Single-cell chromatin state analysis with Signac

2021/11/01 by Tim Stuart, Avi Srivastava, Shaista Madad +2 · 59 citations
Biochemistry, Genetics and Molecular Biology · #Gene Regulatory Network Analysis #Genomics and Chromatin Dynamics #Single-cell and spatial transcriptomics

paper · doi:10.1038/s41592-021-01282-5

crossref issued 2021/11/01 · crossref published 2021/11/01 · crossref published-online 2021/11/01 · crossref published-print 2021/11/01 · openalex publication_date 2021/11/01 · crossref created 2021/11/01 · crossref deposited 2023/02/07 · openalex created_date 2025/10/10 · crossref indexed 2026/07/29 · openalex updated_date 2026/08/02

Citations

• Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin
• ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis
• The GTEx Consortium atlas of genetic regulatory effects across human tissues
• Integrated analysis of multimodal single-cell data

Cited by

• Human haematopoietic stem cells remember inflammatory stress
• Disrupted transcriptional networks regulated by CHD1L during neurodevelopment underlie the mirrored neuroanatomical and growth phenotypes of the 1q21.1 copy number variant
• Charting the transition from in vitro gliogenesis to the in vivo maturation of human glial progenitor cells transplanted into the hypomyelinated mouse brain
• CIRCE: a scalable Python package to predict cis-regulatory DNA interactions from single-cell chromatin accessibility data
• Evolutionary Process Underlying Receptor Gene Expansion and Cellular Divergence of Olfactory Sensory Neurons in Honeybees
• Distinct Gene Regulatory Dynamics Drive Skeletogenic Cell Fate Convergence During Vertebrate Embryogenesis
• Gene regulatory network determinants of rapid recall in human memory CD4+ T cells
• A hitchhiker's guide to single‐cell epigenomics: Methods and applications for cancer research
• Transcription and potential functions of a novel XIST isoform in male peripheral glia
• Single-cell spatiotemporal transcriptomic and chromatin accessibility profiling in developing postnatal human and macaque prefrontal cortex
• Chromatin Accessibility Shapes Developmental-Specific Lineage Plasticity in Hematopoiesis
• Distinct transcriptomic and epigenomic responses of mature oligodendrocytes during disease progression in a mouse model of multiple sclerosis
• Chromatin landscape and epigenetic heterogeneity of acute myeloid leukaemia
• Multiomic analysis of human kidney disease identifies a tractable inflammatory and pro-fibrotic tubular cell phenotype
• Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays
• Stage-specific CAR-mediated signaling generates naïve-like, TCR-null CAR T cells from induced pluripotent stem cells
• A hormetic transcriptional program coregulates invasion, proliferation and dormancy to define metastatic potential
• Gene regulatory landscape dissected by single-cell four-omics sequencing
• Chromatin-mediated anticipatory control of type I interferon production in plasmacytoid dendritic cells
• Human vascularized macrophage-islet organoids to model immune-mediated pancreatic β cell pyroptosis upon viral infection
• MoRE-GNN: Multi-omics Data Integration with a Heterogeneous Graph Autoencoder
• A rare PRIMER cell state in plant immunity
• Frizzled5 controls murine intestinal epithelial cell plasticity through organization of chromatin accessibility
• Lifestyle intervention is associated with attenuation of ER stress/inflammation and enhancement of naive immune cell identity in older adults with metabolic disease
• Cognitive rejuvenation through partial reprogramming of engram cells
• scTAM-seq enables targeted high-confidence analysis of DNA methylation in single cells
• Longitudinal single-cell multiomic atlas of high-risk neuroblastoma reveals chemotherapy-induced tumor microenvironment rewiring
• Direct specification of lymphatic endothelium from mesenchymal progenitors
• Cortical development dynamics across autism spectrum disorder mouse models
• RegVelo: Gene-regulatory-informed dynamics of single cells
• Cell-type- and locus-specific epigenetic editing of memory expression
• Single-nucleus multi-omics identifies shared and distinct pathways in Pick’s and Alzheimer’s disease
• scMitoMut for calling mitochondrial lineage-related mutations in single cells
• RBM39 degrader invigorates innate immunity to eradicate neuroblastoma despite cancer cell plasticity
• Facilitate integrated analysis of single cell multiomic data by binarizing gene expression values
• Tbx1 stabilizes differentiation of the cardiopharyngeal mesoderm and drives morphogenesis in the pharyngeal apparatus
• Kidney multiome-based genetic scorecard reveals convergent coding and regulatory variants
• Generalization of the sci-L3 method to achieve high-throughput linear amplification for replication template strand sequencing, genome conformation capture, and the joint profiling of RNA and chromatin accessibility
• Longitudinal scRNA-seq analysis in mouse and human informs optimization of rapid mouse astrocyte differentiation protocols
• Intelligent label-free droplet microfluidic sorting system for single-cell encapsulation and morphology-guided screening
• Single-nucleus multiome shows motor neuron glutamate overactivation in amyotrophic lateral sclerosis
• Single-cell multiomics reveal divergent effects of DNMT3A- and TET2-mutant clonal hematopoiesis in inflammatory response
• Single-cell multiome profiling reveals neuronal bias of modulatory role of MeCP2 phosphorylation
• Defining the regulatory logic of breast cancer using single-cell epigenetic and transcriptome profiling
• Repurposing of a gill gene regulatory program for outer-ear evolution
• Integrating polygenic signals and single-cell multiomics identifies cell-type-specific regulomes critical for immune- and aging-related diseases
• Meningeal-derived retinoic acid regulates neurogenesis via suppression of Notch and Sox2
• Molecular and genetic insights into human ovarian aging from single-nuclei multi-omics analyses
• A scalable Tn5-based method for genome-wide DNA methylation profiling in development and disease
• Single-cell multiomics of neuron activation reveals context-specific genetics of brain disorders
• A single-cell multiomic analysis identifies molecular and gene-regulatory mechanisms dysregulated in developing Down syndrome neocortex
• Multimodal analyses of early, untreated systemic sclerosis skin identify a proinflammatory vascular niche of macrophage-fibroblast signaling
• Single cell multi-omics reveals rare biosynthetic cell types in the medicinal tree Camptotheca acuminata
• Tbx1 stabilizes differentiation of the cardiopharyngeal mesoderm and drives morphogenesis in the pharyngeal apparatus
• Th1-poised naive CD4 T cell subpopulation reflects anti-tumor immunity and autoimmune disease
• Ursa: A Comprehensive Multiomics Toolbox for High-Throughput Single-Cell Analysis
• FOXR2 Targets LHX6+/DLX+ Neural Lineages to Drive Central Nervous System Neuroblastoma
• ChromFound: Towards A Universal Foundation Model for Single-Cell Chromatin Accessibility Data
• Time-resolved single-cell and spatial gene regulatory atlas of plants under pathogen attack