Single-cell transcriptional profiling: a window into embryonic cell-type specification

Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation

(2018) Ximena Ibarra-Soria et al.   NATURE CELL BIOLOGY

Single-cell analysis reveals lineage segregation in early post-implantation mouse embryos

(2017) Jing Wen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Synthetic recording and in situ readout of lineage information in single cells

(2017) Kirsten L. Frieda et al.   NATURE

Single-cell mRNA quantification and differential analysis with Census

(2017) Xiaojie Qiu et al.   NATURE METHODS

Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos

(2016) Sophie Petropoulos et al.   CELL

Mass Cytometry: Single Cells, Many Features

(2016) Matthew H. Spitzer et al.   CELL

Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos

(2016) Mubeen Goolam et al.   CELL

Single-Cell Resolution of Temporal Gene Expression during Heart Development

(2016) Daniel M. DeLaughter et al.   DEVELOPMENTAL CELL

Spatial Transcriptome for the Molecular Annotation of Lineage Fates and Cell Identity in Mid-gastrula Mouse Embryo

(2016) Guangdun Peng et al.   DEVELOPMENTAL CELL

Asymmetric division of contractile domains couples cell positioning and fate specification

(2016) Jean-Léon Maître et al.   NATURE

Early myeloid lineage choice is not initiated by random PU.1 to GATA1 protein ratios

(2016) Philipp S. Hoppe et al.   NATURE

Resolving early mesoderm diversification through single-cell expression profiling

(2016) Antonio Scialdone et al.   NATURE

Wishbone identifies bifurcating developmental trajectories from single-cell data

(2016) Manu Setty et al.   NATURE BIOTECHNOLOGY

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

Dynamic stem cell states: naive to primed pluripotency in rodents and humans

(2016) Leehee Weinberger et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A decade of transcription factor-mediated reprogramming to pluripotency

(2016) Kazutoshi Takahashi et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Whole-organism lineage tracing by combinatorial and cumulative genome editing

(2016) Aaron McKenna et al.   SCIENCE

Tissue morphodynamics shaping the early mouse embryo

(2016) Ann E. Sutherland   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Serum-Based Culture Conditions Provoke Gene Expression Variability in Mouse Embryonic Stem Cells as Revealed by Single-Cell Analysis

(2016) Guoji Guo et al.   Cell Reports

MERVL/Zscan4 Network Activation Results in Transient Genome-wide DNA Demethylation of mESCs

(2016) Mélanie A. Eckersley-Maslin et al.   Cell Reports

Diffusion maps for high-dimensional single-cell analysis of differentiation data

(2015) Laleh Haghverdi et al.   BIOINFORMATICS

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Single-Cell Transcriptome Analysis Reveals Dynamic Changes in lncRNA Expression during Reprogramming

(2015) Daniel H. Kim et al.   Cell Stem Cell

A Continuous Molecular Roadmap to iPSC Reprogramming through Progression Analysis of Single-Cell Mass Cytometry

(2015) Eli R. Zunder et al.   Cell Stem Cell

Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation

(2015) Aleksandra A. Kolodziejczyk et al.   Cell Stem Cell

Multiple cell and population-level interactions with mouse embryonic stem cell heterogeneity

(2015) D. Cannon et al.   DEVELOPMENT

Defining the three cell lineages of the human blastocyst by single-cell RNA-seq

(2015) P. Blakeley et al.   DEVELOPMENT

Dynamic transcriptional symmetry-breaking in pre-implantation mammalian embryo development revealed by single-cell RNA-seq

(2015) Junchao Shi et al.   DEVELOPMENT

Early reprogramming regulators identified by prospective isolation and mass cytometry

(2015) Ernesto Lujan et al.   NATURE

Decoding the regulatory network of early blood development from single-cell gene expression measurements

(2015) Victoria Moignard et al.   NATURE BIOTECHNOLOGY

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin

(2015) Kaia Achim et al.   NATURE BIOTECHNOLOGY

Network plasticity of pluripotency transcription factors in embryonic stem cells

(2015) Adam Filipczyk et al.   NATURE CELL BIOLOGY

G&T-seq: parallel sequencing of single-cell genomes and transcriptomes

(2015) Iain C Macaulay et al.   NATURE METHODS

Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues

(2015) Je Hyuk Lee et al.   Nature Protocols

Heterogeneities in Nanog Expression Drive Stable Commitment to Pluripotency in the Mouse Blastocyst

(2015) Panagiotis Xenopoulos et al.   Cell Reports

X Chromosome Reactivation Dynamics Reveal Stages of Reprogramming to Pluripotency

(2014) Vincent Pasque et al.   CELL

Genome-wide RNA Tomography in the Zebrafish Embryo

(2014) Jan Philipp Junker et al.   CELL

Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development

(2014) Sean C. Bendall et al.   CELL

Initiation of Hippo signaling is linked to polarity rather than to cell position in the pre-implantation mouse embryo

(2014) Shihadeh Anani et al.   DEVELOPMENT

A gene expression atlas of early craniofacial development

(2014) Eric W. Brunskill et al.   DEVELOPMENTAL BIOLOGY

GATA6 Levels Modulate Primitive Endoderm Cell Fate Choice and Timing in the Mouse Blastocyst

(2014) Nadine Schrode et al.   DEVELOPMENTAL CELL

Cell fate inclination within 2-cell and 4-cell mouse embryos revealed by single-cell RNA sequencing

(2014) Fernando H. Biase et al.   GENOME RESEARCH

Dynamic Heterogeneity and DNA Methylation in Embryonic Stem Cells

(2014) Zakary S. Singer et al.   MOLECULAR CELL

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Early lineage restriction in temporally distinct populations of Mesp1 progenitors during mammalian heart development

(2014) Fabienne Lescroart et al.   NATURE CELL BIOLOGY

Single-cell in situ RNA profiling by sequential hybridization

(2014) Eric Lubeck et al.   NATURE METHODS

Early patterning and specification of cardiac progenitors in gastrulating mesoderm

(2014) W Patrick Devine et al.   eLife

Development: Do Mouse Embryos Play Dice?

(2013) Magdalena Zernicka-Goetz   CURRENT BIOLOGY

High-resolution analysis with novel cell-surface markers identifies routes to iPS cells

(2013) James O’Malley et al.   NATURE

Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing

(2013) Zhigang Xue et al.   NATURE

Chromatin dynamics during cellular reprogramming

(2013) Effie Apostolou et al.   NATURE

Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages

(2013) Yusuke Ohnishi et al.   NATURE CELL BIOLOGY

Quantitative single-cell RNA-seq with unique molecular identifiers

(2013) Saiful Islam et al.   NATURE METHODS

Accounting for technical noise in single-cell RNA-seq experiments

(2013) Philip Brennecke et al.   NATURE METHODS

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

The differential response to Fgf signalling in cells internalized at different times influences lineage segregation in preimplantation mouse embryos

(2013) S. A. Morris et al.   Open Biology

A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells

(2012) Jose M. Polo et al.   CELL

Single-Cell Expression Analyses during Cellular Reprogramming Reveal an Early Stochastic and a Late Hierarchic Phase

(2012) Yosef Buganim et al.   CELL

Developmental Bias in Cleavage-Stage Mouse Blastomeres

(2012) Inna Tabansky et al.   CURRENT BIOLOGY

Analysis of human embryos from zygote to blastocyst reveals distinct gene expression patterns relative to the mouse

(2012) Kathy K. Niakan et al.   DEVELOPMENTAL BIOLOGY

Embryonic stem cell potency fluctuates with endogenous retrovirus activity

(2012) Todd S. Macfarlan et al.   NATURE

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

Single-cell systems biology by super-resolution imaging and combinatorial labeling

(2012) Eric Lubeck et al.   NATURE METHODS

Single-molecule analysis of gene expression using two-color RNA labeling in live yeast

(2012) Sami Hocine et al.   NATURE METHODS

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

(2012) Tamar Hashimshony et al.   Cell Reports

Gene expression heterogeneities in embryonic stem cell populations: origin and function

(2011) Alfonso Martinez Arias et al.   CURRENT OPINION IN CELL BIOLOGY

ER71 directs mesodermal fate decisions during embryogenesis

(2011) T. L. Rasmussen et al.   DEVELOPMENT

Primitive Endoderm Differentiates via a Three-Step Mechanism Involving Nanog and RTK Signaling

(2011) Stephen Frankenberg et al.   DEVELOPMENTAL CELL

Synthetic spike-in standards for RNA-seq experiments

(2011) L. Jiang et al.   GENOME RESEARCH

Oct4 kinetics predict cell lineage patterning in the early mammalian embryo

(2011) Nicolas Plachta et al.   NATURE CELL BIOLOGY

FGF signal-dependent segregation of primitive endoderm and epiblast in the mouse blastocyst

(2010) Y. Yamanaka et al.   DEVELOPMENT

Resolution of Cell Fate Decisions Revealed by Single-Cell Gene Expression Analysis from Zygote to Blastocyst

(2010) Guoji Guo et al.   DEVELOPMENTAL CELL

Zscan4 regulates telomere elongation and genomic stability in ES cells

(2010) Michal Zalzman et al.   NATURE

Dynamic single-cell imaging of direct reprogramming reveals an early specifying event

(2010) Zachary D Smith et al.   NATURE BIOTECHNOLOGY

Origin and formation of the first two distinct cell types of the inner cell mass in the mouse embryo

(2010) S. A. Morris et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Forcing cells to change lineages

(2009) Thomas Graf et al.   NATURE

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Making a commitment: cell lineage allocation and axis patterning in the early mouse embryo

(2009) Sebastian J. Arnold et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Nkx2–5 transactivates the Ets-related protein 71 gene and specifies an endothelial/endocardial fate in the developing embryo

(2009) Anwarul Ferdous et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulated Fluctuations in Nanog Expression Mediate Cell Fate Decisions in Embryonic Stem Cells

(2009) Tibor Kalmar et al.   PLOS BIOLOGY

Formation of the embryonic-abembryonic axis of the mouse blastocyst: relationships between orientation of early cleavage divisions and pattern of symmetric/asymmetric divisions

(2008) M. Bischoff et al.   DEVELOPMENT

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS