Single-cell RNA-sequencing reveals the existence of naive and primed pluripotency in pre-implantation rhesus monkey embryos
暂无分享,去创建一个
Denghui Liu | Jing-Dong J Han | J. Han | P. Zheng | Denghui Liu | Yizhou Li | Ping Zheng | Xinyi Wang | Dajian He | Chunli Sun | Xiechao He | Lanzhen Yan | Yizhou Li | Chunli Sun | Xie-chao He | Lanzhen Yan | Dajian He | Xinyi Wang
[1] Steve Horvath,et al. WGCNA: an R package for weighted correlation network analysis , 2008, BMC Bioinformatics.
[2] D. Bartel,et al. Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species. , 2015, Cell reports.
[3] Anna-Katerina Hadjantonakis,et al. Distinct sequential cell behaviours direct primitive endoderm formation in the mouse blastocyst , 2008, Development.
[4] Angelique M. Nelson,et al. Derivation of naïve human embryonic stem cells , 2014, Proceedings of the National Academy of Sciences.
[5] J. Nichols,et al. NANOG Amplifies STAT3 Activation and They Synergistically Induce the Naive Pluripotent Program , 2014, Current Biology.
[6] J. Rossant,et al. Making the blastocyst: lessons from the mouse. , 2010, The Journal of clinical investigation.
[7] Dan Wang,et al. Integrating genomic, epigenomic, and transcriptomic features reveals modular signatures underlying poor prognosis in ovarian cancer. , 2013, Cell reports.
[8] Lei Wang,et al. Generation of Gene-Modified Cynomolgus Monkey via Cas9/RNA-Mediated Gene Targeting in One-Cell Embryos , 2014, Cell.
[9] Samantha A. Morris,et al. Active cell movements coupled to positional induction are involved in lineage segregation in the mouse blastocyst. , 2009, Developmental biology.
[10] R. Young,et al. Systematic Identification of Culture Conditions for Induction and Maintenance of Naive Human Pluripotency , 2014, Cell stem cell.
[11] Guillaume Marçais,et al. A new rhesus macaque assembly and annotation for next-generation sequencing analyses , 2014, Biology Direct.
[12] B. Doble,et al. The ground state of embryonic stem cell self-renewal , 2008, Nature.
[13] Rickard Sandberg,et al. Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos , 2016, Cell.
[14] Brad T. Sherman,et al. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.
[15] J. Nichols,et al. Lineage-Specific Profiling Delineates the Emergence and Progression of Naive Pluripotency in Mammalian Embryogenesis , 2015, Developmental cell.
[16] Denghui Liu,et al. Transcriptome analyses of rhesus monkey preimplantation embryos reveal a reduced capacity for DNA double-strand break repair in primate oocytes and early embryos. , 2017, Genome research.
[17] Trey Ideker,et al. Cytoscape 2.8: new features for data integration and network visualization , 2010, Bioinform..
[18] J. Hanna,et al. Dynamic stem cell states: naive to primed pluripotency in rodents and humans , 2016, Nature Reviews Molecular Cell Biology.
[19] M. Surani,et al. Regulatory principles of pluripotency: from the ground state up. , 2014, Cell stem cell.
[20] Qi Zhou,et al. Generation of Cynomolgus Monkey Chimeric Fetuses using Embryonic Stem Cells. , 2015, Cell stem cell.
[21] J. Miyazaki,et al. Sox17 plays a substantial role in late-stage differentiation of the extraembryonic endoderm in vitro , 2007, Journal of Cell Science.
[22] J. Nichols,et al. Naive Pluripotent Stem Cells Derived Directly from Isolated Cells of the Human Inner Cell Mass , 2016, Stem cell reports.
[23] L. Hurst,et al. Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells , 2014, Nature.
[24] Austin G Smith,et al. JAK/STAT3 signalling is sufficient and dominant over antagonistic cues for the establishment of naive pluripotency , 2012, Nature Communications.
[25] J. Lebkowski,et al. Basic Fibroblast Growth Factor Supports Undifferentiated Human Embryonic Stem Cell Growth Without Conditioned Medium , 2005, Stem cells.
[26] Paul Theodor Pyl,et al. HTSeq—a Python framework to work with high-throughput sequencing data , 2014, bioRxiv.
[27] A. Puliafito,et al. Heterogeneities in Nanog Expression Drive Stable Commitment to Pluripotency in the Mouse Blastocyst. , 2015, Cell reports.
[28] Toshihiro Sakurai,et al. Regulation of trophoblast-specific factors by GATA2 and GATA3 in bovine trophoblast CT-1 cells. , 2011, The Journal of reproduction and development.
[29] Austin G Smith,et al. FGF stimulation of the Erk1/2 signalling cascade triggers transition of pluripotent embryonic stem cells from self-renewal to lineage commitment , 2007, Development.
[30] W. Ge,et al. TALEN-mediated gene mutagenesis in rhesus and cynomolgus monkeys. , 2014, Cell stem cell.
[31] M. Trotter,et al. Derivation of pluripotent epiblast stem cells from mammalian embryos , 2007, Nature.
[32] Yi Zhang,et al. TET enzymes, TDG and the dynamics of DNA demethylation , 2013, Nature.
[33] Xiang Li,et al. Generation of naive induced pluripotent stem cells from rhesus monkey fibroblasts. , 2014, Cell stem cell.
[34] Kit T. Rodolfa,et al. Sox17 promotes differentiation in mouse embryonic stem cells by directly regulating extraembryonic gene expression and indirectly antagonizing self-renewal. , 2010, Genes & development.
[35] Cole Trapnell,et al. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells , 2014, Nature Biotechnology.
[36] M. Araúzo-Bravo,et al. Inhibition of TGFβ Signaling Promotes Ground State Pluripotency , 2013, Stem Cell Reviews and Reports.
[37] Anna-Katerina Hadjantonakis,et al. The primitive endoderm lineage of the mouse blastocyst: sequential transcription factor activation and regulation of differentiation by Sox17. , 2011, Developmental biology.
[38] Åsa K. Björklund,et al. Full-length RNA-seq from single cells using Smart-seq2 , 2014, Nature Protocols.
[39] Yang Wang,et al. Tet-Mediated Formation of 5-Carboxylcytosine and Its Excision by TDG in Mammalian DNA , 2011, Science.
[40] S. Emmott,et al. Defining an essential transcription factor program for naïve pluripotency , 2014, Science.
[41] G. Faulkner,et al. Transposable elements in the mammalian embryo: pioneers surviving through stealth and service , 2016, Genome Biology.
[42] Luca Pinello,et al. Serum-Based Culture Conditions Provoke Gene Expression Variability in Mouse Embryonic Stem Cells as Revealed by Single-Cell Analysis. , 2016, Cell reports.
[43] M. Araúzo-Bravo,et al. Esrrb Unlocks Silenced Enhancers for Reprogramming to Naive Pluripotency. , 2018, Cell stem cell.
[44] W. Huber,et al. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.
[45] J. Nichols,et al. Resetting Transcription Factor Control Circuitry toward Ground-State Pluripotency in Human , 2014, Cell.
[46] Georg Fuellen,et al. The PluriNetWork: An Electronic Representation of the Network Underlying Pluripotency in Mouse, and Its Applications , 2010, PloS one.
[47] J. Rossant,et al. Intercellular interactions, position, and polarity in establishing blastocyst cell lineages and embryonic axes. , 2012, Cold Spring Harbor perspectives in biology.
[48] S. Pfaff,et al. Transposable elements as genetic regulatory substrates in early development. , 2013, Trends in cell biology.
[49] R. Jaenisch,et al. Human Naive Pluripotent Stem Cells Model X Chromosome Dampening and X Inactivation. , 2017, Cell stem cell.
[50] I. Okamoto,et al. A developmental coordinate of pluripotency among mice, monkeys and humans , 2016, Nature.
[51] Kathleen F. Kerr,et al. The External RNA Controls Consortium: a progress report , 2005, Nature Methods.
[52] Åsa K. Björklund,et al. Smart-seq2 for sensitive full-length transcriptome profiling in single cells , 2013, Nature Methods.
[53] R. Jaenisch,et al. Molecular Criteria for Defining the Naive Human Pluripotent State , 2016, Cell Stem Cell.
[54] S. Nishikawa,et al. Activated Notch1 alters differentiation of embryonic stem cells into mesodermal cell lineages at multiple stages of development , 2006, Mechanisms of Development.
[55] R Core Team,et al. R: A language and environment for statistical computing. , 2014 .
[56] M. Surani,et al. Genome-Wide Reprogramming in the Mouse Germ Line Entails the Base Excision Repair Pathway , 2010, Science.
[57] Ralf Herwig,et al. Primary Differentiation in the Human Blastocyst: Comparative Molecular Portraits of Inner Cell Mass and Trophectoderm Cells , 2005, Stem cells.
[58] William A. Pastor,et al. Naive Human Pluripotent Cells Feature a Methylation Landscape Devoid of Blastocyst or Germline Memory. , 2016, Cell stem cell.
[59] M. Murakami,et al. The Homeoprotein Nanog Is Required for Maintenance of Pluripotency in Mouse Epiblast and ES Cells , 2003, Cell.
[60] S. Horvath,et al. Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing , 2013, Nature.
[61] Janet Rossant,et al. New Insights into Early Human Development: Lessons for Stem Cell Derivation and Differentiation. , 2017, Cell stem cell.
[62] Cole Trapnell,et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.
[63] Ira W. Deveson,et al. The Dimensions, Dynamics, and Relevance of the Mammalian Noncoding Transcriptome. , 2017, Trends in genetics : TIG.
[64] Yang Yu,et al. Transgenic rhesus monkeys produced by gene transfer into early-cleavage–stage embryos using a simian immunodeficiency virus-based vector , 2010, Proceedings of the National Academy of Sciences.
[65] Anna-Katerina Hadjantonakis,et al. Anatomy of a blastocyst: Cell behaviors driving cell fate choice and morphogenesis in the early mouse embryo , 2013, Genesis.
[66] Catalin C. Barbacioru,et al. mRNA-Seq whole-transcriptome analysis of a single cell , 2009, Nature Methods.
[67] Mikael Huss,et al. Resolution of cell fate decisions revealed by single-cell gene expression analysis from zygote to blastocyst. , 2010, Developmental cell.
[68] J. I. Izpisúa Belmonte,et al. Dynamic Pluripotent Stem Cell States and Their Applications. , 2015, Cell stem cell.
[69] Minjung Kang,et al. FGF4 is required for lineage restriction and salt-and-pepper distribution of primitive endoderm factors but not their initial expression in the mouse , 2013, Development.
[70] B. Bavister,et al. Energy substrate requirement for in vitro maturation of oocytes from unstimulated adult rhesus monkeys , 2001, Molecular reproduction and development.
[71] Andrew E. Jaffe,et al. Bioinformatics Applications Note Gene Expression the Sva Package for Removing Batch Effects and Other Unwanted Variation in High-throughput Experiments , 2022 .
[72] The External Rna Controls Consortium. The External RNA Controls Consortium: a progress report , 2005 .
[73] Christopher D. Green,et al. Inference of differentiation time for single cell transcriptomes using cell population reference data , 2017, Nature Communications.
[74] R. McKay,et al. New cell lines from mouse epiblast share defining features with human embryonic stem cells , 2007, Nature.
[75] Brad T. Sherman,et al. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists , 2008, Nucleic acids research.