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

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

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

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

Single-cell spatial transcriptomic analysis reveals common and divergent features of developing postnatal granule cerebellar cells and medulloblastoma

(2021) Wenqin Luo et al.   BMC BIOLOGY

Embryo-scale, single-cell spatial transcriptomics

(2021) Sanjay R. Srivatsan et al.   SCIENCE

An atlas of dynamic chromatin landscapes in mouse fetal development

(2020) David U. Gorkin et al.   NATURE

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

(2020) Sai Ma et al.   CELL

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

(2020) Yang Liu et al.   CELL

Efficient chromatin accessibility mapping in situ by nucleosome-tethered tagmentation

(2020) Steven Henikoff et al.   eLife

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

High-throughput single-cell ChIP-seq identifies heterogeneity of chromatin states in breast cancer

(2019) Kevin Grosselin et al.   NATURE GENETICS

CUT&Tag for efficient epigenomic profiling of small samples and single cells

(2019) Hatice S. Kaya-Okur et al.   Nature Communications

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

Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain

(2017) Blue B Lake et al.   NATURE BIOTECHNOLOGY

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

(2017) Alicia N Schep et al.   NATURE METHODS

Single-cell epigenomics: Recording the past and predicting the future

(2017) Gavin Kelsey et al.   SCIENCE

Cell freezing protocol suitable for ATAC-Seq on motor neurons derived from human induced pluripotent stem cells

(2016) Pamela Milani et al.   Scientific Reports

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

Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state

(2015) Assaf Rotem et al.   NATURE BIOTECHNOLOGY

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Ezh2, the histone methyltransferase of PRC2, regulates the balance between self-renewal and differentiation in the cerebral cortex

(2010) J. D. Pereira et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Characterization of Nkx6-2-Derived Neocortical Interneuron Lineages

(2009) Vitor H. Sousa et al.   CEREBRAL CORTEX

Polycomb Limits the Neurogenic Competence of Neural Precursor Cells to Promote Astrogenic Fate Transition

(2009) Yusuke Hirabayashi et al.   NEURON

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY