduction: what is fat?
    • Fat development
    • Adipocyte precursors
    • Regulation of differentiation
    • Disease and therapeutic use of adipose
    • Conclusions
    • References
  • Adult mesenchymal stem cells
    Ernestina Schipani and Henry M Kronenberg.
    Published January 31, 2009.
    • Introduction
    • Are mesenchymal stem cells distinct from hematopoietic stem cells?
    • Have mesenchymal stem cells specific cell-surface antigens?
    • Are pluripotent stem cells present in the bone marrow?
    • What is the developmental origin of mesenchymal stem cells?
    • Is there a “niche” for mesenchymal stem cells?
    • Why studying MSCs?
    • A future perspective
    • Acknowledgments
    • References
• Niche biology, homing, and migration
  • Hematopoietic stem cell trafficking
    Claire Magnon and Paul S Frenette.
    Published July 14, 2008.
    • Introduction
    • Trafficking of hematopoietic stem cells during embryogenesis and fetal development
    • Post-natal HSC migration to bone marrow
    • Egress of bone marrow HSCs to the periphery
    • Perspectives
    • Acknowledgments
    • References
  • The neural stem cell microenvironment
    Ilias Kazanis, Justin Lathia, Lara Moss, and Charles ffrench-Constant.
    Published August 31, 2008.
    • The embryonic neural stem cell (NSC) microenvironment
    • The adult neural stem cell (NSC) microenvironment
    • The NSC microenvironment in disease
    • Acknowledgements
    • References
• Renewal
  • Aging and stem cell renewal
    Haroldo Silva and Irina M Conboy.
    Published July 15, 2008.
    • Stem cell aging and loss of tissue regenerative potential
    • Aging of stem cell niches and intrinsic aging of stem cells
    • Acknowledgements
    • References
  • Quiescent stem cells in the niche
    Fumio Arai and Toshio Suda.
    Published July 11, 2008.
    • Niche for the quiescent stem cells
    • Quiescent stem cells
    • Signaling for quiescent stem cells
    • Metabolism of quiescent stem cells
    • Biological Function of Quiescence in HSCs
    • Acknowledgement
    • References
  • Mechanisms regulating stem cell polarity and the specification of asymmetric divisions
    Hila Toledano and D Leanne Jones.
    Published March 31, 2009.
    • Drosophila neuroblast divisions
    • Drosophila germline stem cells
    • Mammalian epidermal progenitor cells
    • Asymmetry in other systems
    • Conclusions
    • Acknowledgements
    • References
• Stem cell immunology
  • Immunologic targeting of the cancer stem cell
    Catherine J Wu.
    Published December 15, 2008.
    • Introduction
    • Lessons from CML, a disorder of the hematopoietic stem cell
    • Allogeneic hematopoietic stem cell transplantation: a curative immune-based therapy resulting in eradication of malignant progenitor cells
    • Strategies for immunologic targeting of the stem cell population
    • Acknowledgements
    • References
  • Immunological considerations for cell therapy using human embryonic stem cell derivatives
    Micha Drukker.
    Published December 16, 2008.
    • Introduction
    • Expression of histocompatibility antigens on u/dhESCs
    • Expression of T-cell regulating signals in u/dhESCs
    • T-cell response against u/dhESCs measured by functional assays
    • Interaction of natural killer cells with hESCs
    • Generation of patient-specific isogenic hESC lines
    • Conclusions
    • Acknowledgments
    • References
  • Mouse models of graft-versus-host disease
    Pavan Reddy and James LM Ferrara.
    Published February 28, 2009.
    • Introduction
    • Mouse models
    • Immunobiology
    • Conclusion
    • References
  • Prospects for ensuring acceptance of ES cell-derived tissues
    Kathy O Lui, Paul J Fairchild, and Herman Waldmann.
    Published September 30, 2010.
    • Introduction
    • Central tolerance
    • esDC as a negative vaccine against graft rejection
    • Immunological privilege of ES cell-derived tissues
    • Proposed mechanisms of natural privilege operating in ES cell-derived tissues
    • Induction of donor-specific tolerance for ES cell-derived tissues
    • Conclusion
    • Acknowledgements
    • References
• Therapeutic prospects
  • The hematopoietic stem cell niche
    Louise E Purton and David T Scadden.
    Published November 15, 2008.
    • Hematopoietic inductive microenvironments and the hematopoietic stem cell niche: a historical perspective
    • Cell types that have been identified to form prospective HSC niches
    • Are all HSC niches equal?
    • What regulates the HSC niches?
    • When niches turn bad- evidence for roles of the HSC niches in hematopoietic diseases
    • Acknowledgments
    • References
  • Medical applications of epidermal stem cells
    Gaelle Lapouge and Cédric Blanpain.
    Published November 15, 2008.
    • Introduction
    • The skin stem cells
    • Skin stem cells for the treatment of third-degree burns
    • Cellular therapy for inherited genetic skin diseases
    • Reprogramming of skin stem cells into pluripotent stem cells
    • References
  • Mesenchymal stromal cells as a drug delivery system
    Lata G Menon, Veronica J Shi, and Rona S Carroll.
    Published January 15, 2009.
    • Introduction
    • The potential clinical applications of human MSC
    • Genetically modified MSC for therapy
    • Genetically modified MSC for cancer
    • Summary
    • References
  • Egress and Mobilization of Hematopoietic Stem and Progenitor Cells: A Dynamic Multi-facet Process
    Kfir Lapid, Chen Glait-Santar, Shiri Gur-Cohen, Jonathan Canaani, Orit Kollet, and Tsvee Lapidot.
    Published December 10, 2012.
    • Introduction
    • Cytokine-induced mobilization
    • The SDF-1/CXCR4 pathway
    • HSPC mobilization and intracellular signaling
    • Adhesion molecules and loss of retention
    • Proteolytic activity
    • The fibrinolytic system
    • The dynamics of the HSC niche and BM microenvironment during mobilization
    • Involvement of the innate immunity
    • The nervous system
    • Stem cell mobilization viewed in the clinical context
    • Concluding remarks
    • References
  • Cord blood hematopoietic stem cell transplantation
    Hal E Broxmeyer.
    Published May 26, 2010.
    • Introduction
    • HSCs and HPCs and means to enhance their efficiency of engraftment
    • Other potential uses for CB
    • Perspective/Concluding thoughts
    • References
• Tissue engineering
  • Combining stem cells and biomaterial scaffolds for constructing tissues and cell delivery
    Stephanie M Willerth and Shelly E Sakiyama-Elbert.
    Published July 9, 2008.
    • Introduction
    • Natural biomaterials
    • Synthetic biomaterials
    • Conclusions and future studies
    • Acknowledgements
    • References
  • Autologous Approaches to Tissue Engineering
    Beatrice Dionigi and Dario O Fauza.
    Published December 10, 2012.
    • Introduction
    • Cell sources
    • Translational challenges
    • Regulatory challenges
    • Current clinical applications
    • Future perspectives
    • References
  • Flow perfusion culture of mesenchymal stem cells for bone tissue engineering
    F Kurtis Kasper, Jiehong Liao, James D Kretlow, Vassilios I Sikavitsas, and Antonios G Mikos.
    Published August 15, 2008.
    • Prevalence and significance of bone defects
    • Current clinical strategies for bone regeneration
    • Tissue engineering-based clinical approaches and considerations for bone regeneration
    • Bone regeneration by progenitor cell transplantation
    • Bone tissue induction into polymer scaffolds
    • Flow perfusion culture enhances osteogenic differentiation of mesenchymal stem cells
    • Fluid flow increases mineralized bone-like extracellular matrix deposition in a dose-dependent manner
    • In vitro culture duration and stage of osteogenic differentiation of transplanted mesenchymal stem cells affect in vivo osteogenicity of in vitro generated bone-like extracellular matrix constructs
    • Mineralized matrix deposition by mesenchymal stem cells in flow perfusion culture increases with increasing fluid shear forces
    • Scaffold mesh size affects the osteogenic differentiation of mesenchymal stem cells cultured in a flow perfusion bioreactor
    • The initial cell phenotype and degree of cell adhesion to titanium fiber mesh scaffolds affects the ectopic bone formation response in vivo
    • In vitro generated bone-like extracellular matrix influences the osteogenic differentiation of mesenchymal stem cells in vitro
    • In vitro generated bone-like extracellular matrix and fluid shear stress synergistically enhance osteogenic differentiation of mesenchymal stem cells in vitro
    • Flow perfusion culture of mesenchymal stem cells results in the generation of an extracellular matrix containing bone-related growth factors
    • The preculture period of mesenchymal stem cells in osteogenic media influences the in vivo bone forming potential of the cells
    • An in vitro generated extracellular matrix supports tissue infiltration and promotes blood vessel formation at an ectopic site in vivo
    • An in vitro generated bone-like extracellular matrix enhances the osteogenic gene expression of mesenchymal stem cells
    • Flow perfusion culture promotes infiltration and spatial distribution of mesenchymal stem cells within electrospun poly(ε-caprolactone) microfiber and multilayer nanofiber/microfiber scaffolds
    • Summary
    • Acknowledgements
    • References
  • Engineering microenvironments to control stem cell fate and function
    Shawdee Eshghi and David V Schaffer.
    Published September 11, 2008.
    • Introduction
    • Growth factors and morphogens
    • Direct cell-cell contact
    • ECM presents important biochemical and mechanical cues to stem cells
    • Summary
    • Acknowledgements
    • References
  • The role of bone marrow-derived stem cells in lung regeneration and repair
    Elizabeth K Sage, Michael R Loebinger, Julia Polak, and Sam M Janes.
    Published September 30, 2008.
    • Introduction
    • Lung regeneration
    • Lung injury
    • Acute lung injury
    • Potential complications of stem cells
    • Stem cells as vectors
    • Conclusion
    • References
  • Mechanical control of stem cell differentiation
    Daniel M Cohen and Christopher S Chen.
    Published October 31, 2008.
    • Introduction
    • What are mechanical signals?
    • What are the sources and functional consequences of applied mechanical forces on stem cells in vivo?
    • How do mechanical forces lead to lineage switching?
    • Mechanosensors
    • Conclusions and perspectives
    • Acknowledgements
    • References
  • Skin tissue engineering
    David J Wong and Howard Y Chang.
    Published March 31, 2009.
    • Introduction
    • Current skin substitutes
    • Skin anatomy
    • Skin stem cells
    • Fibroblasts and dermal stem cells
    • Skin morphogenetic signaling
    • Skin gene therapy
    • Future
    • Summary
    • Acknowledgements
    • References
  • Molecular imaging of stem cells
    Martin Rodriguez-Porcel, Joseph C Wu, and Sanjiv Sam Gambhir.
    Published July 30, 2009.
    • Requisites for the ideal imaging modality for stem cell tracking
    • Methodologies for labeling stem cells
    • How to decide which modality to use
    • Translation to clinical applications
    • Summary
    • Acknowledgements
    • References
• Protocols
  • Pluripotent Cells
    • Embryoid body formation from human pluripotent stem cells in chemically defined E8 media
      Yongshun Lin and Guokai Chen.
      Published June 1, 2014.
    • Genome editing in human pluripotent stem cells
      Derek T Peters, Chad A Cowan, and Kiran Musunuru.
      Published April 29, 2013.
    • Splitting hPSCs with Dispase
      Mark Tomishima.
      Published December 10, 2012.
    • Splitting hESC/hiPSC lines with EDTA in feeder free conditions
      Guokai Chen.
      Published December 10, 2012.
    • Splitting hESC/hiPSC lines on MEF using Accutase
      Hyesoo Kim.
      Published December 10, 2012.
    • General Spinfection Protocol
      W Travis Berggren, Margaret Lutz, and Veronica Modesto.
      Published December 10, 2012.
    • Assessment of human pluripotent stem cells with PluriTest
      Franz-Josef Müller, Björn Brändl, and Jeanne F Loring.
      Published December 10, 2012.
    • Conditioning pluripotent stem cell media with mouse embryonic fibroblasts (MEF-CM)
      Mark Tomishima.
      Published June 10, 2012.
    • Feeder-independent culture protocol – EDTA splitting
      WiCell.
      Published June 10, 2012.
    • Feeder dependent (MEF) culture protocol – collagenase passaging
      WiCell.
      Published June 10, 2012.
    • iPSC derivation from fibroblast in chemically defined medium
      Guokai Chen.
      Published June 10, 2012.
    • Cryopreservation of human pluripotent stem cells in defined conditions
      Guokai Chen.
      Published June 10, 2012.
    • Formation of embryoid bodies from Matrigel dots protocol
      Margaret Lutz and Travis Berggren.
      Published June 10, 2012.
    • Teratoma formation: A tool for monitoring pluripotency in stem cell research
      Wendy Y Zhang, Patricia E de Almeida, and Joseph C Wu.
      Published June 10, 2012.
    • Basic pluripotent stem cell culture protocols
      Authors: Maria Borowski, Maria Giovino-Doherty, Lan Ji, Meng-Jiao Shi, Kelly P Smith, and Joseph Laning.
      Published June 10, 2012.
  • Reprogramming
    • iPSC Reprogramming from Human Peripheral Blood Using Sendai Virus Mediated Gene Transfer
      Wenli Yang, Jason A Mills, Spencer Sullivan, Ying Liu, Deborah L French, and Paul Gadue.
      Published June 10, 2012.
    • Protocol for making retroviral reprogramming factors
      Margaret Lutz, Veronica Modesto, and Athanasia Panopoulos.
      Published June 10, 2012.
    • Hematopoietic differentiation
      Kyung-Dal Choi, Maxim Vodyanik, and Igor I Slukvin.
      Published June 10, 2012.
    • Robust generation of hepatocyte-like cells from human embryonic stem cell populations
      CN Medine, B Lucendo-Villarin, W Zhou, CC West, and DC Hay.
      Published June 10, 2012.
    • Monolayer endoderm differentiation from human ESCs
      X Cheng, L Ying, L Lu, AM Galvão, JA Mills, HC Lin, DN Kotton, SS Shen, MC Nostro, JK Choi, MJ Weiss, DL French, and P Gadue.
      Published June 10, 2012.
    • Blood - SeV derived fibroblast generated iPSCs
      Laurence Daheron and Sunita D'Souza.
      Published June 10, 2012.
    • Protocol for directed differentiation of human pluripotent stem cells toward a hepatocyte fate
      Jun Cai, Ann DeLaForest, Joseph Fisher, Amanda Urick, Thomas Wagner, Kirk Twaroski, Max Cayo, Masato Nagaoka, and Stephen A Duncan.
      Published June 10, 2012.
  • Ectoderm
    • Midbrain dopamine neurons from hESCs
      Mark Tomishima.
      Published June 10, 2012.
    • Neural induction – Dual SMAD inhibition
      Mark Tomishima.
      Published June 10, 2012.
  • Endoderm
    • Pancreatic differentiation
      M Cristina Nostro, Farida Sarangi, Shinichiro Ogawa, Audrey Holtzinger, Barbara Corneo, Xueling Li, Suzanne J Micallef, In-Hyun Park, Christina Basford, Michael B Wheeler, George Q Daley, Andrew G Elefanty, Edouard G Stanley, and Gordon Keller.
      Published June 10, 2012.
    • Robust generation of hepatocyte-like cells from human embryonic stem cell populations
      CN Medine, B Lucendo-Villarin, W Zhou, CC West, and DC Hay.
      Published June 10, 2012.
    • Monolayer endoderm differentiation from human ESCs
      X Cheng, L Ying, L Lu, AM Galvão, JA Mills, HC Lin, DN Kotton, SS Shen, MC Nostro, JK Choi, MJ Weiss, DL French, and P Gadue.
      Published June 10, 2012.
    • Protocol for directed differentiation of human pluripotent stem cells toward a hepatocyte fate
      Jun Cai, Ann DeLaForest, Joseph Fisher, Amanda Urick, Thomas Wagner, Kirk Twaroski, Max Cayo, Masato Nagaoka, and Stephen A Duncan.
      Published June 10, 2012.
  • Mesoderm
    • Generation of human induced pluripotent stem cells from peripheral blood using the STEMCCA lentiviral vector
      Andreia Gianotti-Sommer, Sarah S Rozelle, Spencer Sullivan, Jason A Mills, Seon-Mi Park, Brenden W Smith, Amulya M Iyer, Deborah L French, Darrell N Kotton, Paul Gadue, George J Murphy, and Gustavo Mostoslavsky.
      Published April 29, 2013.
    • Hematopoietic differentiation
      Kyung-Dal Choi, Maxim Vodyanik, and Igor I Slukvin.
      Published June 10, 2012.
    • Chondrocyte protocol
      Rachel A Oldershaw, Melissa A Baxter, Emma T Lowe, Nicola Bates, Lisa M Grady, Francesca Soncin, Daniel R Brison, Timothy E Hardingham, and Susan J Kimber.
      Published June 10, 2012.
    • Blood - SeV derived fibroblast generated iPSCs
      Laurence Daheron and Sunita D'Souza.
      Published June 10, 2012.
  • Cell Imaging
    • Analyzing the genomic integrity of stem cells
      Uri Ben-David and Nissim Benvenisty.
      Published June 10, 2012.

Edited by The Stem Cell Research Community