The promise of spatial transcriptomics for neuroscience in the era of molecular cell typing

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

(2017) Kirsten L. Frieda et al.   NATURE

Neuronal cell-type classification: challenges, opportunities and the path forward

(2017) Hongkui Zeng et al.   NATURE REVIEWS NEUROSCIENCE

Integrating Results across Methodologies Is Essential for Producing Robust Neuronal Taxonomies

(2017) Mark S. Cembrowski et al.   NEURON

Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq

(2017) Andrew S. Venteicher et al.   SCIENCE

Single-Cell RNA-Seq Reveals Hypothalamic Cell Diversity

(2017) Renchao Chen et al.   Cell Reports

Multiplexed Intact-Tissue Transcriptional Analysis at Cellular Resolution

(2016) Emily Lauren Sylwestrak et al.   CELL

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

(2016) Gioele La Manno et al.   CELL

Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics

(2016) Karthik Shekhar et al.   CELL

Single-molecule RNA detection at depth by hybridization chain reaction and tissue hydrogel embedding and clearing

(2016) Sheel Shah et al.   DEVELOPMENT

A comprehensive transcriptional map of primate brain development

(2016) Trygve E. Bakken et al.   NATURE

Anatomy and function of an excitatory network in the visual cortex

(2016) Wei-Chung Allen Lee et al.   NATURE

Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma

(2016) Itay Tirosh et al.   NATURE

Nanoscale imaging of RNA with expansion microscopy

(2016) Fei Chen et al.   NATURE METHODS

Molecular interrogation of hypothalamic organization reveals distinct dopamine neuronal subtypes

(2016) Roman A Romanov et al.   NATURE NEUROSCIENCE

Adult mouse cortical cell taxonomy revealed by single cell transcriptomics

(2016) Bosiljka Tasic et al.   NATURE NEUROSCIENCE

Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons

(2016) Suguna Rani Krishnaswami et al.   Nature Protocols

High-Throughput Mapping of Single-Neuron Projections by Sequencing of Barcoded RNA

(2016) Justus M. Kebschull et al.   NEURON

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

(2016) Sheel Shah et al.   NEURON

smiFISH and FISH-quant – a flexible single RNA detection approach with super-resolution capability

(2016) Nikolay Tsanov et al.   NUCLEIC ACIDS RESEARCH

High-performance multiplexed fluorescence in situ hybridization in culture and tissue with matrix imprinting and clearing

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

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

Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain

(2016) B. B. Lake et al.   SCIENCE

Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons

(2016) Naomi Habib et al.   SCIENCE

Reconstruction and Simulation of Neocortical Microcircuitry

(2015) Henry Markram et al.   CELL

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

(2015) Evan Z. Macosko et al.   CELL

Mapping Synapses by Conjugate Light-Electron Array Tomography

(2015) F. Collman et al.   JOURNAL OF NEUROSCIENCE

Integration of electrophysiological recordings with single-cell RNA-seq data identifies neuronal subtypes

(2015) János Fuzik et al.   NATURE BIOTECHNOLOGY

Electrophysiological, transcriptomic and morphologic profiling of single neurons using Patch-seq

(2015) Cathryn R Cadwell 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

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

(2015) Je Hyuk Lee et al.   Nature Protocols

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

A survey of human brain transcriptome diversity at the single cell level

(2015) Spyros Darmanis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

(2015) A. Zeisel et al.   SCIENCE

Principles of connectivity among morphologically defined cell types in adult neocortex

(2015) X. Jiang et al.   SCIENCE

Expansion microscopy

(2015) F. Chen et al.   SCIENCE

Next-Generation in Situ Hybridization Chain Reaction: Higher Gain, Lower Cost, Greater Durability

(2014) Harry M. T. Choi et al.   ACS Nano

Single-Cell Phenotyping within Transparent Intact Tissue through Whole-Body Clearing

(2014) Bin Yang et al.   CELL

Single-cell in situ RNA profiling by sequential hybridization

(2014) Eric Lubeck et al.   NATURE METHODS

Spatially resolved transcriptomics and beyond

(2014) Nicola Crosetto et al.   NATURE REVIEWS GENETICS

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

(2014) A. P. Patel et al.   SCIENCE

The human splicing code reveals new insights into the genetic determinants of disease

(2014) H. Y. Xiong et al.   SCIENCE

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee et al.   SCIENCE

Genetic Approaches to Neural Circuits in the Mouse

(2013) Z. Josh Huang et al.   Annual Review of Neuroscience

In situ sequencing for RNA analysis in preserved tissue and cells

(2013) Rongqin Ke et al.   NATURE METHODS

Single-chromosome transcriptional profiling reveals chromosomal gene expression regulation

(2013) Marshall J Levesque et al.   NATURE METHODS

Single-molecule mRNA detection and counting in mammalian tissue

(2013) Anna Lyubimova et al.   Nature Protocols

An anatomically comprehensive atlas of the adult human brain transcriptome

(2012) Michael J. Hawrylycz et al.   NATURE

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

(2012) Eric Lubeck et al.   NATURE METHODS

Sequencing the Connectome

(2012) Anthony M. Zador et al.   PLOS BIOLOGY

Spatio-temporal transcriptome of the human brain

(2011) Hyo Jung Kang et al.   NATURE

Temporal dynamics and genetic control of transcription in the human prefrontal cortex

(2011) Carlo Colantuoni et al.   NATURE

Network anatomy and in vivo physiology of visual cortical neurons

(2011) Davi D. Bock et al.   NATURE

Single-molecule transcript counting of stem-cell markers in the mouse intestine

(2011) Shalev Itzkovitz et al.   NATURE CELL BIOLOGY

A Transcriptomic Atlas of Mouse Neocortical Layers

(2011) T. Grant Belgard et al.   NEURON

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS