Single-cell transcriptomic profiling of the aging mouse brain

Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap

(2019) Jüri Reimand et al.   Nature Protocols

Oligodendrocyte Progenitor Cells Become Regionally Diverse and Heterogeneous with Age

(2019) Sonia Olivia Spitzer et al.   NEURON

An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics

(2019) Ilias Angelidis et al.   Nature Communications

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

(2019) Samuel G. Rodriques et al.   SCIENCE

Quiescence Modulates Stem Cell Maintenance and Regenerative Capacity in the Aging Brain

(2019) Georgios Kalamakis et al.   CELL

Single-cell analysis reveals T cell infiltration in old neurogenic niches

(2019) Ben W. Dulken et al.   NATURE

Gene expression hallmarks of cellular ageing

(2018) Stephen Frenk et al.   BIOGERONTOLOGY

Single-Cell Transcriptomics and Fate Mapping of Ependymal Cells Reveals an Absence of Neural Stem Cell Function

(2018) Prajay T. Shah et al.   CELL

A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain

(2018) Kristofer Davie et al.   CELL

Mapping the Mouse Cell Atlas by Microwell-Seq

(2018) Xiaoping Han et al.   CELL

Hallmarks of Brain Aging: Adaptive and Pathological Modification by Metabolic States

(2018) Mark P. Mattson et al.   Cell Metabolism

High-Dimensional Single-Cell Mapping of Central Nervous System Immune Cells Reveals Distinct Myeloid Subsets in Health, Aging, and Disease

(2018) Dunja Mrdjen et al.   IMMUNITY

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing

(2018) Hannah Hochgerner et al.   NATURE NEUROSCIENCE

Normal aging induces A1-like astrocyte reactivity

(2018) Laura E. Clarke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lysosome activation clears aggregates and enhances quiescent neural stem cell activation during aging

(2018) Dena S. Leeman et al.   SCIENCE

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

(2018) Alexander B. Rosenberg et al.   SCIENCE

A transcriptomic atlas of aged human microglia

(2018) Marta Olah et al.   Nature Communications

The Aging Astrocyte Transcriptome from Multiple Regions of the Mouse Brain

(2018) Matthew M. Boisvert et al.   Cell Reports

Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain

(2018) Arpiar Saunders et al.   CELL

Molecular Architecture of the Mouse Nervous System

(2018) Amit Zeisel et al.   CELL

A molecular atlas of cell types and zonation in the brain vasculature

(2018) Michael Vanlandewijck et al.   NATURE

Single-Cell RNA Sequencing of Microglia throughout the Mouse Lifespan and in the Injured Brain Reveals Complex Cell-State Changes

(2018) Timothy R. Hammond et al.   IMMUNITY

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

(2018) et al.   NATURE

Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells

(2018) Ishaan Gupta et al.   NATURE BIOTECHNOLOGY

Single-Cell RNA-Seq of Mouse Olfactory Bulb Reveals Cellular Heterogeneity and Activity-Dependent Molecular Census of Adult-Born Neurons

(2018) Burak Tepe et al.   Cell Reports

Single-Cell Transcriptomics Characterizes Cell Types in the Subventricular Zone and Uncovers Molecular Defects Impairing Adult Neurogenesis

(2018) Vera Zywitza et al.   Cell Reports

Anti-ACSA-2 defines a novel monoclonal antibody for prospective isolation of living neonatal and adult astrocytes

(2017) Christina G. Kantzer et al.   GLIA

BAIAP3, a C2 domain–containing Munc13 protein, controls the fate of dense-core vesicles in neuroendocrine cells

(2017) Xingmin Zhang et al.   JOURNAL OF CELL BIOLOGY

Alterations of the translation apparatus during aging and stress response

(2017) Yulia Gonskikh et al.   MECHANISMS OF AGEING AND DEVELOPMENT

Massively parallel single-nucleus RNA-seq with DroNc-seq

(2017) Naomi Habib et al.   NATURE METHODS

A molecular census of arcuate hypothalamus and median eminence cell types

(2017) John N Campbell et al.   NATURE NEUROSCIENCE

Single-cell analysis of experience-dependent transcriptomic states in the mouse visual cortex

(2017) Sinisa Hrvatin et al.   NATURE NEUROSCIENCE

Detecting Activated Cell Populations Using Single-Cell RNA-Seq

(2017) Ye Emily Wu et al.   NEURON

Aging increases cell-to-cell transcriptional variability upon immune stimulation

(2017) Celia Pilar Martinez-Jimenez et al.   SCIENCE

Nucleolar expansion and elevated protein translation in premature aging

(2017) Abigail Buchwalter et al.   Nature Communications

Major Shifts in Glial Regional Identity Are a Transcriptional Hallmark of Human Brain Aging

(2017) Lilach Soreq et al.   Cell Reports

A Single-Cell RNA Sequencing Study Reveals Cellular and Molecular Dynamics of the Hippocampal Neurogenic Niche

(2017) Benedetta Artegiani et al.   Cell Reports

Temporal Tracking of Microglia Activation in Neurodegeneration at Single-Cell Resolution

(2017) Hansruedi Mathys et al.   Cell Reports

Cystatin C in aging and in Alzheimer’s disease

(2016) Paul M. Mathews et al.   AGEING RESEARCH REVIEWS

A Ribosomal Perspective on Proteostasis and Aging

(2016) Kristan K. Steffen et al.   Cell Metabolism

End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data

(2016) Alan Derr et al.   GENOME RESEARCH

Ageing, neurodegeneration and brain rejuvenation

(2016) Tony Wyss-Coray   NATURE

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

Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system

(2016) S. Marques et al.   SCIENCE

Identification of cell types from single-cell transcriptomes using a novel clustering method

(2015) Chen Xu et al.   BIOINFORMATICS

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

(2015) Evan Z. Macosko et al.   CELL

Single-Cell Transcriptomics Reveals a Population of Dormant Neural Stem Cells that Become Activated upon Brain Injury

(2015) Enric Llorens-Bobadilla et al.   Cell Stem Cell

Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells

(2015) Monika S. Kowalczyk et al.   GENOME RESEARCH

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Cell type– and brain region–resolved mouse brain proteome

(2015) Kirti Sharma et al.   NATURE NEUROSCIENCE

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

(2015) A. Zeisel et al.   SCIENCE

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

The transcriptional landscape of age in human peripheral blood

(2015) Marjolein J. Peters et al.   Nature Communications

Induction of a common microglia gene expression signature by aging and neurodegenerative conditions: a co-expression meta-analysis

(2015) Inge R Holtman et al.   Acta Neuropathologica Communications

Epigenomic Profiling of Young and Aged HSCs Reveals Concerted Changes during Aging that Reinforce Self-Renewal

(2014) Deqiang Sun et al.   Cell Stem Cell

Young blood reverses age-related impairments in cognitive function and synaptic plasticity in mice

(2014) Saul A Villeda et al.   NATURE MEDICINE

Prospective Identification and Purification of Quiescent Adult Neural Stem Cells from Their In Vivo Niche

(2014) Paolo Codega et al.   NEURON

A circadian gene expression atlas in mammals: Implications for biology and medicine

(2014) Ray Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Aging-induced type I interferon response at the choroid plexus negatively affects brain function

(2014) K. Baruch et al.   SCIENCE

Vascular and Neurogenic Rejuvenation of the Aging Mouse Brain by Young Systemic Factors

(2014) L. Katsimpardi et al.   SCIENCE

The Hallmarks of Aging

(2013) Carlos López-Otín et al.   CELL

Human housekeeping genes, revisited

(2013) Eli Eisenberg et al.   TRENDS IN GENETICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Trehalose-enhanced isolation of neuronal sub-types from adult mouse brain

(2012) Alka Saxena et al.   BIOTECHNIQUES

Programmatic features of aging originating in development: aging mechanisms beyond molecular damage?

(2012) João Pedro de Magalhães   FASEB JOURNAL

Endothelial cell expression of haemoglobin α regulates nitric oxide signalling

(2012) Adam C. Straub et al.   NATURE

Chemokine CXCL12 in neurodegenerative diseases: an SOS signal for stem cell-based repair

(2012) Meizhang Li et al.   TRENDS IN NEUROSCIENCES

In Vivo Fate Mapping and Expression Analysis Reveals Molecular Hallmarks of Prospectively Isolated Adult Neural Stem Cells

(2010) Ruth Beckervordersandforth et al.   Cell Stem Cell

Dynamic interaction networks in a hierarchically organized tissue

(2010) Daniel C Kirouac et al.   Molecular Systems Biology

Pathway Commons, a web resource for biological pathway data

(2010) E. G. Cerami et al.   NUCLEIC ACIDS RESEARCH

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Meta-analysis of age-related gene expression profiles identifies common signatures of aging

(2009) João Pedro de Magalhães et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Age-related effects on hippocampal precursor cell subpopulations and neurogenesis

(2009) Josephine Walter et al.   NEUROBIOLOGY OF AGING

iRefIndex: A consolidated protein interaction database with provenance

(2008) Sabry Razick et al.   BMC BIOINFORMATICS

Early age-related changes in adult hippocampal neurogenesis in C57 mice

(2008) Nada M.-B. Ben Abdallah et al.   NEUROBIOLOGY OF AGING

Age-dependent accumulation of lipofuscin in perivascular and subretinal microglia in experimental mice

(2007) Heping Xu et al.   AGING CELL