Cell type
View article: Single-cell data: Antigen-reactive CD4 T cells after SARS-CoV-2 vaccination show divergent phenotypic states with or without restimulation
Single-cell data: Antigen-reactive CD4 T cells after SARS-CoV-2 vaccination show divergent phenotypic states with or without restimulation Open
Understanding T cell fate requires precise knowledge of antigen reactivity. For CD4+ T cells, conventional identification of antigen reactivity by peptide restimulation relies on cellular activation, but thereby also introduces…
View article: Mapping single cell eQTLs by using MatrixEQTL with pseudo-bulk cell type
Mapping single cell eQTLs by using MatrixEQTL with pseudo-bulk cell type Open
These scripts are implementing a two-step approach for detecting eQTL and conditional eQTL analysis for cell type gene expression in single cell RNA seq study. Relevant R packages: SVA (version 3.52.0, DOI: 10.18129/B9.bioc.sva), MatrixEQT…
View article: Supplementary Figures 1-6 from Comparative Tumor Microenvironment Analysis of Primary and Recurrent Ovarian Granulosa Cell Tumors
Supplementary Figures 1-6 from Comparative Tumor Microenvironment Analysis of Primary and Recurrent Ovarian Granulosa Cell Tumors Open
S1. Heatmap of unsupervised hierarchical clustering of the top 1000 most variable genes.S2. Violin plots showing the expression levels of genes previously identified as differentially expressed genes between primary and recurrent tumors in…
View article: Supplementary Table 18 from Disruption of the MYC Superenhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia
Supplementary Table 18 from Disruption of the MYC Superenhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia Open
Single Cell ATAC Cell Type Populations
View article: Supplementary Figure S2 from Single-Cell Evolutionary Analysis Reveals Drivers of Plasticity and Mediators of Chemoresistance in Small Cell Lung Cancer
Supplementary Figure S2 from Single-Cell Evolutionary Analysis Reveals Drivers of Plasticity and Mediators of Chemoresistance in Small Cell Lung Cancer Open
Characterization of cell types isolated from the autochthonous scRNA-seq data.
View article: Supplementary Figures 1 - 12, Supplementary Tables 1-5 from BLEACH&STAIN 15-marker Multiplexed Imaging in 3,098 Human Carcinomas Reveals Six Major PD-L1–driven Immune Phenotypes with Distinct Spatial Orchestration
Supplementary Figures 1 - 12, Supplementary Tables 1-5 from BLEACH&STAIN 15-marker Multiplexed Imaging in 3,098 Human Carcinomas Reveals Six Major PD-L1–driven Immune Phenotypes with Distinct Spatial Orchestration Open
Figure S1a: Representative images of the BLEACH&STAIN 15+1 staining.Figure S1b: BLEACH&STAIN 15+1 validation.Figure S2: Deep learning framework for automated cell type identification.Figure S3: Performance of a Deep Learning-based framewor…
View article: Single-cell transcriptome analysis reveals elongation and ossification characteristics of antlers
Single-cell transcriptome analysis reveals elongation and ossification characteristics of antlers Open
Introduction Antlers are specialized bony appendages in mammals that exhibit the remarkable ability to periodically regenerate from the pedicles and then rapidly elongate to form bone. Previous studies have demonstrated that this intricate…
View article: Topography as a Cue for Driving Osteochondral Unit Regeneration
Topography as a Cue for Driving Osteochondral Unit Regeneration Open
Osteochondral defects are injuries generally affecting to the surface of hyaline cartilage and progressing throughout the tissue until the underlying subchondral bone. The osteochondral unit is a multizonal tissue in which cells within eac…
View article: Supplementary Figure from Characterization of Epigenomic Alterations in HPV16<sup>+</sup> Head and Neck Squamous Cell Carcinomas
Supplementary Figure from Characterization of Epigenomic Alterations in HPV16<sup>+</sup> Head and Neck Squamous Cell Carcinomas Open
Supplementary Figure from Characterization of Epigenomic Alterations in HPV16+ Head and Neck Squamous Cell Carcinomas
View article: Extracellular vesicles from long COVID patients promote RUNX2-mediated cellular stress via dysregulated miR-204 and p53 pathway activation
Extracellular vesicles from long COVID patients promote RUNX2-mediated cellular stress via dysregulated miR-204 and p53 pathway activation Open
Background Subjects with Long COVID, also known as post-acute sequelae of SARS-CoV-2 infection (PASC), experience a wide range of symptoms, including fatigue and respiratory disturbances, affecting their quality of life. Despite the increa…
View article: Single cell and machine learning identify type II pneumocyte-derived biomarkers HN1/OCIAD2/SFTA2 for non-small cell lung cancer prognosis and immune regulation
Single cell and machine learning identify type II pneumocyte-derived biomarkers HN1/OCIAD2/SFTA2 for non-small cell lung cancer prognosis and immune regulation Open
View article: Figure S7 from Application of Novel Breast Biospecimen Cell-Type Adjustment Identifies Shared DNA Methylation Alterations in Breast Tissue and Milk with Breast Cancer–Risk Factors
Figure S7 from Application of Novel Breast Biospecimen Cell-Type Adjustment Identifies Shared DNA Methylation Alterations in Breast Tissue and Milk with Breast Cancer–Risk Factors Open
Distribution of the estimated relative proportion of each component cell type in (A) solid breast tissue (n = 95) and (B) breast milk (n = 48) by subject family history of breast cancer. Component cell types include epithelial cells, endot…
View article: A longitudinal single-nucleus transcriptomic atlas of the bovine placenta reveals dynamic cellular hierarchies and regulatory networks during gestation
A longitudinal single-nucleus transcriptomic atlas of the bovine placenta reveals dynamic cellular hierarchies and regulatory networks during gestation Open
Elucidation of the cellular hierarchy and the underlying regulatory mechanisms for placentas during gestation can tremendously contribute to healthy pregnancy outcomes in mammalian species including cows. Here, we constructed a single-nucl…
View article: Figure 1 from Tissue-Resident Memory T Cells in Pancreatic Ductal Adenocarcinoma Coexpress PD-1 and TIGIT and Functional Inhibition Is Reversible by Dual Antibody Blockade
Figure 1 from Tissue-Resident Memory T Cells in Pancreatic Ductal Adenocarcinoma Coexpress PD-1 and TIGIT and Functional Inhibition Is Reversible by Dual Antibody Blockade Open
High-level cell type atlas of the PDAC tumor microenvironment. A, UMAP embedding of scRNA-seq data from 3 PDAC patient samples overlaid with high level cell type annotation (i). UMAP embedding overlaid with sample identification, an…
View article: From pathogenesis to treatment: the emerging role of ferroptosis in Parkinson’s disease
From pathogenesis to treatment: the emerging role of ferroptosis in Parkinson’s disease Open
Parkinson’s disease (PD), the second most common neurodegenerative disorder worldwide, features gradual loss of dopaminergic neurons in the substantia nigra pars compacta (SNpc) along with pathological α-synuclein (α-syn) aggregation. Rece…
View article: Investigating the neuronal role of the proteasomal ATPase subunit gene PSMC5 in neurodevelopmental proteasomopathies
Investigating the neuronal role of the proteasomal ATPase subunit gene PSMC5 in neurodevelopmental proteasomopathies Open
Neurodevelopmental proteasomopathies are a group of disorders caused by variants in proteasome subunit genes, that disrupt protein homeostasis and brain development through poorly characterized mechanisms. Here, we report 26 distinct varia…
View article: Figure S4 from Application of Novel Breast Biospecimen Cell-Type Adjustment Identifies Shared DNA Methylation Alterations in Breast Tissue and Milk with Breast Cancer–Risk Factors
Figure S4 from Application of Novel Breast Biospecimen Cell-Type Adjustment Identifies Shared DNA Methylation Alterations in Breast Tissue and Milk with Breast Cancer–Risk Factors Open
Correlation between subject BMI (kg/m2) and estimated relative proportions of cells in solid breast tissue (n = 95). Component cell types include epithelial cells, endothelial cells, fibroblasts, adipocytes, B cells, CD4+ T cells, CD8+ T c…
View article: Data from Characterization of Epigenomic Alterations in HPV16<sup>+</sup> Head and Neck Squamous Cell Carcinomas
Data from Characterization of Epigenomic Alterations in HPV16<sup>+</sup> Head and Neck Squamous Cell Carcinomas Open
Background:Epigenetic changes associated with human papillomavirus (HPV)–driven tumors have been described; however, HPV type–specific alterations are less well understood. We sought to compare HPV16-specific methylation changes with those…
View article: Single-cell transcriptomics identifies FOSL1-regulated IGFBP3+ melanoma subtype as a neuro-immunoregulatory signaling hub facilitating tumor progression
Single-cell transcriptomics identifies FOSL1-regulated IGFBP3+ melanoma subtype as a neuro-immunoregulatory signaling hub facilitating tumor progression Open
Background The most aggressive type of skin cancer, melanoma, has a high prevalence of metastases and a poor prognosis. Despite advancements in treatment, drug resistance and tumor microenvironment heterogeneity, especially involving neuro…
View article: NF-κB is a central regulator of hypoxia-induced gene expression
NF-κB is a central regulator of hypoxia-induced gene expression Open
Hypoxia is both a physiological and pathological signal in cells. Changes in gene expression play a critical role in the cellular response to hypoxia, enabling cells to adapt to reduced oxygen availability. These changes are primarily medi…
View article: Figure S6 from Application of Novel Breast Biospecimen Cell-Type Adjustment Identifies Shared DNA Methylation Alterations in Breast Tissue and Milk with Breast Cancer–Risk Factors
Figure S6 from Application of Novel Breast Biospecimen Cell-Type Adjustment Identifies Shared DNA Methylation Alterations in Breast Tissue and Milk with Breast Cancer–Risk Factors Open
Distribution of the estimated relative proportion of each component cell type in (A) solid breast tissue (n = 95) and (B) breast milk (n = 48) by subject parity. Component cell types include epithelial cells, endothelial cells, fibroblasts…
View article: The Role of Radial Astroglia During a Critical Period of Visual System Development
The Role of Radial Astroglia During a Critical Period of Visual System Development Open
The development of the nervous system is carefully coordinated to create a complex network of cells that allow an organism to perceive, interpret, and interact with their environment. One of the strategies employed to create this complex s…
View article: GM-CSF and specific type 2 cytokines induce CD103+ and CD301b+ cell states in cDC1s and cDC2s
GM-CSF and specific type 2 cytokines induce CD103+ and CD301b+ cell states in cDC1s and cDC2s Open
View article: Unravelling the reversion mechanisms of activated hepatic stellate cell properties by extracellular vesicles from mesenchymal stem cells
Unravelling the reversion mechanisms of activated hepatic stellate cell properties by extracellular vesicles from mesenchymal stem cells Open
Hepatic fibrosis is a pathological process characterized by an imbalance between the deposition and degradation of extracellular matrix components. This process is initiated by chronic liver injuries resulting from viral infections, alcoho…
View article: Supplementary Figure from Characterization of Epigenomic Alterations in HPV16<sup>+</sup> Head and Neck Squamous Cell Carcinomas
Supplementary Figure from Characterization of Epigenomic Alterations in HPV16<sup>+</sup> Head and Neck Squamous Cell Carcinomas Open
Supplementary Figure from Characterization of Epigenomic Alterations in HPV16+ Head and Neck Squamous Cell Carcinomas
View article: CTCF-RNA interactions orchestrate cell-specific chromatin loop organization
CTCF-RNA interactions orchestrate cell-specific chromatin loop organization Open
CCCTC-binding factor (CTCF) is essential for chromatin organization. CTCF interacts with endogenous RNAs, and deletion of its ZF1 RNA binding region (∆ZF1) disrupts chromatin loops in mouse embryonic stem cells (ESCs). However, the functio…
View article: Intracellular Osteopontin of Macrophages Promotes Carotid Plaques Formation by Inducing Foam Cells and Releasing Proinflammatory Cytokines
Intracellular Osteopontin of Macrophages Promotes Carotid Plaques Formation by Inducing Foam Cells and Releasing Proinflammatory Cytokines Open
Background Atherosclerotic carotid plaque is the main cause of cerebrovascular diseases, but the molecular and cellular mechanisms involving in carotid plaque formation have not yet been fully uncovered. Methods Single cell RNA sequencing …
View article: DiCoLo: Integration-free and cluster-free detection of localized differential gene co-expression in single-cell data
DiCoLo: Integration-free and cluster-free detection of localized differential gene co-expression in single-cell data Open
Detecting changes in gene coordination patterns between biological conditions and identifying the cell populations in which these changes occur are key challenges in single-cell analysis. Existing approaches often compare gene co-expressio…
View article: Endothelial senescence drives intrinsic skin aging via the neuroimmune CGRP-mast cell axis in mice
Endothelial senescence drives intrinsic skin aging via the neuroimmune CGRP-mast cell axis in mice Open
View article: Impact of vascular density on pancreatic islet viability: a computational study
Impact of vascular density on pancreatic islet viability: a computational study Open
Introduction Pancreatic islets are densely vascularized clusters of cells that secrete insulin, glucagon, and somatostatin, hormones essential to glucose metabolism. The viability and function of islet cells rely on the availability of oxy…