Differentiation of human embryonic stem cells to HOXA+ hemogenic vasculature that resembles the aorta-gonad-mesonephros

[1]  F. Tang,et al.  Tracing haematopoietic stem cell formation at single-cell resolution , 2016, Nature.

[2]  J. Zack,et al.  Medial HOXA genes demarcate haematopoietic stem cell fate during human development , 2016, Nature Cell Biology.

[3]  S. Rybtsov,et al.  Concealed expansion of immature precursors underpins acute burst of adult HSC activity in foetal liver , 2016, Development.

[4]  Crispin J. Miller,et al.  GFI1 proteins orchestrate the emergence of haematopoietic stem cells through recruitment of LSD1 , 2015, Nature Cell Biology.

[5]  Kechun Liu,et al.  Identification and Expression Analysis of Zebrafish (Danio rerio) E-Selectin during Embryonic Development , 2015, Molecules.

[6]  Young Chul Kim,et al.  Alternative Wnt Signaling Activates YAP/TAZ , 2015, Cell.

[7]  S. Orkin,et al.  Hemoglobin switching's surprise: the versatile transcription factor BCL11A is a master repressor of fetal hemoglobin. , 2015, Current opinion in genetics & development.

[8]  J. Klusmann,et al.  Lost in translation: pluripotent stem cell-derived hematopoiesis , 2015, EMBO molecular medicine.

[9]  E. Stanley,et al.  HUMAN DEFINITIVE HAEMOGENIC ENDOTHELIUM AND ARTERIAL VASCULAR ENDOTHELIUM REPRESENT DISTINCT LINEAGES , 2015, Nature Cell Biology.

[10]  Matthew E. Ritchie,et al.  limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.

[11]  W. V. van IJcken,et al.  Whole-transcriptome analysis of endothelial to hematopoietic stem cell transition reveals a requirement for Gpr56 in HSC generation , 2015, The Journal of experimental medicine.

[12]  G. Crooks,et al.  GPI-80 defines self-renewal ability in hematopoietic stem cells during human development. , 2015, Cell stem cell.

[13]  Howard Y. Chang,et al.  ATAC‐seq: A Method for Assaying Chromatin Accessibility Genome‐Wide , 2015, Current protocols in molecular biology.

[14]  B. Bruneau,et al.  Ezh2-mediated repression of a transcriptional pathway upstream of Mmp9 maintains integrity of the developing vasculature , 2014, Development.

[15]  N. Soshnikova,et al.  Hox gene regulation and timing in embryogenesis. , 2014, Seminars in cell & developmental biology.

[16]  P. Real,et al.  HOXA9 promotes hematopoietic commitment of human embryonic stem cells , 2014 .

[17]  Loren Gragert,et al.  HLA match likelihoods for hematopoietic stem-cell grafts in the U.S. registry. , 2014, The New England journal of medicine.

[18]  G. Keller,et al.  Wnt Signaling Controls the Specification of Definitive and Primitive Hematopoiesis From Human Pluripotent Stem Cells , 2014, Nature Biotechnology.

[19]  Rafael A. Irizarry,et al.  Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays , 2014, Bioinform..

[20]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[21]  M. Turner,et al.  Identification of the Niche and Phenotype of the First Human Hematopoietic Stem Cells , 2014, Stem Cell Reports.

[22]  A. Iwama,et al.  Sox17-Mediated Maintenance of Fetal Intra-Aortic Hematopoietic Cell Clusters , 2014, Molecular and Cellular Biology.

[23]  S. Nilsson,et al.  Analyzing hematopoietic stem cell homing, lodgment, and engraftment to better understand the bone marrow niche , 2014, Annals of the New York Academy of Sciences.

[24]  I. Weissman,et al.  Efficient endoderm induction from human pluripotent stem cells by logically directing signals controlling lineage bifurcations. , 2014, Cell stem cell.

[25]  Charity W. Law,et al.  voom: precision weights unlock linear model analysis tools for RNA-seq read counts , 2014, Genome Biology.

[26]  B. Göttgens,et al.  Early dynamic fate changes in haemogenic endothelium characterized at the single-cell level , 2013, Nature Communications.

[27]  James J Collins,et al.  Induction of multipotential hematopoietic progenitors from human pluripotent stem cells via respecification of lineage-restricted precursors. , 2013, Cell stem cell.

[28]  G. Keller,et al.  Retinoic Acid Signaling Is Essential for Embryonic Hematopoietic Stem Cell Development , 2013, Cell.

[29]  A. Regev,et al.  Transcriptome Analysis Identifies Regulators of Hematopoietic Stem and Progenitor Cells , 2013, Stem cell reports.

[30]  David K. Gifford,et al.  Saltatory remodeling of Hox chromatin in response to rostro-caudal patterning signals , 2013, Nature Neuroscience.

[31]  E. Stanley,et al.  WNT3A Promotes Hematopoietic or Mesenchymal Differentiation from hESCs Depending on the Time of Exposure , 2013, Stem cell reports.

[32]  Wei Shi,et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features , 2013, Bioinform..

[33]  Y. Yashiro‐Ohtani,et al.  The expression of Sox17 identifies and regulates haemogenic endothelium , 2013, Nature Cell Biology.

[34]  Gordon Keller,et al.  T lymphocyte potential marks the emergence of definitive hematopoietic progenitors in human pluripotent stem cell differentiation cultures. , 2012, Cell reports.

[35]  Mitchell D. Probasco,et al.  Identification of the hemogenic endothelial progenitor and its direct precursor in human pluripotent stem cell differentiation cultures. , 2012, Cell reports.

[36]  E. Stanley,et al.  APELIN promotes hematopoiesis from human embryonic stem cells. , 2012, Blood.

[37]  J. Navarro-González,et al.  Expression of FGF23/KLOTHO system in human vascular tissue , 2012 .

[38]  M. Kaplan,et al.  Autonomous murine T-cell progenitor production in the extra-embryonic yolk sac before HSC emergence. , 2012, Blood.

[39]  J. Tost,et al.  Complete pipeline for Infinium(®) Human Methylation 450K BeadChip data processing using subset quantile normalization for accurate DNA methylation estimation. , 2012, Epigenomics.

[40]  I. Khazaal,et al.  Angiotensin-converting enzyme (CD143) specifies emerging lympho-hematopoietic progenitors in the human embryo. , 2012, Blood.

[41]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[42]  P. Dollé,et al.  Retinoic acid signalling during development , 2012, Development.

[43]  Richard A. Anderson,et al.  Highly potent human hematopoietic stem cells first emerge in the intraembryonic aorta-gonad-mesonephros region , 2011, The Lancet.

[44]  J. Frampton,et al.  Hierarchical organization and early hematopoietic specification of the developing HSC lineage in the AGM region , 2011, The Journal of experimental medicine.

[45]  N. Friedman,et al.  Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis , 2011, Cell.

[46]  G. Sauvageau,et al.  HoxA cluster is haploinsufficient for activity of hematopoietic stem and progenitor cells. , 2010, Experimental hematology.

[47]  T. Townes,et al.  KLF1 regulates BCL11A expression and γ- to β-globin gene switching , 2010, Nature Genetics.

[48]  F. Grosveld,et al.  Haploinsufficiency for the erythroid transcription factor KLF1 causes Hereditary Persistence of Fetal Hemoglobin , 2010, Nature Genetics.

[49]  D. Duboule,et al.  Additive and global functions of HoxA cluster genes in mesoderm derivatives. , 2010, Developmental biology.

[50]  G. Swiers,et al.  Nonredundant roles for Runx1 alternative promoters reflect their activity at discrete stages of developmental hematopoiesis. , 2010, Blood.

[51]  H. Nakase,et al.  Direct Comparison of Dll1- and Dll4-Mediated Notch Activation Levels Shows Differential Lymphomyeloid Lineage Commitment Outcomes , 2010, The Journal of Immunology.

[52]  N. Galjart,et al.  In vivo imaging of haematopoietic cells emerging from the mouse aortic endothelium , 2010, Nature.

[53]  M. Robinson,et al.  A scaling normalization method for differential expression analysis of RNA-seq data , 2010, Genome Biology.

[54]  V. Kouskoff,et al.  The differential activities of Runx1 promoters define milestones during embryonic hematopoiesis. , 2009, Blood.

[55]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[56]  Stuart H. Orkin,et al.  Developmental and species-divergent globin switching are driven by BCL11A , 2009, Nature.

[57]  J. Hirschhorn,et al.  Supporting Online Material Materials and Methods Figs. S1 to S10 Tables S1 to S7 References Human Fetal Hemoglobin Expression Is Regulated by the Developmental Stage-specific Repressor Bcl11a , 2022 .

[58]  M. Dickinson,et al.  Cell signaling directing the formation and function of hemogenic endothelium during murine embryogenesis. , 2008, Blood.

[59]  K. Moore,et al.  Extensive hematopoietic stem cell generation in the AGM region via maturation of VE-cadherin+CD45+ pre-definitive HSCs. , 2008, Cell stem cell.

[60]  Pan Du,et al.  lumi: a pipeline for processing Illumina microarray , 2008, Bioinform..

[61]  E. Stanley,et al.  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 , 2008, Nature Protocols.

[62]  E. Stanley,et al.  Targeting a GFP reporter gene to the MIXL1 locus of human embryonic stem cells identifies human primitive streak-like cells and enables isolation of primitive hematopoietic precursors. , 2008, Blood.

[63]  R. Humphries,et al.  Hox genes in hematopoiesis and leukemogenesis , 2007, Oncogene.

[64]  S. Morrison,et al.  Sox17 Dependence Distinguishes the Transcriptional Regulation of Fetal from Adult Hematopoietic Stem Cells , 2007, Cell.

[65]  J. Lotem,et al.  Developmentally regulated promoter-switch transcriptionally controls Runx1 function during embryonic hematopoiesis , 2007, BMC Developmental Biology.

[66]  D. Grier,et al.  Analysis of HSC activity and compensatory Hox gene expression profile in Hoxb cluster mutant fetal liver cells. , 2006, Blood.

[67]  J. van Nes,et al.  Developmental regulation of the Hox genes during axial morphogenesis in the mouse , 2005, Development.

[68]  Takuro Nakamura,et al.  Bcl11a is essential for normal lymphoid development , 2003, Nature Immunology.

[69]  Elaine Dzierzak,et al.  Runx1 expression marks long-term repopulating hematopoietic stem cells in the midgestation mouse embryo. , 2002, Immunity.

[70]  M. Taniwaki,et al.  Identification of an alternatively spliced form of the mouse AML1/RUNX1 gene transcript AML1c and its expression in early hematopoietic development. , 2001, Biochemical and biophysical research communications.

[71]  L. Barnett,et al.  Homeodomain factor Nkx2-3 controls regional expression of leukocyte homing coreceptor MAdCAM-1 in specialized endothelial cells of the viscera. , 2000, Developmental biology.

[72]  J. Sotto,et al.  Fitting limiting dilution experiments with generalized linear models results in a test of the single-hit Poisson assumption. , 1996, Journal of immunological methods.

[73]  M. Marín‐Padilla,et al.  Disruption of the Cbfa2 gene causes necrosis and hemorrhaging in the central nervous system and blocks definitive hematopoiesis. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[74]  A. Mccarthy.  Development , 1996, Current Opinion in Neurobiology.

[75]  E. Soeda,et al.  Alternative splicing and genomic structure of the AML1 gene involved in acute myeloid leukemia. , 1995, Nucleic acids research.

[76]  A. Müller,et al.  An early pre-liver intraembryonic source of CFU-S in the developing mouse , 1993, Nature.

[77]  J. Saavedra,et al.  Changes in expression of angiotensin receptor subtypes in the rat aorta during development. , 1991, Biochemical and biophysical research communications.

[78]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[79]  Xabier Agirre,et al.  Unraveling a novel transcription factor code determining the human arterial-specific endothelial cell signature. , 2013, Blood.

[80]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[81]  W. Liang,et al.  TM4 microarray software suite. , 2006, Methods in enzymology.

[82]  W. Liang,et al.  9) TM4 Microarray Software Suite , 2006 .

[83]  D. Luton,et al.  Aorta-associated CD34+ hematopoietic cells in the early human embryo. , 1996, Blood.