Chromatin accessibility profiling methods
L Minnoye, GK Marinov, T Krausgruber, L Pan… - Nature Reviews …, 2021 - nature.com
Chromatin accessibility, or the physical access to chromatinized DNA, is a widely studied
characteristic of the eukaryotic genome. As active regulatory DNA elements are generally …
characteristic of the eukaryotic genome. As active regulatory DNA elements are generally …
[HTML][HTML] Distinct regulatory programs control the latent regenerative potential of dermal fibroblasts during wound healing
Dermal fibroblasts exhibit considerable heterogeneity during homeostasis and in response
to injury. Defining lineage origins of reparative fibroblasts and regulatory programs that drive …
to injury. Defining lineage origins of reparative fibroblasts and regulatory programs that drive …
[HTML][HTML] Ovarian cancer immunogenicity is governed by a narrow subset of progenitor tissue-resident memory T cells
Despite repeated associations between T cell infiltration and outcome, human ovarian
cancer remains poorly responsive to immunotherapy. We report that the hallmarks of tumor …
cancer remains poorly responsive to immunotherapy. We report that the hallmarks of tumor …
[HTML][HTML] Single-nucleus RNA-sequencing of autosomal dominant Alzheimer disease and risk variant carriers
Genetic studies of Alzheimer disease (AD) have prioritized variants in genes related to the
amyloid cascade, lipid metabolism, and neuroimmune modulation. However, the cell …
amyloid cascade, lipid metabolism, and neuroimmune modulation. However, the cell …
[HTML][HTML] Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM
Single-cell transcriptomic assays have enabled the de novo reconstruction of lineage
differentiation trajectories, along with the characterization of cellular heterogeneity and state …
differentiation trajectories, along with the characterization of cellular heterogeneity and state …
[HTML][HTML] Integrative analyses of single-cell transcriptome and regulome using MAESTRO
Abstract We present Model-based AnalysEs of Transcriptome and RegulOme (MAESTRO),
a comprehensive open-source computational workflow (http://github. com/liulab …
a comprehensive open-source computational workflow (http://github. com/liulab …
VISTA is a checkpoint regulator for naïve T cell quiescence and peripheral tolerance
INTRODUCTION A central tenet of the clonal selection theory (CST), the current cornerstone
of adaptive immunity, states that naïve T cells are selected on the basis of specificity to …
of adaptive immunity, states that naïve T cells are selected on the basis of specificity to …
[HTML][HTML] Single-cell analysis of chromatin accessibility in the adult mouse brain
Recent advances in single-cell technologies have led to the discovery of thousands of brain
cell types; however, our understanding of the gene regulatory programs in these cell types is …
cell types; however, our understanding of the gene regulatory programs in these cell types is …
Multimodal single-cell chromatin analysis with Signac
The recent development of experimental methods for measuring chromatin state at single-
cell resolution has created a need for computational tools capable of analyzing these …
cell resolution has created a need for computational tools capable of analyzing these …
[HTML][HTML] Endothelial reprogramming by disturbed flow revealed by single-cell RNA and chromatin accessibility study
Disturbed flow (d-flow) induces atherosclerosis by regulating gene expression in endothelial
cells (ECs). For further mechanistic understanding, we carried out a single-cell RNA …
cells (ECs). For further mechanistic understanding, we carried out a single-cell RNA …