From whole-mount to single-cell spatial assessment of gene expression in 3D

Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids

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

Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas

(2020) Reuben Moncada et al.   NATURE BIOTECHNOLOGY

Cell Atlas technologies and insights into tissue architecture

(2020) Anna Wilbrey-Clark et al.   BIOCHEMICAL JOURNAL

Spatially Resolved Transcriptomes—Next Generation Tools for Tissue Exploration

(2020) Michaela Asp et al.   BIOESSAYS

The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas

(2020) Quanxin Wang et al.   CELL

Identification of genomic enhancers through spatial integration of single‐cell transcriptomics and epigenomics

(2020) Carmen Bravo González‐Blas et al.   Molecular Systems Biology

Inferring spatial and signaling relationships between cells from single cell transcriptomic data

(2020) Zixuan Cang et al.   Nature Communications

Uncovering an Organ’s Molecular Architecture at Single-Cell Resolution by Spatially Resolved Transcriptomics

(2020) Jie Liao et al.   TRENDS IN BIOTECHNOLOGY

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

(2019) Samuel G. Rodriques et al.   SCIENCE

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

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

Navigating the non-coding genome in heart development and Congenital Heart Disease

(2019) Gulrez Chahal et al.   DIFFERENTIATION

Advanced fluorescence microscopy for in vivo imaging of neuronal activity

(2019) Giuseppe Sancataldo et al.   Optica

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

DNA Microscopy: Optics-free Spatio-genetic Imaging by a Stand-Alone Chemical Reaction

(2019) Joshua A. Weinstein et al.   CELL

Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity

(2019) Joshua D. Welch et al.   CELL

MorphoNet: an interactive online morphological browser to explore complex multi-scale data

(2019) Bruno Leggio et al.   Nature Communications

NASC-seq monitors RNA synthesis in single cells

(2019) Gert-Jan Hendriks et al.   Nature Communications

Multiplexed detection of RNA using MERFISH and branched DNA amplification

(2019) Chenglong Xia et al.   Scientific Reports

High-definition spatial transcriptomics for in situ tissue profiling

(2019) Sanja Vickovic 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

A single-cell transcriptome atlas for zebrafish development

(2019) Dylan R. Farnsworth et al.   DEVELOPMENTAL BIOLOGY

Gene expression cartography

(2019) Mor Nitzan et al.   NATURE

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart

(2019) Michaela Asp et al.   CELL

Oct4 regulates the embryonic axis and coordinates exit from pluripotency and germ layer specification in the mouse embryo

(2018) Carla Mulas et al.   DEVELOPMENT

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

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

Standards and Guidelines for Validating Next-Generation Sequencing Bioinformatics Pipelines

(2018) Somak Roy et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Epigenomics in 3D: importance of long-range spreading and specific interactions in epigenomic maintenance

(2018) Daniel Jost et al.   NUCLEIC ACIDS RESEARCH

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

(2018) Xiao Wang et al.   SCIENCE

Systemic Loss and Gain of Chromatin Architecture throughout Zebrafish Development

(2018) Lucas J.T. Kaaij et al.   Cell Reports

Spatially resolved RNA-sequencing of the embryonic heart identifies a role for Wnt/β-catenin signaling in autonomic control of heart rate

(2018) Silja Barbara Burkhard et al.   eLife

ClampFISH detects individual nucleic acid molecules using click chemistry–based amplification

(2018) Sara H Rouhanifard et al.   NATURE BIOTECHNOLOGY

Spatial organization of the somatosensory cortex revealed by osmFISH

(2018) Simone Codeluppi et al.   NATURE METHODS

Single cell RNA-sequencing identifies a metabolic aspect of apoptosis in Rbf mutant

(2018) Majd M. Ariss et al.   Nature Communications

A rapid and robust method for single cell chromatin accessibility profiling

(2018) Xi Chen et al.   Nature Communications

A guide to light-sheet fluorescence microscopy for multiscale imaging

(2017) Rory M Power et al.   NATURE METHODS

Quantifying transcription factor–DNA binding in single cells in vivo with photoactivatable fluorescence correlation spectroscopy

(2017) Ziqing Winston Zhao et al.   Nature Protocols

Spatial transcriptomic analysis of cryosectioned tissue samples with Geo-seq

(2017) Jun Chen et al.   Nature Protocols

TheDrosophilaembryo at single-cell transcriptome resolution

(2017) Nikos Karaiskos et al.   SCIENCE

Identification of a neural crest stem cell niche by Spatial Genomic Analysis

(2017) Antti Lignell et al.   Nature Communications

A Fluorescence in Situ Hybridization Method To Quantify mRNA Translation by Visualizing Ribosome–mRNA Interactions in Single Cells

(2017) Kelly S. Burke et al.   ACS Central Science

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

Comprehensive cellular-resolution atlas of the adult human brain

(2016) Song-Lin Ding et al.   JOURNAL OF COMPARATIVE NEUROLOGY

A comprehensive transcriptional map of primate brain development

(2016) Trygve E. Bakken et al.   NATURE

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

(2016) P. L. Stahl et al.   SCIENCE

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

(2015) Evan Z. Macosko et al.   CELL

The evolution of standards and data management practices in systems biology

(2015) N. J. Stanford et al.   Molecular Systems Biology

Kidney organoids from human iPS cells contain multiple lineages and model human nephrogenesis

(2015) Minoru Takasato et al.   NATURE

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

Whole-animal functional and developmental imaging with isotropic spatial resolution

(2015) Raghav K Chhetri et al.   NATURE METHODS

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

Transcription Factor Activity Mapping of a Tissue-Specific In Vivo Gene Regulatory Network

(2015) Lesley T. MacNeil et al.   Cell Systems

Technical Review:In SituHybridization

(2014) Ellen Jensen   Anatomical Record-Advances in Integrative Anatomy and Evolutionary Biology

Genome-wide RNA Tomography in the Zebrafish Embryo

(2014) Jan Philipp Junker et al.   CELL

Proteogenomics: concepts, applications and computational strategies

(2014) Alexey I Nesvizhskii   NATURE METHODS

Heterogeneous gene expression signatures correspond to distinct lung pathologies and biomarkers of disease severity in idiopathic pulmonary fibrosis

(2014) Daryle J DePianto et al.   THORAX

Ribogenomics: the Science and Knowledge of RNA

(2014) Jiayan Wu et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

The regulation of Hox gene expression during animal development

(2013) Moisés Mallo et al.   DEVELOPMENT

Single-molecule mRNA detection and counting in mammalian tissue

(2013) Anna Lyubimova et al.   Nature Protocols

Sequencing mRNA from Cryo-Sliced Drosophila Embryos to Determine Genome-Wide Spatial Patterns of Gene Expression

(2013) Peter A. Combs et al.   PLoS One

The role of HOX genes in normal hematopoiesis and acute leukemia

(2012) R A Alharbi et al.   LEUKEMIA

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy

(2012) Raju Tomer et al.   NATURE METHODS

5′ end–centered expression profiling using cap-analysis gene expression and next-generation sequencing

(2012) Hazuki Takahashi et al.   Nature Protocols

The Virtual Fly Brain browser and query interface

(2011) N. Milyaev et al.   BIOINFORMATICS

RNAscope

(2011) Fay Wang et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Xenbase: gene expression and improved integration

(2009) Jeff B. Bowes et al.   NUCLEIC ACIDS RESEARCH

WormBase: a comprehensive resource for nematode research

(2009) Todd W. Harris et al.   NUCLEIC ACIDS RESEARCH

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS