Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis

Imaging cell lineage with a synthetic digital recording system

(2021) Ke-Huan K. Chow et al.   SCIENCE

Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids

(2020) Susanne C. van den Brink et al.   NATURE

Cell-fate plasticity, adhesion and cell sorting complementarily establish a sharp midbrain-hindbrain boundary

(2020) Gokul Kesavan et al.   DEVELOPMENT

The lateral plate mesoderm

(2020) Karin D. Prummel et al.   DEVELOPMENT

Epigenetic regulator function through mouse gastrulation

(2020) Stefanie Grosswendt et al.   NATURE

Investigating higher-order interactions in single-cell data with scHOT

(2020) Shila Ghazanfar et al.   NATURE METHODS

Delineating the early transcriptional specification of the mammalian trachea and esophagus

(2020) Akela Kuwahara et al.   eLife

Single cell transcriptomics identifies a signaling network coordinating endoderm and mesoderm diversification during foregut organogenesis

(2020) Lu Han et al.   Nature Communications

Diverse Routes toward Early Somites in the Mouse Embryo

(2020) Carolina Guibentif et al.   DEVELOPMENTAL CELL

Fgf4 maintains Hes7 levels critical for normal somite segmentation clock function

(2020) Matthew J Anderson et al.   eLife

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

(2019) Samuel G. Rodriques et al.   SCIENCE

A single-cell molecular map of mouse gastrulation and early organogenesis

(2019) Blanca Pijuan-Sala et al.   NATURE

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

(2019) Chee-Huat Linus Eng et al.   NATURE

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Molecular recording of mammalian embryogenesis

(2019) Michelle M. Chan et al.   NATURE

The emergent landscape of the mouse gut endoderm at single-cell resolution

(2019) Sonja Nowotschin et al.   NATURE

Molecular architecture of lineage allocation and tissue organization in early mouse embryo

(2019) Guangdun Peng et al.   NATURE

ilastik: interactive machine learning for (bio)image analysis

(2019) Stuart Berg et al.   NATURE METHODS

Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression

(2019) Chenglong Xia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In situ readout of DNA barcodes and single base edits facilitated by in vitro transcription

(2019) Amjad Askary et al.   NATURE BIOTECHNOLOGY

Isl1 Regulation of Nkx2.1 in the Early Foregut Epithelium Is Required for Trachea-Esophageal Separation and Lung Lobation

(2019) Eugene Kim et al.   DEVELOPMENTAL CELL

Endosome-Mediated Epithelial Remodeling Downstream of Hedgehog-Gli Is Required for Tracheoesophageal Separation

(2019) Talia Nasr et al.   DEVELOPMENTAL CELL

Multi-omics profiling of mouse gastrulation at single-cell resolution

(2019) Ricard Argelaguet et al.   NATURE

Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH

(2018) Sheel Shah et al.   CELL

Multidimensional quantitative analysis of mRNA expression within intact vertebrate embryos

(2018) Vikas Trivedi et al.   DEVELOPMENT

Third-generationin situhybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust

(2018) Harry M. T. Choi et al.   DEVELOPMENT

Whole-organism clone tracing using single-cell sequencing

(2018) Anna Alemany et al.   NATURE

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain

(2018) Bushra Raj et al.   NATURE BIOTECHNOLOGY

Simultaneous lineage tracing and cell-type identification using CRISPR–Cas9-induced genetic scars

(2018) Bastiaan Spanjaard et al.   NATURE BIOTECHNOLOGY

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

Three-dimensional intact-tissue sequencing of single-cell transcriptional states

(2018) Xiao Wang et al.   SCIENCE

Multiplexed imaging of high-density libraries of RNAs with MERFISH and expansion microscopy

(2018) Guiping Wang et al.   Scientific Reports

Developmental barcoding of whole mouse via homing CRISPR

(2018) Reza Kalhor et al.   SCIENCE

Profiling the transcriptome with RNA SPOTs

(2017) Chee-Huat Linus Eng et al.   NATURE METHODS

Multicut brings automated neurite segmentation closer to human performance

(2017) Thorsten Beier et al.   NATURE METHODS

Efficient in situ barcode sequencing using padlock probe-based BaristaSeq

(2017) Xiaoyin Chen et al.   NUCLEIC ACIDS RESEARCH

Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation

(2017) Hisham Mohammed et al.   Cell Reports

Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells

(2016) Gioele La Manno et al.   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

Resolving early mesoderm diversification through single-cell expression profiling

(2016) Antonio Scialdone et al.   NATURE

Protein-retention expansion microscopy of cells and tissues labeled using standard fluorescent proteins and antibodies

(2016) Paul W Tillberg et al.   NATURE BIOTECHNOLOGY

Nanoscale imaging of RNA with expansion microscopy

(2016) Fei Chen et al.   NATURE METHODS

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus

(2016) Sheel Shah et al.   NEURON

High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization

(2016) Jeffrey R. Moffitt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

(2016) P. L. Stahl et al.   SCIENCE

A Cranial Mesoderm Origin for Esophagus Striated Muscles

(2015) Swetha Gopalakrishnan et al.   DEVELOPMENTAL CELL

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

The initial establishment and epithelial morphogenesis of the esophagus: a new model of tracheal-esophageal separation and transition of simple columnar into stratified squamous epithelium in the developing esophagus

(2015) Jianwen Que   Wiley Interdisciplinary Reviews-Developmental Biology

Pax genes: regulators of lineage specification and progenitor cell maintenance

(2014) J. A. Blake et al.   DEVELOPMENT

Novel mechanisms that pattern and shape the midbrain-hindbrain boundary

(2013) Sebastian Dworkin et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Tbx18 regulates development of the epicardium and coronary vessels

(2013) San-Pin Wu et al.   DEVELOPMENTAL BIOLOGY

In situ sequencing for RNA analysis in preserved tissue and cells

(2013) Rongqin Ke et al.   NATURE METHODS

EMAGE mouse embryo spatial gene expression database: 2014 update

(2013) Lorna Richardson et al.   NUCLEIC ACIDS RESEARCH

Altered Tbx1 gene expression is associated with abnormal oesophageal development in the adriamycin mouse model of oesophageal atresia/tracheo-oesophageal fistula

(2013) Danielle Mc Laughlin et al.   PEDIATRIC SURGERY INTERNATIONAL

A novel role for FOXA2 and SHH in organizing midbrain signaling centers

(2012) Roy D. Bayly et al.   DEVELOPMENTAL BIOLOGY

Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes

(2012) B. J. Beliveau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gbx2 and Fgf8 are sequentially required for formation of the midbrain-hindbrain compartment boundary

(2011) N. A. Sunmonu et al.   DEVELOPMENT

Signaling through BMP receptors promotes respiratory identity in the foregut via repression of Sox2

(2011) E. T. Domyan et al.   DEVELOPMENT

Notch signaling: simplicity in design, versatility in function

(2011) E. R. Andersson et al.   DEVELOPMENT

Wt1 controls retinoic acid signalling in embryonic epicardium through transcriptional activation of Raldh2

(2011) J. A. Guadix et al.   DEVELOPMENT

A High-Resolution Anatomical Atlas of the Transcriptome in the Mouse Embryo

(2011) Graciana Diez-Roux et al.   PLOS BIOLOGY

Analysis of the Hand1 cell lineage reveals novel contributions to cardiovascular, neural crest, extra-embryonic, and lateral mesoderm derivatives

(2010) Ralston M. Barnes et al.   DEVELOPMENTAL DYNAMICS

Wnt1-lmx1a Forms a Novel Autoregulatory Loop and Controls Midbrain Dopaminergic Differentiation Synergistically with the SHH-FoxA2 Pathway

(2009) Sangmi Chung et al.   Cell Stem Cell

Wnt2/2b and β-Catenin Signaling Are Necessary and Sufficient to Specify Lung Progenitors in the Foregut

(2009) Ashley M. Goss et al.   DEVELOPMENTAL CELL

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

Spatial Analysis of Expression Patterns Predicts Genetic Interactions at the Mid-Hindbrain Boundary

(2009) Dominik M. Wittmann et al.   PLoS Computational Biology

Characterization and Classification of Zebrafish Brain Morphology Mutants

(2008) Laura Anne Lowery et al.   Anatomical Record-Advances in Integrative Anatomy and Evolutionary Biology

Microarray analysis of Foxa2 mutant mouse embryos reveals novel gene expression and inductive roles for the gastrula organizer and its derivatives

(2008) Owen J Tamplin et al.   BMC GENOMICS

Identification of presomitic mesoderm (PSM)-specific Mesp1 enhancer and generation of a PSM-specific Mesp1/Mesp2-null mouse using BAC-based rescue technology

(2008) Masayuki Oginuma et al.   MECHANISMS OF DEVELOPMENT

A myocardial lineage derives from Tbx18 epicardial cells

(2008) Chen-Leng Cai et al.   NATURE