Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

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

(2017) Andrew S. Venteicher et al.   SCIENCE

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics

(2016) Karthik Shekhar et al.   CELL

The late and dual origin of cerebrospinal fluid-contacting neurons in the mouse spinal cord

(2016) Yanina L. Petracca et al.   DEVELOPMENT

RNA-seq analysis of developing olfactory bulb projection neurons

(2016) Yuka Imamura Kawasawa et al.   MOLECULAR AND CELLULAR NEUROSCIENCE

Adult mouse cortical cell taxonomy revealed by single cell transcriptomics

(2016) Bosiljka Tasic et al.   NATURE NEUROSCIENCE

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

(2016) Sheel Shah et al.   NEURON

Gamma motor neurons survive and exacerbate alpha motor neuron degeneration in ALS

(2016) Melanie Lalancette-Hebert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system

(2016) S. Marques et al.   SCIENCE

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

(2016) B. B. Lake et al.   SCIENCE

Microglia development follows a stepwise program to regulate brain homeostasis

(2016) O. Matcovitch-Natan et al.   SCIENCE

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

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

(2016) Naomi Habib et al.   SCIENCE

Nuclear RNA-seq of single neurons reveals molecular signatures of activation

(2016) Benjamin Lacar et al.   Nature Communications

Hipposeq: a comprehensive RNA-seq database of gene expression in hippocampal principal neurons

(2016) Mark S Cembrowski et al.   eLife

Analysis of the brain mural cell transcriptome

(2016) Liqun He et al.   Scientific Reports

The astrocytic transporter SLC7A10 (Asc-1) mediates glycinergic inhibition of spinal cord motor neurons

(2016) Jeffrey T. Ehmsen et al.   Scientific Reports

Starcode: sequence clustering based on all-pairs search

(2015) Eduard Zorita et al.   BIOINFORMATICS

Molecular anatomy of the thalamic complex and the underlying transcription factors

(2015) Andrzej Nagalski et al.   Brain Structure & Function

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

Ascl1 and Helt act combinatorially to specify thalamic neuronal identity by repressing Dlxs activation

(2015) Hobeom Song et al.   DEVELOPMENTAL BIOLOGY

Cerebellar granule cells are predominantly generated by terminal symmetric divisions of granule cell precursors

(2015) Kie Nakashima et al.   DEVELOPMENTAL DYNAMICS

Mitotic Events in Cerebellar Granule Progenitor Cells That Expand Cerebellar Surface Area Are Critical for Normal Cerebellar Cortical Lamination in Mice

(2015) Joshua C. Chang et al.   JOURNAL OF NEUROPATHOLOGY AND EXPERIMENTAL NEUROLOGY

Single-cell messenger RNA sequencing reveals rare intestinal cell types

(2015) Dominic Grün et al.   NATURE

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

(2015) Victoria Moignard et al.   NATURE BIOTECHNOLOGY

Fixed single-cell transcriptomic characterization of human radial glial diversity

(2015) Elliot R Thomsen et al.   NATURE METHODS

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

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

(2015) A. Zeisel et al.   SCIENCE

Foxp2 regulates neuronal differentiation and neuronal subtype specification

(2014) Yi-Chi Chiu et al.   Developmental Neurobiology

Transcription factor Runx1 inhibits proliferation and promotes developmental maturation in a selected population of inner olfactory nerve layer olfactory ensheathing cells

(2014) Manjari Murthy et al.   GENE

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

A High-Resolution Spatiotemporal Atlas of Gene Expression of the Developing Mouse Brain

(2014) Carol L. Thompson et al.   NEURON

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

(2014) D. A. Jaitin et al.   SCIENCE

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

(2013) Alex K. Shalek et al.   NATURE

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

(2013) Simone Picelli et al.   NATURE METHODS

Identification of a unique TGF-β–dependent molecular and functional signature in microglia

(2013) Oleg Butovsky et al.   NATURE NEUROSCIENCE

The microglial sensome revealed by direct RNA sequencing

(2013) Suzanne E Hickman et al.   NATURE NEUROSCIENCE

Review: Could neurotransmitters influence neurogenesis and neurorepair after stroke?

(2013) E. Sánchez-Mendoza et al.   NEUROPATHOLOGY AND APPLIED NEUROBIOLOGY

Mitral and Tufted Cells Are Potential Cellular Targets of Nitration in the Olfactory Bulb of Aged Mice

(2013) Myung Jae Yang et al.   PLoS One

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Prox1 postmitotically defines dentate gyrus cells by specifying granule cell identity over CA3 pyramidal cell fate in the hippocampus

(2012) T. Iwano et al.   DEVELOPMENT

Dopaminergic neurons inhibit striatal output through non-canonical release of GABA

(2012) Nicolas X. Tritsch et al.   NATURE

Bergmann Glial AMPA Receptors Are Required for Fine Motor Coordination

(2012) A. S. Saab et al.   SCIENCE

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

(2012) Tamar Hashimshony et al.   Cell Reports

GRIK4/KA1 protein expression in human brain and correlation with bipolar disorder risk variant status

(2011) Helen M. Knight et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART B-NEUROPSYCHIATRIC GENETICS

Isolation, characterization, and genetic profiling of subpopulations of olfactory ensheathing cells from the olfactory bulb

(2011) Axel Honoré et al.   GLIA

Complement Receptor 2 Is Expressed in Neural Progenitor Cells and Regulates Adult Hippocampal Neurogenesis

(2011) M. Moriyama et al.   JOURNAL OF NEUROSCIENCE

A Transcriptomic Atlas of Mouse Neocortical Layers

(2011) T. Grant Belgard et al.   NEURON

AP-2δ Is a Crucial Transcriptional Regulator of the Posterior Midbrain

(2011) Katrin Hesse et al.   PLoS One

Identification of novel spinal cholinergic genetic subtypes disclose Chodl and Pitx2 as markers for fast motor neurons and partition cells

(2010) Anders Enjin et al.   JOURNAL OF COMPARATIVE NEUROLOGY

LEF1/ -Catenin Complex Regulates Transcription of the Cav3.1 Calcium Channel Gene (Cacna1g) in Thalamic Neurons of the Adult Brain

(2010) M. B. Wisniewska et al.   JOURNAL OF NEUROSCIENCE

Prdm16 promotes stem cell maintenance in multiple tissues, partly by regulating oxidative stress

(2010) Sergei Chuikov et al.   NATURE CELL BIOLOGY

Zbtb20 is essential for the specification of CA1 field identity in the developing hippocampus

(2010) Z. Xie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Prox1 Is Required for Granule Cell Maturation and Intermediate Progenitor Maintenance During Brain Neurogenesis

(2010) Alfonso Lavado et al.   PLOS BIOLOGY

Neurotrophin-3 Is Involved in the Formation of Apical Dendritic Bundles in Cortical Layer 2 of the Rat

(2009) Toshio Miyashita et al.   CEREBRAL CORTEX

Zbtb20-Induced CA1 Pyramidal Neuron Development and Area Enlargement in the Cerebral Midline Cortex of Mice

(2009) Jakob V. Nielsen et al.   CEREBRAL CORTEX

The human brain in numbers: a linearly scaled-up primate brain

(2009) Suzana Herculano-Houzel   Frontiers in Human Neuroscience

Injury-induced mechanical hypersensitivity requires C-low threshold mechanoreceptors

(2009) Rebecca P. Seal et al.   NATURE

Alteration of Glial Fibrillary Acidic Proteins Immunoreactivity in Astrocytes of the Spinal Cord Diabetic Rats

(2008) Zainab H. Afsari et al.   Anatomical Record-Advances in Integrative Anatomy and Evolutionary Biology

Dynamic expression of Dab2 in the mouse embryonic central nervous system

(2008) Kwok-Kuen Cheung et al.   BMC DEVELOPMENTAL BIOLOGY

Identification of a set of genes showing regionally enriched expression in the mouse brain

(2008) Cletus A D'Souza et al.   BMC NEUROSCIENCE

Mechanisms and Functional Implications of Adult Neurogenesis

(2008) Chunmei Zhao et al.   CELL

Application of a Translational Profiling Approach for the Comparative Analysis of CNS Cell Types

(2008) Joseph P. Doyle et al.   CELL

Besides Purkinje cells and granule neurons: an appraisal of the cell biology of the interneurons of the cerebellar cortex

(2008) Karl Schilling et al.   HISTOCHEMISTRY AND CELL BIOLOGY

A Transcriptome Database for Astrocytes, Neurons, and Oligodendrocytes: A New Resource for Understanding Brain Development and Function

(2008) J. D. Cahoy et al.   JOURNAL OF NEUROSCIENCE

Satb2 Regulates Callosal Projection Neuron Identity in the Developing Cerebral Cortex

(2008) Elizabeth A. Alcamo et al.   NEURON

Control of the Reversibility of Cellular Quiescence by the Transcriptional Repressor HES1

(2008) L. Sang et al.   SCIENCE