snRNA-seq

Cell Type- and Tissue-specific Enhancers in Craniofacial Development

The paper identifies 14,000 human craniofacial enhancers across developmental stages and shows 56% are conserved in mice, providing cell type- and stage-specific activity profiles.

Loss of endothelial cell heterogeneity in arteries after obesogenic diet

The paper investigates how an obesogenic diet affects endothelial cell heterogeneity in arteries, finding convergence in transcriptional profiles between mesenteric and adipose arterial endothelial cells in obesity.

Integrative Multi-omic Profiling of Two Human Decedents Receiving Pig Heart Xenografts Reveals Strong Perturbations in Early Immune-Cell and Cellular Metabolism Responses.

The paper analyzes multi-omic data from two pig heart xenografts in human decedents to identify immune and metabolic responses associated with rejection and injury.

Sex-specific Proximal Tubular Cell differentiation pathways identified by single-nucleus RNA

This study identifies sex-specific differentiation pathways in proximal tubular cells using single-nucleus RNA sequencing in mice.

Deciphering deep-sea chemosynthetic symbiosis by single-nucleus RNA-sequencing

This study uses single-nucleus RNA sequencing to create a cell atlas of deep-sea mussel gills, revealing cell types and their roles in supporting chemosynthetic symbiosis and environmental adaptation.

Activity-regulated gene expression across cell types of the mouse hippocampus

The paper identifies cell type-specific activity-regulated gene expression patterns in mouse hippocampal neurons using snRNA-seq and ECS, revealing divergent transcriptomic responses and enriched biological pathways.

Comparative analysis of single-cell and single-nucleus RNA-sequencing in a rabbit model of retinal detachment-related proliferative vitreoretinopathy.

This study compares single-cell and single-nucleus RNA-seq in a rabbit PVR model, finding similar gene expression profiles but differences in cell type capture rates and fibrotic cell representation.

Single-nucleus resolution mapping of the adult C. elegans and its application to elucidate inter- and trans-generational response to alcohol.

This study uses single-nucleus RNA-seq to map the adult C. elegans transcriptome and assess inter- and trans-generational effects of alcohol exposure at cell type resolution.

A comprehensive mouse kidney atlas enables rare cell population characterization and robust marker discovery

The paper builds a comprehensive mouse kidney atlas using scRNA-seq and snRNA-seq data to identify rare cell populations and their markers.

Single-nucleus chromatin accessibility identifies a critical role for TWIST1 in idiopathic pulmonary fibrosis myofibroblast activity

The paper identifies TWIST1 as a critical regulator of myofibroblast activity in IPF using single-nucleus ATAC-seq and scRNA-seq integration.

Cell-attribute aware community detection improves differential abundance testing from single-cell RNA-Seq data

ELVAR improves differential abundance testing in single-cell RNA-Seq by using cell attribute aware clustering to detect DA shifts in aging and disease.

Transcriptomic Analysis Of The Ocular Posterior Segment Completes A Cell Atlas Of The Human Eye

This paper completes a cell atlas of the human eye by analyzing the posterior segment using snRNA-seq, identifying 37 cell types and mapping glaucoma-associated gene expression.

Avoiding false discoveries: Revisiting an Alzheimer's disease snRNA-Seq dataset

The paper reanalyzes an Alzheimer's disease snRNA-Seq dataset using improved methods, finding 549 times fewer differentially expressed genes at an FDR of 0.05.

Slide-tags: scalable, single-nucleus barcoding for multi-modal spatial genomics

Slide-tags enables spatial localization of single nuclei for multi-modal spatial genomics, achieving high-resolution mapping and multiomic profiling in various tissues.

Distinct subpopulations of D1 medium spiny neurons exhibit unique transcriptional responsiveness to cocaine

The paper uses snRNA-seq to identify distinct D1-MSN subpopulations with differential transcriptional responses to cocaine in rats.

Purkinje-Enriched snRNA-seq in SCA7 Cerebellum Reveals Zebrin Identity Loss as a Central Feature of Polyglutamine Ataxias

The paper uses snRNA-seq to study Purkinje cells in SCA7 mice, revealing zebrin-II subtype loss as a key feature of polyglutamine ataxias.

Distinct myofibre domains of the human myotendinous junction revealed by single nucleus RNA-seq

The paper uses single nucleus RNA-seq to identify distinct myonuclei profiles at the human myotendinous junction, revealing gene expression patterns and subclusters associated with specific proteins and fibre types.

A Protocol for Single Nucleus RNAseq from Frozen Skeletal Muscle

This paper presents a method for snRNAseq from frozen human skeletal muscle, enabling analysis of cell types despite tissue degradation and pathological changes.

Molecular Consequences of Peripheral Influenza A Infection on Cell Populations in the Murine Hypothalamus

This study investigates the molecular changes in the murine hypothalamus following Influenza A virus infection using single-nucleus RNA sequencing, revealing transcriptional responses in cell populations and immune-related gene activity shifts.

Molecular and spatial profiling of the paraventricular nucleus of the thalamus

The paper identifies five molecularly distinct PVT neuronal subtypes using snRNA-seq and reveals their spatial organization and connectivity with cortical areas.

Decoding Duchenne muscular dystrophy transcriptome to single nuclei level reveals clinical-genetic correlations

This study uses single nuclei RNA sequencing to analyze DMD muscle samples and identifies clinical-genetic correlations by comparing gene expression profiles across cell populations.

Multimodal decoding of human liver regeneration

This study uses single-nuclei RNA sequencing and spatial profiling to create a single-cell atlas of human liver regeneration, identifying a novel migratory hepatocyte subpopulation and demonstrating that wound closure precedes hepatocyte proliferation.

Neuronal Transcriptome Disruption, Tau Accumulation and Synapse Loss in Alzheimer's Knock-in Mice Require Cellular Prion Protein

This study shows that PrPC is necessary for synapse loss, phospho-tau accumulation, and neuronal gene expression changes in Alzheimer's knock-in mice, suggesting targeting the Aβo-PrPC interaction could prevent these pathologies.

Single nucleus multiomics identifies ZEB1 and MAFB as candidate regulators of Alzheimer's disease-specific cis regulatory elements.

Emergent dynamics of adult stem cell lineages from single nucleus and single cell RNA-Seq of Drosophila testes

The paper provides single nucleus and single cell RNA-seq data from Drosophila testes to study spermatogenesis, identifying rare cell types and developmental transitions.

Bacterial meningitis in the early postnatal mouse studied at single-cell resolution

This study examines the response of meningeal cell types to early postnatal E. coli infection in mice using single nucleus RNA sequencing and other methods, revealing transcriptomic changes and vascular responses.

TCDD dysregulation of lncRNA expression, liver zonation and intercellular communication across the liver lobule

This study uses snRNA-seq to analyze TCDD-induced dysregulation of lncRNAs, liver zonation, and intercellular communication in mouse liver.

Understanding and evaluating ambiguity in single-cell and single-nucleus RNA-sequencing

The paper evaluates a new method for classifying splicing status in single-cell and single-nucleus RNA-seq data, finds it conservative but ambiguous, and introduces new tools to improve classification.

Single nucleus and spatial transcriptomic profiling of human healthy hamstring tendon

This study profiles the transcriptome and spatial distribution of cell types in healthy human hamstring tendon using snRNA-seq and spatial transcriptomics, identifying 12 cell types and highlighting fibroblasts' role in tissue homeostasis.

Single-nucleus co-expression networks of dopaminergic neurons support iron accumulation as a plausible explanation to their vulnerability in Parkinson's disease

The paper introduces scCoExpNets and CovCoExpNets to analyze cell-type specific gene co-expression networks from single-cell RNA-seq data, identifying iron accumulation as a factor in dopaminergic neuron vulnerability in Parkinson's disease.