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Protocols Archive

  • Technology: Isolation and preparation

    • From Nature Protocols: Peer reviewed & editorially enhanced

    • Identification and propagation of haploid human pluripotent stem cells

      Published online: 20 October 2016 | doi:10.1038/nprot.2016.145

      - This protocol was used in a related article published in Nature

    • Isolation and Cultivation of Naïve-like Human Pluripotent Stem Cells based on LTR7/HERVH Expression

      Published online: 21 January 2016 | doi:10.1038/nprot.2016.016

      - This protocol was used in a related article published in Nature

    • Direct conversion of human amniotic cells into endothelial cells without transitioning through a pluripotent state

      Published online: 5 November 2015 | doi:10.1038/nprot.2015.126

      - This protocol was used in a related article published in Cell

    • Efficient delivery of nuclease proteins for genome editing in human stem cells and primary cells

      Published online: 22 October 2015 | doi:10.1038/nprot.2015.117

    • MicroRNA-based conversion of human fibroblasts into striatal medium spiny neurons

      Published online: 17 September 2015 | doi:10.1038/nprot.2015.102

      - This protocol was used in a related article published in Neuron

    • Molecular beacon–enabled purification of living cells

      Published online: 18 September 2014 | doi:10.1038/nprot.2014.154

      - This protocol was used in a related article published in Circulation

    • Efficient gene delivery into cell lines and stem cells using baculovirus

      Published online: 10 July 2014 | doi:10.1038/nprot.2014.130

    • Isolation and characterization of resident endogenous c-kit-positive cardiac stem cells (eCSCs) from the adult mouse and rat heart

      Published online: 19 June 2014 | doi:10.1038/nprot.2014.113

    • Chemical ablation of tumor-initiating human pluripotent stem cells

      Published online: 27 February 2014 | doi:10.1038/nprot.2014.050

      - This protocol was used in related articles published in Cell Stem Cell and Nature Communications

    • Derivation and characterization of mouse embryonic stem cells (mESCs) from permissive and non-permissive strains

      Published online: 06 February 2014 | doi:10.1038/nprot.2014.030

      - This protocol was used in a related article published in PLoS One

    • Engineering cells with intracellular agent-loaded microparticles to control cell phenotype

      Published online: 09 January 2014 | doi:10.1038/nprot.2014.002

      - This protocol was used in a related article published in Nanoletters

    • In vitro expansion and genetic modification of gastrointestinal stem cells in spheroid culture

      Published online: 07 November 2013 | doi:10.1038/nprot.2013.153

      - This protocol was used in a related article published in Science

    • Isolation, culture and evaluation of Multilineage-differentiating Stress Enduring (Muse) cells

      Published online: 20 June 2013 | doi:10.1038/nprot.2013.076

      - This protocol was used in a related article published in Proc. Natl. Acad. Sci.

    • Derivation of Human Embryonic Stem Cells using a Post-Inner Cell Mass Intermediate

      Published online: 10 January 2013 | doi:10.1038/nprot.2012.157

      - This protocol was used in a related article published in Nature Biotech

    • Identification, isolation and in vitro expansion of human and nonhuman primate T stem cell memory cells

      Published online: 06 December 2012 | doi:10.1038/nprot.2012.143

      - This protocol was used in a related article published in Nature Medicine

    • Isolation of murine mesenchymal stem cells based on positive expression of Sca-1 and PDGFRα

      Published online: 15 November 2012 | doi:10.1038/nprot.2012.125

    • Generation of human induced pluripotent stem cells from urine samples

      Published online: 08 November 2012 | doi:10.1038/nprot.2012.115

    • Passaging and colony expansion of human pluripotent stem cells

      Published online: 25 October 2012 | doi:10.1038/nprot.2012.130

    • Isolation of multipotent neural stem/progenitor cells from the dentate gyrus and subventricular zone of a single adult mouse

      Published online: 18 October 2012 | doi:10.1038/nprot.2012.123

    • hES derivation from embryos in an animal product-free environment

      Published online: 21 June 2012 | doi:10.1038/nprot.2012.080

    • Prospective isolation of adult neural stem cells from the mouse subependymal zone

      Published online: 26 May 2011 | doi:10.1038/nprot.2011.412

      - This protocol was used in a related article published in Cytotherapy

    • Generating gene knockout rats by homologous recombination in embryonic stem cells

      Published online: 26 May 2011 | doi:10.1038/nprot.2011.338

      - This protocol was used in a related article published in Nature

    • Faster generation of hiPSCs by coupling high-titer lentivirus and column-based positive selection

      Published online: 5 May 2011 | doi:10.1038/nprot.2011.320

      - This protocol was used in a related article published in Stem Cell Res.

    • Feeder-dependent and feeder-independent iPS cell derivation from human and mouse adipose stem cells

      Published online: 24 February 2011 | doi:10.1038/nprot.2010.199

      - This protocol was used in a related article published in Proc. Natl. Acad. Sci.

    • Optimized multiparametric immunophenotyping of umbilical cord blood cells by flow cytometry

      Published online: 24 June 2010 | doi:10.1038/nprot.2010.88

      - This protocol was used in a related article published in Early Human Development

    • Derivation and Characterization of Haploid Embryonic Stem Cell Cultures in Medaka Fish

      Published online: 17 July 2010 | doi:10.1038/nprot.2010.104

      - This protocol was used in a related article published in Science

    • Isolation of adipose derived stem cells and their induction to a chondrogenic phenotype

      Published online: 17 June 2010 | doi:10.1038/nprot.2010.81

    • Immobilization of growth factors on solid supports for the modulation of stem cell fate

      Published online: 13 May 2010 | doi:10.1038/nprot.2010.70

      - This protocol was used in a related article published in Biomacromolecules

    • Production of mice using iPS cells and tetraploid complementation

      Published online: 29 April 2010 | doi:10.1038/nprot.2010.61

      - This protocol was used in a related article published in Nature

    • Generation of induced pluripotent stem cells from human cord blood cells with only two factors: Oct4 and Sox2

      Published online: 1 April 2010 | doi:10.1038/nprot.2010.16

      - This protocol was used in a related article published in Cell Stem Cell

    • Isolation, cultivation and characterization of adult murine prostate stem cells

      Published online: 25 March 2010 | doi:10.1038/nprot.2010.11

    • Generation of mouse induced pluripotent stem (iPS) cells with plasmid vectors

      Published online: 11 February 2010 | doi:10.1038/nprot.2009.231

      - This protocol was used in a related article published in Science

    • Isolation and cultivation of human keratinocytes from skin or plucked hair for the generation of induced pluripotent stem cells

      Published online: 4 February 2010 | doi:10.1038/nprot.2009.241

      - This protocol was used in a related article published in Nature Biotechnology

    • EOS lentiviral vector selection system for human induced pluripotent stem cells

      Published online: 3 December 2009 | doi:10.1038/nprot.2009.201

    • Generation of induced pluripotent stem cells from neural stem cells

      Published online: 17 September 2009 | doi:10.1038/nprot.2009.173

    • Isolation and cultivation of stem cells from adult mouse testes

      Published online: 15 January 2009 | doi:10.1038/nprot.2008.242

      - This protocol was used in a related article published in Nature

    • A protocol for isolation and culture of mesenchymal stem cells from mouse bone marrow

      Published online: 8 January 2009 | doi:10.1038/nprot.2008.221

      - This protocol was used in a related article published in Int. J. Dev. Biol.

    • Isolation of a slowly adhering cell fraction containing stem cells from murine skeletal muscle by the preplate technique

      Published online: 4 September 2008 | doi:10.1038/nprot.2008.142

    • Generation of human-induced pluripotent stem cells

      Published online: 26 June 2008 | Corrected online: 4 September 2008 | doi:10.1038/nprot.2008.92

      - This protocol was used in a related article published in Nature Biotechnology

    • Derivation and maintenance of human embryonic stem cells from poor-quality in vitro fertilization embryos

      Published online: 1 May 2008 | doi:10.1038/nprot.2008.60

      - This protocol was used in a related article published in Nature Biotechnology

    • Culture of embryonic-like stem cells from human umbilical cord blood and onward differentiation to neural cells in vitro

      Published online: 29 May 2008 | doi:10.1038/nprot.2008.69

    • Induction of pluripotent stem cells from fibroblast cultures

      Published online: 29 November 2007 | doi:10.1038/nprot.2007.418

      - This protocol was used in a related article published in Cell

    • Derivation of human embryonic stem cells from single blastomeres

      Published online: 9 August 2007 | doi:10.1038/nprot.2007.274

      - This protocol was used in a related article published in Nature

    • Adult mouse hematopoietic stem cells: purification and single-cell assays

      Published online: 25 January 2007 | doi:10.1038/nprot.2006.447

      - This protocol was used in a related article published in Science

    • Derivation of mouse embryonic stem cells

      Published online: 30 November 2006 | doi:10.1038/nprot.2006.355

    • From The Protocols Exchange: Uploaded directly by recent Nature authors & other researchers

    • Comprehensive Protocols to Isolate, Characterize, and Culture pure-population of Multi-potent Stem Cell from Mouse Epidermis

      Lab/Group: Environmental Carcinogenesis Laboratory

      DOI: 10.1038/nprot.2010.58

    • Approaches to isolate porcine skeletal muscle stem and progenitor cells

      Lab/Group: Roelen Lab

      DOI: 10.1038/nprot.2010.53

    • Generation of stem/progenitor cultures from mouse lungs

      Lab/Group: Nebreda Lab

      DOI: 10.1038/nprot.2007.216

      - This protocol was used in a related article published in Nature Genetics

  • Technology: Culturing and imaging cells

    • From Nature Protocols: Peer reviewed & editorially enhanced

    • Self-organization of human embryonic stem cells on micropatterns

      Published online: 13 October 2016 | doi:10.1038/nprot.2016.131

      - This protocol was used in a related article published in Nature Methods

    • Monolayer culturing and cloning of human pluripotent stem cells on laminin-521 based matrices under xeno-free and chemically defined conditions

      Published online: 11 September 2014 | doi:10.1038/nprot.2014.159

      - This protocol was used in related articles published in Nature Biotechnology and Nature Communications

    • Microinjection of membrane-impermeable molecules into single neural stem cells in brain tissue

      Published online: 24 April 2014 | doi:10.1038/nprot.2014.074

      - This protocol was used in a related article published in Nat. Neuroscience

    • Adapting human pluripotent stem cells to high-throughput and high-content screening

      Published online: 20 December 2012 | doi:10.1038/nprot.2012.139

      - This protocol was used in a related article published in Cell Stem Cell

    • Increased initiation and growth of tumor cell lines, cancer stem cells, and biopsy material in mice using basement membrane matrix protein (Cultrex®/Matrigel™) coinjection

      Published online: 17 May 2012 | doi:10.1038/nprot.2012.053

    • Arrayed cellular microenvironments for identifying culture and differentiation conditions for stem, primary, and rare cell populations

      Published online: 17 November 2011 | doi:10.1038/nprot.2011.422

    • Vertebrate Neural Stem Cell Segmentation, Tracking and Lineaging with Validation and Editing

      Published online: 17 November 2011 | doi:10.1038/nprot.2011.422

      - This protocol was used in a related article published in Nature Methods

    • Studying cell behavior in whole zebrafish embryos by confocal live imaging including an application to hematopoietic stem cell emergence

      Published online: 10 November 2011 | doi:10.1038/nprot.2011.408

      - This protocol was used in a related article published in Nature

    • Ex vivo time lapse confocal imaging of the mouse embryo aorta.

      Published online: 27 October 2011 | doi:10.1038/nprot.2011.401

      - This protocol was used in a related article published in Nature

    • An adherent cell culture of the mouse subependymal zone to study the behavior of adult neural stem cells at a single cell level

      Published online: 03 November 2011 | doi:10.1038/nprot.2011.404

      - This protocol was used in a related article published in Development

    • Primary culture of chick, mouse or human neural crest cells

      Published online: 22 September 2011 | doi:10.1038/nprot.2011.398

      - This protocol was used in a related article published in Hum Mol Genet

    • Embryonic and induced pluripotent stem cell staining and sorting using live cell fluorescence imaging probe CDy1.

      Published online: 30 June 2011 | doi:10.1038/nprot.2011.350

      - This protocol was used in a related article published in Angew. Chem., Int. Ed. Engl.

    • Fabrication of synthetic polymer coatings and their use in feeder-free culture of human embryonic stem cells

      Published online: 23 June 2011 | doi:10.1038/nprot.2011.342

      - This protocol was used in a related article published in Nature Biotechnology

    • Scalable expansion of human pluripotent stem cells in suspension culture

      Published online: 28 April 2011 | doi:10.1038/nprot.2011.318

    • Dynamic suspension culture for scalable expansion of undifferentiated human pluripotent stem cells

      Published online: 07 April 2011 | doi:10.1038/nprot.2011.325

      - This protocol was used in a related article published in Stem Cells Reviews and Reports

    • Assaying stem cell mechanobiology on microfabricated elastomeric substrates with geometrically modulated rigidity

      Published online: 27 January 2011 | doi:10.1038/nprot.2010.189

      - This protocol was used in a related article published in Nature Methods

    • In vivo imaging of transplanted hematopoietic stem and progenitor cells in mouse calvarium bone marrow

      Published online: 09 December 2010 | doi:10.1038/nprot.2010.168

      - This protocol was used in a related article published in Nature

    • Quantitation of human mammary epithelial stem cells with in vivo regenerative properties using a subrenal capsule xenotransplantation assay

      Published online: 10 November 2010 | doi:10.1038/nprot.2010.148

      - This protocol was used in a related article published in Nature Medicine

    • A protocol describing the genetic correction of somatic human cells and subsequent generation of iPS cells

      Published online: 11 March 2010 | doi:10.1038/nprot.2010.9

      - This protocol was used in a related article published in Nature

    • An efficient and easy-to-use cryopreservation protocol for human ES and iPS cells

      Published online: 4 March 2010 | doi:10.1038/nprot.2009.247

      - This protocol was used in a related article published in Human Reproduction

    • Long term non-invasive imaging of embryonic stem cells using reporter genes

      Published online: 23 July 2009 | doi:10.1038/nprot.2009.100

    • In vivo evaluation of human hematopoiesis through xenotransplantation of purified hematopoietic stem cells from umbilical cord blood

      Published online: 20 November 2008 | doi:10.1038/nprot.2008.194

      - This protocol was used in a related article published in Cell Stem Cell

    • Feeder-free culture of human embryonic stem cells in conditioned medium for efficient genetic modification

      Published online: 14 August 2008 | doi:10.1038/nprot.2008.140

      - This protocol was used in a related article published in Nature Methods

    • Optimized mouse ES cell culture system by suspension growth in a fully defined medium

      Published online: 22 May 2008 | doi:10.1038/nprot.2008.65

    • A protocol describing the use of a recombinant protein-based, animal product-free medium (APEL) for human embryonic stem cell differentiation as spin embryoid bodies

      Published online: 10 April 2008 | doi:10.1038/nprot.2008.42

      - This protocol was used in a related article published in Blood

    • A combined ex/in vivo assay to detect effects of exogenously added factors in neural stem cells

      Published online: 5 April 2007 | doi:10.1038/nprot.2007.104

    • In vitro generation of germ cells from murine embryonic stem cells

      Published online: 30 November 2006 | doi:10.1038/nprot.2006.303

      - This protocol was used in a related article published in Nature

    • Production of chimeras by aggregation of embryonic stem cells with diploid or tetraploid mouse embryos

      Published online: 7 September 2006 | doi:10.1038/nprot.2006.173

  • Differentiation of stem cells to specific lineages

    • From Nature Protocols: Peer reviewed & editorially enhanced

    • Using a neonatal rat system as a bioincubator to generate adult-like mature cardiomyocytes from human and mouse pluripotent stem cells

      Published online: 7 September 2017 | doi:10.1038/nprot.2017.089

      This protocol was used in a related article published in Cell Reports.

    • Generation of human high-purity ventral midbrain dopaminergic progenitors for in vitro maturation and intracerebral transplantation

      Published online: 31 August 2017 | doi:10.1038/nprot.2017.078

      This protocol was used in a related article published in Cell Stem Cell.

    • Directed differentiation and long-term maintenance of epicardial cells from human pluripotent stem cells under fully defined conditions

      Published online: 17 August 2017 | doi:10.1038/nprot.2017.080

      This protocol was used in a related article published in Nature Biomedical Engineering.

    • Reconstitution of mouse oogenesis in a dish from pluripotent stem cells

      Published online: 10 August 2017 | doi:10.1038/nprot.2017.070

      This protocol was used in a related article published in Nature and is an Extension of an earlier Nature Protocols article.

    • Constructing cellular niche properties by localized presentation of Wnt proteins on synthetic surfaces

      Published online: 29 June 2017 | doi:10.1038/nprot.2017.061

      This protocol was used in a related article published in Stem Cell Reports

    • Differentiation of cardiomyocytes and generation of human Engineered Heart Tissue

      Published online: 11 May 2017 | doi:10.1038/nprot.2017.033

    • Generation of multipotent induced cardiac progenitor cells from mouse fibroblasts and potency testing in ex vivo mouse embryos

      Published online: 20 April 2017 | doi:10.1038/nprot.2017.021

      - This protocol was used in a related article published in Cell Stem Cell 10.1016/j.stem.2015.12.001

    • Directed differentiation of human induced pluripotent stem cells into functional cholangiocyte-like cells

      Published online: 23 March 2017 | doi:10.1038/nprot.2017.011

      - This protocol was used in a related article published in Nature Biotechnology 10.1038/nbt.3275

    • Co-ordinated generation of multiple ocular-like cell lineages and fabrication of functional corneal epithelial cell sheets from human iPS cells

      Published online: 2 March 2017 | doi:10.1038/nprot.2017.007

      - This protocol was used in a related article published in Nature 10.1038/nature17000

    • Generation of nephron progenitor cells and kidney organoids from human pluripotent stem cells

      Published online: 22 December 2016 | doi:10.1038/nprot.2016.170

      - This protocol was used in a related article published in Nature Biotechnology 10.1038/nbt.3392

    • Reprogramming of mouse retinal neurons and standardized quantification of their differentiation in 3D retinal cultures

      Published online: 15 September 2016 | doi:10.1038/nprot.2016.109

      - This protocol was used in a related article published in Cell Stem Cell 10.1016/j.stem.2015.05.015

    • Generation of human muscle fibers and satellite-like cells from human pluripotent stem cells in vitro

      Published online: 1 September 2016 | doi:10.1038/nprot.2016.109

      - This protocol was used in a related article published in Nature Biotechnology 10.1098/nbt.3297

    • From Nature Protocols: Peer reviewed & editorially enhanced

    • Organoid culture systems for prostate epithelial and cancer tissue

      Published online: 21 January 2016 | doi:10.1038/nprot.2016.006

      - This protocol was used in related articles published in Cell 10.1016/j.cell.2014.08.017 and 10.1016/j.cell.2014.08.016

    • Efficient gene engineering of human intestinal organoids using electroporation

      Published online: 3 September 2015 | doi:10.1038/nprot.2015.088

    • Cardiac differentiation of human pluripotent stem cells in scalable suspension culture

      Published online: 13 August 2015 | doi:10.1038/nprot.2015.089

    • Generation and isolation of oligodendrocyte progenitor cells from human pluripotent stem cells

      Published online: 2 July 2015 | doi:10.1038/nprot.2015.075

      - This protocol was used in a related article published in Stem cell reports

    • Intravital imaging of hair follicle regeneration in the mouse

      Published online: 25 June 2015 | doi:10.1038/nprot.2015.070

    • A 3D human neural cell culture system for modeling Alzheimer’s disease

      Published online: 11 June 2015 | doi:10.1038/nprot.2015.065

      - This protocol was used in a related article published in Nature

    • Efficient Derivation and Inducible Differentiation of Expandable Skeletal Myogenic Cells from Human ES and Patient-Specific iPS Cells

      Published online: 4 June 2015 | doi:10.1038/nprot.2015.057

      - This protocol was used in a related article published in Science Translational Medicine

    • Reprogramming fibroblasts toward cardiomyocytes, neural stem cells, and hepatocytes by cell activation and signaling directed lineage conversion

      Published online: 4 June 2015 | doi:10.1038/nprot.2015.059

    • Efficient generation of functional CFTR-expressing airway epithelial cells from human pluripotent stem cells

      Published online: 5 February 2015 | doi:10.1038/nprot.2015.021

      - This protocol was used in a related article published in Nature Biotechnology

    • The in vitro generation of lung and airway progenitor cells from human pluripotent stem cells

      Published online: 5 February 2015 | doi:10.1038/nprot.2015.023

      - This protocol was used in related articles published by Green et al. and Huang et al. Nature Biotechnology

    • The generation of kidney organoids by differentiation of human pluripotent cells to ureteric bud progenitor-like cells

      Published online: 23 October 2014 | doi:10.1038/nprot.2014.182

      - This protocol was used in a related article published in Nature Cell Biology

    • Generation of cerebral organoids from human pluripotent stem cells

      Published online: 4 September 2014 | doi:10.1038/nprot.2014.158

    • Generation, expansion and functional analysis of endothelial cells and pericytes derived from human pluripotent stem cells

      Published online: 29 May 2014 | doi:10.1038/nprot.2014.102

      - This protocol was used in a related article published in Arterioscler. Thromb. Vasc. Biol.

    • 3D mouse embryonic stem cell culture for generating inner ear organoids

      Published online: 01 May 2014 | doi:10.1038/nprot.2014.100

      - This protocol was used in a related article published in Nature

    • Directed differentiation of embryonic origin-specific vascular smooth muscle subtypes from human pluripotent stem cells

      Published online: 27 March 2014 | doi:10.1038/nprot.2014.059

      - This protocol was used in a related article published in Nature Biotechnology

    • Direct conversion of mouse fibroblasts into induced neural stem cells

      Published online: 20 March 2014 | doi:10.1038/nprot.2014.056

      - This protocol was used in a related article published in Cell Stem Cell

    • Generation of a vascularized and functional human liver from an iPSC-derived organ bud transplant

      Published online: 23 January 2014 | doi:10.1038/nprot.2014.020

      - This protocol was used in a related article published in Nature

    • In vitro sperm production from murine spermatogonial stem cell lines using an organ culture method

      Published online: 03 October 2013 | doi:10.1038/nprot.2013.138

      - This protocol was used in related articles published in Nature and Nature Communications

    • Directed differentiation of forebrain GABA interneurons from human pluripotent stem cells

      Published online: 08 August 2013 | doi:10.1038/nprot.2013.106

      - This protocol was used in a related article published in Nature Biotechnology

    • Generation of eggs from mouse embryonic stem cells and induced pluripotent stem cells

      Published online: 11 July 2013 | doi:10.1038/nprot.2013.090

      - This protocol was used in a related article published in Cell

    • Derivation of extraembryonic endoderm stem (XEN) cells from mouse embryos and embryonic stem cells

      Published online: 02 May 2013 | doi:10.1038/nprot.2013.049

    • Production of hepatocyte-like cells from human pluripotent stem cells

      Published online: 31 January 2013 | doi:10.1038/nprot.2012.153

      - This protocol was used in a related article published in Nature

    • Directed differentiation of human pluripotent cells to neural crest stem cells

      Published online: 03 January 2013 | doi:10.1038/nprot.2012.156

      - This protocol was used in a related article published in Proc. Natl, Acad. Sci.

    • Differentiation of human pluripotent stem cells to cerebral cortex neurons

      Published online: 13 September 2012 | doi:10.1038/nprot.2012.116

      - This protocol was used in a related article published in Nature Neuroscience

    • Efficient introduction of specific p53 mutations into murine embryonic fibroblasts and embryonic stem cells

      Published online: 17 May 2012 | doi:10.1038/nprot.2012.042

    • Combining competition assays with genetic complementation strategies to dissect mouse embryonic stem cell self-renewal and pluripotency

      Published online: 22 March 2012 | doi:10.1038/nprot.2012.018

    • Mouse ES cell culture for generation of three-dimensional retinal and cortical tissues

      Published online: 15 December 2011 | doi:10.1038/nprot.2011.429

      - This protocol was used in a related article published in Nature

    • Generation and differentiation of microtissues from multipotent precursor cells for use in tissue engineering

      Published online: 13 October 2011 | doi:10.1038/nprot.2011.394

      - This protocol was used in a related article published in J. Biomater. Appl.

    • From Nature Protocols: Peer reviewed & editorially enhanced

    • Directed Differentiation of Functional Astroglial Subtypes from Human Pluripotent Stem Cells

      Published online: 13 October 2011 | doi:10.1038/nprot.2011.405

      - This protocol was used in a related article published in Nat. Biotech

    • Efficient derivation of neural precursor cells, spinal motor neurons and midbrain dopaminergic neurons from human ES cells at 3% oxygen

      Published online: 28 July 2011 | doi:10.1038/nprot.2011.380

      - This protocol was used in a related article published in Cell Death. Differ.

    • The validated embryonic stem cell test to predict embryotoxicity in vitro

      Published online: 16 June 2011 | doi:10.1038/nprot.2011.348

      - This protocol was used in a related article published in Reprod. Toxicol.

    • OLIG gene targeting in human pluripotent stem cells for motor neuron and oligodendrocyte differentiation

      Published online: 21 April 2011 | doi:10.1038/nprot.2011.310

      - This protocol was used in a related article published in Stem Cells

    • Hematopoietic differentiation and production of mature myeloid cells from human pluripotent stem cells

      Published online: 17 February 2011 | doi:10.1038/nprot.2010.184

      - This protocol was used in a related article published in J. Clin. Invest.

    • Differentiation of rat multipotent adult progenitor cells to functional hepatocyte-like cells by mimicking embryonic liver development

      Published online: 24 June 2010 | doi:10.1038/nprot.2010.80

    • Generation of microglial cells from mouse embryonic stem cells

      Published online: 05 August 2010 | doi:10.1038/nprot.2010.90

      - This protocol was used in a related article published in Glia

    • Isolation, differentiation, and characterization of vascular cells derived from human embryonic stem cells

      Published online: 27 May 2010 | doi:10.1038/nprot.2010.31

    • Assaying proliferation and differentiation capacity of stem cells using disaggregated adult mouse epidermis

      Published online: 22 April 2010 | doi:10.1038/nprot.2010.39

    • Derivation of neural crest cells from human pluripotent stem cells

      Published online: 18 March 2010 | doi:10.1038/nprot.2010.35

    • The generation of hepatocytes from mesenchymal stem cells and engraftment into murine liver

      Published online: 11 March 2010 | doi:10.1038/nprot.2010.7

    • Differentiation of human oligodendrocytes from pluripotent stem cells

      Published online: 15 October 2009 | doi:10.1038/nprot.2009.186

    • Generation of cortical neurons from mouse embryonic stem cells

      Published online: 17 September 2009 | doi:10.1038/nprot.2009.157

    • Differentiation of spinal motor neurons from pluripotent human stem cells

      Published online: 20 August 2009 | doi:10.1038/nprot.2009.127.

    • Stepwise differentiation of pluripotent stem cells into retinal cells

      Published online: 7 May 2009 | doi:10.1038/nprot.2009.51

    • Efficient derivation of functional dopaminergic neurons from human embryonic stem cells on a large scale

      Published online: 13 November 2008 | doi:10.1038/nprot.2008.188

      - This protocol was used in a related article published in Proc. Natl. Acad. Sci. USA

    • Cardiac commitment of primate embryonic stem cells

      Published online: 7 August 2008 | doi:10.1038/nprot.2008.116

      - This protocol was used in a related article published in Stem Cells

    • Production of neurons, astrocytes and oligodendrocytes from mammalian CNS stem cells

      Published online: 8 May 2008 | doi:10.1038/nprot.2008.55

      - This protocol was used in a related article published in Science

    • Generation of a defined and uniform population of CNS progenitors and neurons from mouse embryonic stem cells

      Published online: 26 April 2007 | doi:10.1038/nprot.2007.147

    • Differentiation of mouse embryonic stem cells to hepatocyte-like cells by co-culture with human liver nonparenchymal cell lines

      Published online: 8 March 2007 | doi:10.1038/nprot.2007.18

      - This protocol was used in a related article published in Nature Biotechnology

    • In vitro generation of germ cells from murine embryonic stem cells

      Published online: 30 November 2006 | doi:10.1038/nprot.2006.303

      - This protocol was used in a related article published in Nature

    • Differentiation of mouse embryonic stem cells to insulin-producing cells

      Published online: 29 June 2006 | Corrected online: 5 October 2006 | doi:10.1038/nprot.2006.71

      - This protocol was used in a related article published in Blood

    • From The Protocols Exchange: Uploaded directly by recent Nature authors & other researchers

    • A chemically-defined protocol for generating chondrocytes from human embryonic stem cells

      Lab/Group: Kimber/Brison/Hardingham Labs

      DOI: 10.1038/protex.2010.201

      - This protocol was used in a related article published in Nature Biotechnology

    • Neural Stem Cell Culture: Neurosphere generation, microscopical analysis and cryopreservation

      Lab/Group: Department of Pathology and Molecular Medicine, McMaster University

      DOI: 10.1038/nprot.2006.215

      - This protocol was used in a related article published in Nature Biotechnology

    • Generation of neurospheres from embryonic stem cells for investigating the temporal specification of neural stem/progenitor cells

      Lab/Group: Okano Lab (Keio)

      DOI: 10.1038/nprot.2008.168

      - This protocol was used in a related article published in Nature Neuroscience

    • Isolation of neural crest cells derived from human embryonic stem cells

      Lab/Group: Studer Lab (SKI)

      DOI: 10.1038/nprot.2009.49

      - This protocol was used in a related article published in Nature Biotechnology

  • Stem cells and progenitor cells isolated from adult tissues

    • From Nature Protocols: Peer reviewed & editorially enhanced

    • Isolation of Skeletal Muscle Stem Cells by Fluorescence-Activated Cell Sorting

      Published online: 24 Sept 2015 | doi:10.1038/nprot.2015.110

      - This protocol was used in related articles published in Nature (1) (2)

    • Reprogramming of mouse fibroblasts into cardiomyocyte-like cells in vitro

      Published online: 30 May 2013 | doi:10.1038/nprot.2013.067

      - This protocol was used in a related article published in Cell

    • Isolation, characterization and propagation of mitotically active germ cells from adult mouse and human ovaries

      Published online: 21 February 2013 | doi:10.1038/nprot.2013.047

      - This protocol was used in a related article published in Nature Medicine

    • Reprogramming human fibroblasts to pluripotency using modified-mRNA

      Published online: 21 February 2013 | doi:10.1038/nprot.2013.019

      - This protocol was used in a related article published in Cell Stem Cell

    • Generation of induced pluripotent stem cells from a small amount of human peripheral blood using a combination of activated T cells and Sendai virus

      Published online: 15 March 2012 | doi:10.1038/nprot.2012.015

      - This protocol was used in a related article published in Cell Stem Cell

    • Feeder-dependent and feeder-independent iPS cell derivation from human and mouse adipose stem cells

      Published online: 24 February 2011 | doi:10.1038/nprot.2010.199

      - This protocol was used in a related article published in Proc. Natl. Acad. Sci.

    • Generation of adult human induced pluripotent stem cells using nonviral minicircle DNA vectors

      Published online: 23 December 2010 | doi:10.1038/nprot.2010.173

      - This protocol was used in a related article published in Nature Methods

    • Conversion of adult mouse unipotent germline stem cells into pluripotent stem cells

      Published online: 22 April 2010 | doi:10.1038/nprot.2010.44

    • A protocol for isolation and culture of mesenchymal stem cells (MSCs) from mouse compact bone

      Published online: 25 February 2010 | doi:10.1038/nprot.2009.238

    • Isolation and cultivation of stem cells from adult mouse testes

      Published online: 15 January 2009 | doi:10.1038/nprot.2008.242

      - This protocol was used in a related article published in Nature

    • Human cardiomyocyte progenitor cells differentiate into functional mature cardiomyocytes: an in vitro model for studying human cardiac physiology and pathophysiology

      Published online: 5 February 2009 | doi:10.1038/nprot.2008.229

    • A protocol for isolation and culture of mesenchymal stem cells from mouse bone marrow

      Published online: 8 January 2009 | doi:10.1038/nprot.2008.221

      - This protocol was used in a related article published in Int. J. Dev. Biol.

    • Isolation of a slowly adhering cell fraction containing stem cells from murine skeletal muscle by the preplate technique

      Published online: 4 September 2008 | doi:10.1038/nprot.2008.142

    • Production of neurons, astrocytes and oligodendrocytes from mammalian CNS stem cells

      Published online: 8 May 2008 | doi:10.1038/nprot.2008.55

      - This protocol was used in a related article published in Science

    • Retrovirally mediated telomerase immortalization of neural progenitor cells

      Published online: 1 November 2007 | doi:10.1038/nprot.2007.402

      - This protocol was used in a related article published in Nature Biotechnology

    • Establishment of 3D organotypic cultures using human neonatal epidermal cells

      Published online: 8 February 2007 | doi:10.1038/nprot.2006.448

    • Adult mouse hematopoietic stem cells: purification and single-cell assays

      Published online: 25 January 2007 | doi:10.1038/nprot.2006.447

      - This protocol was used in a related article published in Science

    • Isolation and culture of rat and mouse oligodendrocyte precursor cells

      Published online: 26 April 2007 | doi:10.1038/nprot.2007.149

    • Isolation of skin-derived precursors (SKPs) and differentiation and enrichment of their Schwann cell progeny

      Published online: 25 January 2007 | doi:10.1038/nprot.2006.422

      - This protocol was used in a related article published in Nature Cell Biology

    • From The Protocols Exchange: Uploaded directly by recent Nature authors & other researchers

    • Generation of stem/progenitor cultures from mouse lungs

      Lab/Group: Nebreda Lab

      DOI: 10.1038/nprot.2007.216

      - This protocol was used in a related article published in Nature Genetics

    • Neural Stem Cell Culture: Neurosphere generation, microscopical analysis and cryopreservation

      Lab/Group: Department of Pathology and Molecular Medicine, McMaster University

      DOI: 10.1038/nprot.2006.215

    • Cell staining for sorting of hematopoietic stem cells (HSC) and myeloid progenitors and isolating RNA from sorted cells

      Lab/Group: Hurles Lab (Sanger Institute)

      DOI: 10.1038/nprot.2006.139

      - This protocol was used in a related article published in Nature Immunology

  • Tissue regeneration

    • From Nature Protocols: Peer reviewed & editorially enhanced

    • Engineering a humanized bone organ model in mice to study bone metastases

      Published online: 2 March 2017 | doi:10.1038/nprot.2017.002

      - This protocol was used in related articles published in Biomaterials and Disease Models and Mechanisms

    • Generation of cerebral organoids from human pluripotent stem cells

      Published online: 4 September 2014 | doi:10.1038/nprot.2014.158

    • Tracheal tissue engineering in rats

      Published online: 14 August 2014 | doi:10.1038/nprot.2014.149

    • Generation of a vascularized and functional human liver from an iPSC-derived organ bud transplant

      Published online: 23 January 2014 | doi:10.1038/nprot.2014.020

      - This protocol was used in a related article published in Nature

    • Engineering cells with intracellular agent-loaded microparticles to control cell phenotype

      Published online: 09 January 2014 | doi:10.1038/nprot.2014.002

      - This protocol was used in a related article published in Nanoletters

    • The mouse excisional wound splinting model including applications for stem cell transplantation

      Published online: 17 January 2013 | doi:10.1038/nprot.2013.002

    • Stem cell therapy for heart failure

      Published online: 12 July 2012 | doi:10.1038/nprot.2012.075

    • Generating human in1inal tissue from pluripotent stem cells in vitro

      Published online: 10 November 2011 | doi:10.1038/nprot.2010.410

      - This protocol was used in a related article published in Nature

    • The use of mesenchymal stem cells in collagen-based scaffolds for tissue-engineered repair of tendons

      Published online: 15 April 2010 | doi:10.1038/nprot.2010.14

    • Electrophysiological evaluation of engrafted stem cell-derived neurons

      Published online: 21 June 2007 | doi:10.1038/nprot.2007.230

    • A rodent model of myocardial infarction for testing the efficacy of cells and polymers for myocardial reconstruction

      Published online: 9 November 2006 | doi:10.1038/nprot.2006.188

  • Stem cells and molecular biology

    • From Nature Protocols: Peer reviewed & editorially enhanced

    • Assessment of engineered cells using CellNet and RNA-seq

      Published online: 27 April 2017 | doi:10.1038/nprot.2017.022

      - This protocol was used in a related article published in Cell

    • Precise and efficient scarless genome editing in stem cells using CORRECT

      Published online: 19 January 2017 | doi:10.1038/nprot.2016.171

      - This protocol was used in related articles published in Nature

    • Efficient, footprint-free human iPSC genome editing by consolidation of Cas9/CRISPR and piggyBac technologies

      Published online: 08 December 2016 | doi:10.1038/nprot.2016.152

      - This protocol was used in related articles published in Nature Communications, Science, and Nature Medicine

    • Modeling and correction of structural variations in patient-derived iPSCs using CRISPR/Cas9

      Published online: 06 October 2016 | doi:10.1038/nprot.2015.114

      - This protocol was used in related articles published in Cell Stem Cell and Cell Reports

    • Using the GEMM-ESC strategy to study gene function in mouse models

      Published online: 15 October 2015 | doi:10.1038/nprot.2015.114

    • Profiling DNA methylome landscapes of mammalian cells with single-cell reduced representation bisulfite sequencing

      Published online: 2 April 2015 | doi:10.1038/nprot.2015.039

      - This protocol was used in related articles published in Genome Research and Nature

    • Multiplexed locus-specific analysis of DNA methylation in single cells

      Published online: 26 March 2015 | doi:10.1038/nprot.2015.041

      - This protocol was used in a related article published in Science

    • Antibody-based detection of protein phosphorylation status to track efficacy of novel therapies using nanogram protein quantities from stem cells and cell lines

      Published online: 18 December 2014 | doi:10.1038/nprot.2015.007

      - This protocol was used in related articles published in European Journal of Haematology and Molecular & Cellular Proteomics

    • Molecular beacon–enabled purification of living cells

      Published online: 18 September 2014 | doi:10.1038/nprot.2014.154

      - This protocol was used in a related article published in Circulation

    • Seamless genome editing in human pluripotent stem cells using custom endonuclease-based gene targeting and the piggyBac transposon

      Published online: 26 September 2013 | doi:10.1038/nprot.2013.126

      - This protocol was used in a related article published in Nature

    • Virtual karyotyping of pluripotent stem cells based on their global gene expression profiles

      Published online: 25 April 2012 | doi:10.1038/nprot.2013.051

      - This protocol was used in a related article published in Cell Stem Cell

    • Measuring energy metabolism in cultured cells, including human pluripotent stem cells and differentiated cells

      Published online: 10 May 2012 | doi:10.1038/nprot.2012.048

      - This protocol was used in a related article published in EMBO J.

    • Comprehensive qPCR profiling of gene expression in single neuronal cells

      Published online: 22 December 2011 | doi:10.1038/nprot.2011.430

      - This protocol was used in a related article published in Nature

    • Derivation of genetically modified human pluripotent stem cells with integrated transgenes at unique mapped genomic sites

      Published online: 04 August 2011 | doi:10.1038/nprot.2011.362

      - This protocol was used in a related article published in Nat. Biotech.

    • Generation of transgene-free human induced pluripotent stem cells with an excisable single polycistronic vector

      Published online: 04 August 2011 | doi:10.1038/nprot.2011.374

      - This protocol was used in a related article published in Nat. Biotech.

    • The validated embryonic stem cell test to predict embryotoxicity in vitro

      Published online: 16 June 2011 | doi:10.1038/nprot.2011.348

      - This protocol was used in a related article published in Reprod. Toxicol.

    • Generating gene knockout rats by homologous recombination in embryonic stem cells

      Published online: 26 May 2011 | doi:10.1038/nprot.2011.338

      - This protocol was used in a related article published in Nature

    • OLIG gene targeting in human pluripotent stem cells for motor neuron and oligodendrocyte differentiation

      Published online: 21 April 2011 | doi:10.1038/nprot.2011.310

    • Efficient siRNA-mediated prolonged gene silencing in human amniotic fluid stem cells

      Published online: 20 May 2010 | doi:10.1038/nprot.2010.74

    • Attachment of stem cells to scaffold particles for intracerebral transplantation

      Published online: 17 September 2009 | doi:10.1038/nprot.2009.156

    • Long term non-invasive imaging of embryonic stem cells using reporter genes

      Published online: 23 July 2009 | doi:10.1038/nprot.2009.100

    • Use of in vivo biotinylation to study protein–protein and protein–DNA interactions in mouse embryonic stem cells

      Published online: 26 March 2009 | doi:10.1038/nprot.2009.23

      - This protocol was used in a related article published in Nature

    • A protocol for removal of antibiotic resistance cassettes from human embryonic stem cells genetically modified by homologous recombination or transgenesis

      Published online: 11 September 2008 | doi:10.1038/nprot.2008.146

    • An optimized procedure for whole-mount in situ hybridization on mouse embryos and embryoid bodies

      Published online: 26 June 2008 | doi:10.1038/nprot.2008.103

      - This protocol was used in a related article published in Developmental Dynamics

    • A method for genetic modification of human embryonic stem cells using electroporation

      Published online: 5 April 2007 | doi:10.1038/nprot.2007.105

      - This protocol was used in a related article published in Nature Methods

    • From The Protocols Exchange: Uploaded directly by recent Nature authors & other researchers

    • Two-photon microscopy and spectral detection for ex vivo imaging of individual stem cells

      DOI: 10.1038/nprot.2009.48

      Lab/Group: Linheng Li Lab, Advanced Instrumentation & Physics Facility

      This protocols was used in a related article published in Nature

    • Cell staining for sorting of hematopoietic stem cells (HSC) and myeloid progenitors and isolating RNA from sorted cells

      DOI: 10.1038/nprot.2006.139

      Lab/Group: Hurles Lab (Sanger Institute)

      - This protocol was used in a related article published in Nature Immunology

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