Spatial epigenome–transcriptome co-profiling of mammalian tissues

Integration of whole transcriptome spatial profiling with protein markers

(2023) Nir Ben-Chetrit et al.   NATURE BIOTECHNOLOGY

Epigenomic priming of immune genes implicates oligodendroglia in multiple sclerosis susceptibility

(2022) Mandy Meijer et al.   NEURON

Spatial-CUT&Tag: Spatially resolved chromatin modification profiling at the cellular level

(2022) Yanxiang Deng et al.   SCIENCE

Expanding the mutation and phenotype spectrum of MYH3-associated skeletal disorders

(2022) Sen Zhao et al.   npj Genomic Medicine

Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays

(2022) Ao Chen et al.   CELL

NEAT-seq: simultaneous profiling of intra-nuclear proteins, chromatin accessibility and gene expression in single cells

(2022) Amy F. Chen et al.   NATURE METHODS

Spatial profiling of chromatin accessibility in mouse and human tissues

(2022) Yanxiang Deng et al.   NATURE

Neuronal splicing regulator RBFOX3 mediates seizures via regulating Vamp1 expression preferentially in NPY-expressing GABAergic neurons

(2022) De-Fong Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conservation and divergence of cortical cell organization in human and mouse revealed by MERFISH

(2022) Rongxin Fang et al.   SCIENCE

Spatially resolved epigenomic profiling of single cells in complex tissues

(2022) Tian Lu et al.   CELL

Belayer: Modeling discrete and continuous spatial variation in gene expression from spatially resolved transcriptomics

(2022) Cong Ma et al.   Cell Systems

Polony gels enable amplifiable DNA stamping and spatial transcriptomics of chronic pain

(2022) Xiaonan Fu et al.   CELL

Medin co-aggregates with vascular amyloid-β in Alzheimer’s disease

(2022) Jessica Wagner et al.   NATURE

Multimodal chromatin profiling using nanobody-based single-cell CUT&Tag

(2022) Marek Bartosovic et al.   NATURE BIOTECHNOLOGY

Integrated spatial genomics reveals global architecture of single nuclei

(2021) Yodai Takei et al.   NATURE

ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis

(2021) Jeffrey M. Granja et al.   NATURE GENETICS

Joint profiling of histone modifications and transcriptome in single cells from mouse brain

(2021) Chenxu Zhu et al.   NATURE METHODS

Spatially mapped single-cell chromatin accessibility

(2021) Casey A. Thornton et al.   Nature Communications

Single-cell CUT&Tag analysis of chromatin modifications in differentiation and tumor progression

(2021) Steven J. Wu et al.   NATURE BIOTECHNOLOGY

Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues

(2021) Marek Bartosovic et al.   NATURE BIOTECHNOLOGY

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

Microscopic examination of spatial transcriptome using Seq-Scope

(2021) Chun-Seok Cho et al.   CELL

Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution

(2021) Alexandro E. Trevino et al.   CELL

An atlas of gene regulatory elements in adult mouse cerebrum

(2021) Yang Eric Li et al.   NATURE

Genetic and epigenetic coordination of cortical interneuron development

(2021) Kathryn C. Allaway et al.   NATURE

Single-cell chromatin state analysis with Signac

(2021) Tim Stuart et al.   NATURE METHODS

A MYT1L syndrome mouse model recapitulates patient phenotypes and reveals altered brain development due to disrupted neuronal maturation

(2021) Jiayang Chen et al.   NEURON

Transcriptomic taxonomy and neurogenic trajectories of adult human, macaque, and pig hippocampal and entorhinal cells

(2021) Daniel Franjic et al.   NEURON

Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin

(2020) Sai Ma et al.   CELL

Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer’s and Parkinson’s diseases

(2020) M. Ryan Corces et al.   NATURE GENETICS

High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue

(2020) Yang Liu et al.   CELL

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell

(2019) Song Chen et al.   NATURE BIOTECHNOLOGY

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Molecular Architecture of the Mouse Nervous System

(2018) Amit Zeisel et al.   CELL

Transcriptional Convergence of Oligodendrocyte Lineage Progenitors during Development

(2018) Sueli Marques et al.   DEVELOPMENTAL CELL

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Joint profiling of chromatin accessibility and gene expression in thousands of single cells

(2018) Junyue Cao et al.   SCIENCE

Shared and distinct transcriptomic cell types across neocortical areas

(2018) Bosiljka Tasic et al.   NATURE

Six3 and Six6 Are Jointly Required for the Maintenance of Multipotent Retinal Progenitors through Both Positive and Negative Regulation

(2018) Raven Diacou et al.   Cell Reports

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

(2017) Alicia N Schep et al.   NATURE METHODS

Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system

(2016) S. Marques et al.   SCIENCE

Major depressive disorder

(2016) Christian Otte et al.   Nature Reviews Disease Primers

SOX2 primes the epigenetic landscape in neural precursors enabling proper gene activation during hippocampal neurogenesis

(2015) Alejandro Amador-Arjona et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Sox2 and Pax6 maintain the proliferative and developmental potential of gliogenic neural stem cells In vitro

(2011) Sandra Gómez-López et al.   GLIA

Phosphorylation of microtubule-associated protein tau by AMPK-related kinases

(2011) Hirotaka Yoshida et al.   JOURNAL OF NEUROCHEMISTRY

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

The Glial Nature of Embryonic and Adult Neural Stem Cells

(2009) Arnold Kriegstein et al.   Annual Review of Neuroscience

Novel SOX2 partner-factor domain mutation in a four-generation family

(2009) Marija Mihelec et al.   EUROPEAN JOURNAL OF HUMAN GENETICS