J. Nichols and A. Smith, Naive and Primed Pluripotent States, Cell Stem Cell, vol.4, issue.6, pp.487-492, 2009.
DOI : 10.1016/j.stem.2009.05.015

L. Weinberger, M. Ayyash, N. Novershtern, and J. H. Hanna, 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

H. Chen, 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

Y. S. Chan, 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

O. Gafni, Derivation of novel human ground state naive pluripotent stem cells, Nature, vol.138, issue.7479, pp.282-286, 2013.
DOI : 10.1242/dev.064741

B. Valamehr, 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

Y. Takashima, 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

T. W. Theunissen, 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

C. B. Ware, Derivation of naive human embryonic stem cells, Proc. Natl. Acad. Sci. USA, pp.4484-4489, 2014.
DOI : 10.1016/S1534-5807(03)00330-7

P. Blakeley, 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

L. Yan, 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

S. Petropoulos, 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

H. Guo, The DNA methylation landscape of human early embryos, Nature, vol.511, issue.7511, pp.606-610, 2014.
DOI : 10.1038/nprot.2008.211

Z. D. Smith, DNA methylation dynamics of the human preimplantation embryo, Nature, vol.454, issue.7511, pp.611-615, 2014.
DOI : 10.1073/pnas.1530509100

C. Vallot, 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

A. De-los-angeles, Hallmarks of pluripotency, Nature, vol.158, issue.7570, pp.469-478, 2015.
DOI : 10.1016/j.cell.2014.07.020

W. A. Pastor, 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

A. Sahakyan, 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

G. Guo, 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

A. J. Collier, 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

K. Okita, T. Ichisaka, and S. Yamanaka, Generation of germline-competent induced pluripotent stem cells, Nature, vol.62, issue.7151, pp.313-317, 2007.
DOI : 10.1038/nature05934

N. Maherali, 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

M. Wernig, 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

Q. L. Ying, The ground state of embryonic stem cell self-renewal, Nature, vol.113, issue.7194, pp.519-523, 2008.
DOI : 10.1038/nature06968

G. Guo, Epigenetic resetting of human pluripotency, Development, vol.15, issue.15, pp.2748-2763, 2017.
DOI : 10.1242/dev.138982

|. Doi, 10.1038/s41467-017-02107-w ARTICLE, NATURE COMMUNICATIONS NATURE COMMUNICATIONS |, vol.9, 2018.
URL : https://hal.archives-ouvertes.fr/in2p3-00652853

J. Choi, 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

D. Cacchiarelli, 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

M. Soumillon, D. Cacchiarelli, and S. Semrau, Characterization of directed differentiation by high-throughput single-cell RNA-Seq. Preprint at bioRxiv https://www.biorxiv.org/content, p.3236, 2014.

K. K. Niakan, J. Han, R. A. Pedersen, C. Simon, and R. A. Pera, 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

T. W. Theunissen, 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

H. Ogata, 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

W. Gu, 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

J. Durruthy-durruthy, 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

I. Okamoto, 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

C. Vallot, 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

S. Mekhoubad, 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

S. Patel, Human embryonic stem cells do not change their X inactivation status during differentiation. Cell Rep, pp.54-67, 2017.

A. Smith, Formative pluripotency: the executive phase in a developmental continuum, Development, vol.144, issue.3, pp.365-373, 2017.
DOI : 10.1242/dev.142679

C. Buecker, 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

J. Wu, Interspecies Chimerism with Mammalian Pluripotent Stem Cells, Cell, vol.168, issue.3, pp.473-486, 2017.
DOI : 10.1016/j.cell.2016.12.036

Y. Yang, 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

F. Von-meyenn, 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

G. Q. Daley, 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

P. Samavarchi-tehrani, 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

S. Picelli, 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

S. Picelli, 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

J. J. Trombetta, 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

C. Trapnell, 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

B. Langmead and S. L. Salzberg, Fast gapped-read alignment with Bowtie 2, Nature Methods, vol.9, issue.4, pp.357-359, 2012.
DOI : 10.1093/bioinformatics/btp352

S. Anders, P. T. Pyl, and W. Huber, 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. T. Lun, D. J. Mccarthy, and J. C. Marioni, A step-by-step workflow for lowlevel analysis of single-cell RNA-seq data with Bioconductor, p.2122, 2016.

M. D. Robinson, D. J. Mccarthy, and G. Smyth, 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

M. I. Love, W. Huber, and S. Anders, 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

T. Suomi, F. Seyednasrollah, M. K. Jaakkola, T. Faux, and L. L. Elo, 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

R. Suzuki and H. Shimodaira, Pvclust: an R package for assessing the uncertainty in hierarchical clustering, Bioinformatics, vol.32, issue.3, pp.1540-1542, 2006.
DOI : 10.1214/009053604000000823

A. Alexa, J. Rahnenfuhrer, and T. Lengauer, 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

W. Luo, M. S. Friedman, K. Shedden, K. D. Hankenson, and P. J. Woolf, 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

I. Nantes, L. , and U. Cnrs-;-cnrs, 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

K. Center-pkwy and #. , Stéphanie Kilens and Dimitri Meistermann contributed equally to this work. A full list of consortium members appears at the end of the paper

N. Branch and I. U1163, 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.

F. Bobigny, 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

I. Pasteur, I. U932, and . Curie, 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.