Naive and Primed Pluripotent States, Cell Stem Cell, vol.4, issue.6, pp.487-492, 2009. ,
DOI : 10.1016/j.stem.2009.05.015
Dynamic stem cell states: naive to primed pluripotency in rodents and humans, Nature Reviews Molecular Cell Biology, vol.4, issue.3, pp.155-169, 2016. ,
DOI : 10.1038/nature13551
Reinforcement of STAT3 activity reprogrammes human embryonic stem cells to naive-like pluripotency, Nature Communications, vol.6, issue.1, p.7095, 2015. ,
DOI : 10.1038/nprot.2010.190
Induction of a Human Pluripotent State with Distinct Regulatory Circuitry that Resembles Preimplantation Epiblast, Cell Stem Cell, vol.13, issue.6, pp.663-675, 2013. ,
DOI : 10.1016/j.stem.2013.11.015
Derivation of novel human ground state naive pluripotent stem cells, Nature, vol.138, issue.7479, pp.282-286, 2013. ,
DOI : 10.1242/dev.064741
Platform for Induction and Maintenance of Transgene-free hiPSCs Resembling Ground State Pluripotent Stem Cells, Stem Cell Reports, vol.2, issue.3, pp.366-381, 2014. ,
DOI : 10.1016/j.stemcr.2014.01.014
Resetting Transcription Factor Control Circuitry toward Ground-State Pluripotency in Human, Cell, vol.158, issue.6, pp.1254-1269, 2014. ,
DOI : 10.1016/j.cell.2014.08.029
Systematic Identification of Culture Conditions for Induction and Maintenance of Naive Human Pluripotency, Cell Stem Cell, vol.15, issue.4, pp.471-487, 2014. ,
DOI : 10.1016/j.stem.2014.07.002
Derivation of naive human embryonic stem cells, Proc. Natl. Acad. Sci. USA, pp.4484-4489, 2014. ,
DOI : 10.1016/S1534-5807(03)00330-7
Defining the three cell lineages of the human blastocyst by single-cell RNA-seq, Development, vol.142, issue.18, pp.3151-3165, 2015. ,
DOI : 10.1242/dev.123547
Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells, Nature Structural & Molecular Biology, vol.57, issue.9, pp.1131-1139, 2013. ,
DOI : 10.1038/nprot.2008.211
Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos, Cell, vol.165, issue.4, pp.1012-1026, 2016. ,
DOI : 10.1016/j.cell.2016.03.023
The DNA methylation landscape of human early embryos, Nature, vol.511, issue.7511, pp.606-610, 2014. ,
DOI : 10.1038/nprot.2008.211
DNA methylation dynamics of the human preimplantation embryo, Nature, vol.454, issue.7511, pp.611-615, 2014. ,
DOI : 10.1073/pnas.1530509100
XACT Noncoding RNA Competes with XIST in the Control of X Chromosome Activity during Human Early Development, Cell Stem Cell, vol.20, issue.1, pp.102-111, 2017. ,
DOI : 10.1016/j.stem.2016.10.014
URL : https://hal.archives-ouvertes.fr/hal-01607750
Hallmarks of pluripotency, Nature, vol.158, issue.7570, pp.469-478, 2015. ,
DOI : 10.1016/j.cell.2014.07.020
Naive Human Pluripotent Cells Feature a Methylation Landscape Devoid of Blastocyst or Germline Memory, Cell Stem Cell, vol.18, issue.3, pp.323-329, 2016. ,
DOI : 10.1016/j.stem.2016.01.019
Human Naive Pluripotent Stem Cells Model X Chromosome Dampening and X Inactivation, Cell Stem Cell, vol.20, issue.1, pp.87-101, 2016. ,
DOI : 10.1016/j.stem.2016.10.006
Naive Pluripotent Stem Cells Derived Directly from Isolated Cells of the Human Inner Cell Mass, Stem Cell Reports, vol.6, issue.4, pp.437-446, 2016. ,
DOI : 10.1016/j.stemcr.2016.02.005
Comprehensive Cell Surface Protein Profiling Identifies Specific Markers of Human Naive and Primed Pluripotent States, Cell Stem Cell, vol.20, issue.6, pp.874-890, 2017. ,
DOI : 10.1016/j.stem.2017.02.014
Generation of germline-competent induced pluripotent stem cells, Nature, vol.62, issue.7151, pp.313-317, 2007. ,
DOI : 10.1038/nature05934
Directly Reprogrammed Fibroblasts Show??Global??Epigenetic??Remodeling and??Widespread??Tissue??Contribution, Cell Stem Cell, vol.1, issue.1, pp.55-70, 2007. ,
DOI : 10.1016/j.stem.2007.05.014
In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state, Nature, vol.70, issue.7151, pp.318-324, 2007. ,
DOI : 10.1038/nature05944
The ground state of embryonic stem cell self-renewal, Nature, vol.113, issue.7194, pp.519-523, 2008. ,
DOI : 10.1038/nature06968
Epigenetic resetting of human pluripotency, Development, vol.15, issue.15, pp.2748-2763, 2017. ,
DOI : 10.1242/dev.138982
10.1038/s41467-017-02107-w ARTICLE, NATURE COMMUNICATIONS NATURE COMMUNICATIONS |, vol.9, 2018. ,
URL : https://hal.archives-ouvertes.fr/in2p3-00652853
DUSP9 Modulates DNA Hypomethylation in Female Mouse Pluripotent Stem Cells, Cell Stem Cell, vol.20, issue.5, pp.706-719, 2017. ,
DOI : 10.1016/j.stem.2017.03.002
Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency, Cell, vol.162, issue.2, pp.412-424, 2015. ,
DOI : 10.1016/j.cell.2015.06.016
Characterization of directed differentiation by high-throughput single-cell RNA-Seq. Preprint at bioRxiv https://www.biorxiv.org/content, p.3236, 2014. ,
Human pre-implantation embryo development, Development, vol.139, issue.5, pp.829-841, 2012. ,
DOI : 10.1242/dev.060426
URL : http://dev.biologists.org/content/develop/139/5/829.full.pdf
Molecular Criteria for Defining the Naive Human Pluripotent State, Cell Stem Cell, vol.19, issue.4, pp.502-515, 2016. ,
DOI : 10.1016/j.stem.2016.06.011
KEGG: Kyoto Encyclopedia of Genes and Genomes, Nucleic Acids Research, vol.26, issue.1, pp.29-34, 1999. ,
DOI : 10.1093/nar/26.1.38
Glycolytic Metabolism Plays a Functional Role in Regulating Human Pluripotent Stem Cell State, Cell Stem Cell, vol.19, issue.4, pp.476-490, 2016. ,
DOI : 10.1016/j.stem.2016.08.008
Spatiotemporal Reconstruction of the Human Blastocyst by Single-Cell Gene-Expression Analysis Informs Induction of Naive Pluripotency, Developmental Cell, vol.38, issue.1, pp.100-115, 2016. ,
DOI : 10.1016/j.devcel.2016.06.014
Eutherian mammals use diverse strategies to initiate X-chromosome inactivation during development, Nature, vol.104, issue.7343, pp.370-374, 2011. ,
DOI : 10.1073/pnas.0610946104
URL : https://hal.archives-ouvertes.fr/hal-01019321
Erosion of X Chromosome Inactivation in Human Pluripotent Cells Initiates with XACT Coating and Depends on a Specific Heterochromatin Landscape, Cell Stem Cell, vol.16, issue.5, pp.533-546, 2015. ,
DOI : 10.1016/j.stem.2015.03.016
Erosion of Dosage Compensation Impacts Human iPSC Disease Modeling, Cell Stem Cell, vol.10, issue.5, pp.595-609, 2012. ,
DOI : 10.1016/j.stem.2012.02.014
Human embryonic stem cells do not change their X inactivation status during differentiation. Cell Rep, pp.54-67, 2017. ,
Formative pluripotency: the executive phase in a developmental continuum, Development, vol.144, issue.3, pp.365-373, 2017. ,
DOI : 10.1242/dev.142679
A Murine ESC-like State Facilitates Transgenesis and Homologous Recombination in Human Pluripotent Stem Cells, Cell Stem Cell, vol.6, issue.6, pp.535-546, 2010. ,
DOI : 10.1016/j.stem.2010.05.003
Interspecies Chimerism with Mammalian Pluripotent Stem Cells, Cell, vol.168, issue.3, pp.473-486, 2017. ,
DOI : 10.1016/j.cell.2016.12.036
Derivation of Pluripotent Stem Cells with In??Vivo Embryonic and Extraembryonic Potency, Cell, vol.169, issue.2, pp.243-257, 2017. ,
DOI : 10.1016/j.cell.2017.02.005
Comparative Principles of DNA Methylation Reprogramming during Human and Mouse In??Vitro Primordial Germ Cell Specification, Developmental Cell, vol.39, issue.1, pp.104-115, 2016. ,
DOI : 10.1016/j.devcel.2016.09.015
Setting Global Standards for Stem Cell Research and Clinical Translation: The??2016 ISSCR Guidelines, Stem Cell Reports, vol.6, issue.6, pp.787-797, 2016. ,
DOI : 10.1016/j.stemcr.2016.05.001
Functional Genomics Reveals a BMP-Driven Mesenchymal-to-Epithelial Transition in the Initiation of Somatic Cell Reprogramming, Cell Stem Cell, vol.7, issue.1, pp.64-77, 2010. ,
DOI : 10.1016/j.stem.2010.04.015
Full-length RNA-seq from single cells using Smart-seq2, Nature Protocols, vol.30, issue.1, pp.171-181, 2014. ,
DOI : 10.1038/nprot.2012.016
URL : http://www.nature.com/nprot/journal/v9/n1/pdf/nprot.2014.006.pdf
Smart-seq2 for sensitive full-length transcriptome profiling in single cells, Nature Methods, vol.22, issue.1, pp.1096-1098, 2013. ,
DOI : 10.1016/j.stem.2010.03.015
Preparation of Single-Cell RNA-Seq Libraries for Next Generation Sequencing, Curr. Protoc. Mol. Biol, vol.30, issue.4, pp.22-43, 2014. ,
DOI : 10.1038/nprot.2012.016
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks, Nature Protocols, vol.7, issue.3, pp.562-578, 2012. ,
DOI : 10.1038/nbt0710-691
Fast gapped-read alignment with Bowtie 2, Nature Methods, vol.9, issue.4, pp.357-359, 2012. ,
DOI : 10.1093/bioinformatics/btp352
HTSeq--a Python framework to work with high-throughput sequencing data, Bioinformatics, vol.13, issue.1, pp.166-169, 2015. ,
DOI : 10.1093/bioinformatics/btp616
A step-by-step workflow for lowlevel analysis of single-cell RNA-seq data with Bioconductor, p.2122, 2016. ,
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics, vol.9, issue.2, pp.139-140, 2010. ,
DOI : 10.1093/bib/bbm046
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biology, vol.14, issue.12, p.550, 2014. ,
DOI : 10.1186/gb-2013-14-4-r36
ROTS: An R package for reproducibility-optimized statistical testing, PLOS Computational Biology, vol.16, issue.1, pp.13-1005562, 2017. ,
DOI : 10.1371/journal.pcbi.1005562.t001
Pvclust: an R package for assessing the uncertainty in hierarchical clustering, Bioinformatics, vol.32, issue.3, pp.1540-1542, 2006. ,
DOI : 10.1214/009053604000000823
Improved scoring of functional groups from gene expression data by decorrelating GO graph structure, Bioinformatics, vol.4, issue.4, pp.1600-1607, 2006. ,
DOI : 10.1186/gb-2003-4-4-r28
GAGE: generally applicable gene set enrichment for pathway analysis, BMC Bioinformatics, vol.10, issue.1, p.161, 2009. ,
DOI : 10.1186/1471-2105-10-161
Service de Biologie de la Reproduction 7 Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR 7216 CNRS 8 INSERM UMS 016, SFR Francois Bonamy, MicroPicell Core Facility, 10 INSERM UMR1087, CNRS UMR6291 Université de Nantes l'institut du thorax Present address: 10x Genomics, pp.5-016 ,
Stéphanie Kilens and Dimitri Meistermann contributed equally to this work. A full list of consortium members appears at the end of the paper ,
25 Laboratory of Dendritic Cell Immunobiology, Department of Immunology Center for Translational Research 26 Immunobiology of Infection Unit, 33 Unité de Biologie des Populations Lymphocytaires, Department of Immunology Institut Pasteur, and Centre National pour la Recherche Scientifique Inra (U1125), Cnam, pp.31-35, 1153. ,
37 Laboratoire d'Immunologie clinique, CIC-4218 et Unité INSERM 932 38 Institut Pasteur, Unité de Régulation Immunitaire et Vaccinologie, Institut Curie Bioinformatics Biostatistics, and Integrative Biology Institut Pasteur, p.75015 ,
45 Virus & Immunity Unit, Department of Virology 51 Center for Translational Research, ICAReB Platform, Center for Translational Research, 49 Department of Immunology, Hôpital Européen Georges Pompidou, pp.10-1038, 2018. ,