snRNA-seq

Aging alters the distribution, stability, and transcriptional signature of engram cells

The paper examines how aging affects engram cell distribution, stability, and gene expression in mice, finding altered engram allocation and distinct transcriptional patterns in aged brains.

Sexually Dimorphic Transdifferentiation of Endothelial Cells in Atherosclerosis

This study identifies sex-specific endothelial cell transdifferentiation trajectories in atherosclerosis, revealing distinct fates in males and females and a novel direct EC-to-adipocyte transition.

SUMO2 Deletion Changes Chromatin Accessibility and Enhances Cytotoxic T Cell Activation and Tumor Infiltration

This study shows that deleting SUMO2 in CD8+ T cells enhances their activation, tumor infiltration, and anti-tumor effects by altering chromatin accessibility and gene expression.

A DNA Typewriter records the cell lineage history of a mouse, from zygote to late organogenesis

A prime-editing recorder in one mouse embryo yields a dated, zygote-rooted lineage tree of 1.28M cells at E13.5, enabling clonal dominance, sibling-fate and cell-type coupling analyses.

Spatial Transcriptomics Reveal Developmental Dynamics of the Human Cerebral Cortex and Striatum

This study uses spatial transcriptomics and snRNA-seq to identify 25 forebrain regions and characterize dynamic changes in the human fetal cortex and striatum during late first and early second trimesters.

Single-nucleus transcriptome-wide association study of human brain disorders

This study performs a single-nucleus transcriptome-wide association study to identify gene-trait associations in brain disorders, revealing cell-type-specific genetic regulation and ancestry-specific patterns.

Pirfenidone treatment attenuates fibrosis in autosomal dominant polycystic kidney disease

This study shows pirfenidone reduces fibrosis and improves kidney function in ADPKD by targeting myofibroblast activation and ECM production.

Maternal-fetal immune conflict contributes to male-specific impairments in a mouse model of neurodevelopmental disorders

A poly(I:C) dose at E12.5 causes placental junctional-zone breakdown, amniotic inflammation and developmental defects in a male-only subset of embryos within 24 hours, dependent on maternal IL-6.

Cell-type-specific circadian and light-responsive transcriptional dynamics in adult Drosophila neurons

The paper profiles circadian neuron transcriptomes across timepoints under different light conditions to reveal transcriptional and light-dependent gene regulation in Drosophila.

Amygdalostriatal transition zone neurons encode sustained cue responses to guide defensive behaviors

The paper identifies the amygdalostriatal transition zone (ASt) as a critical structure for encoding sustained cue responses that guide defensive behaviors.

Conserved Neuronal-like and Secretory Programs Define the Spatial Architecture of Gastroenteropancreatic Neuroendocrine Tumors

This study identifies conserved neuronal-like and secretory programs in GEP-NETs and links them to spatial microenvironmental niches and metastatic potential.

The extreme diversity of retinal amacrine cells has deep evolutionary roots

The paper reconstructs the evolutionary origins of retinal amacrine cell diversity using transcriptomic data from 24 vertebrate species, identifying 42 orthologous cell types and suggesting a hybrid precursor origin.

Single-nucleus transcriptome analysis provides new insights into B chromosome elimination in sorghum

The paper uses snRNA-seq to study B chromosome elimination in sorghum embryos, identifying two subpopulations of B-containing nuclei with distinct transcriptional profiles.

Single-nucleus transcriptomics reveal disrupted pathways in the prefrontal cortex of Scn2a-deficient mice

This study uses snRNA-seq to analyze gene expression changes in Scn2a-deficient mice, identifying disrupted pathways in neuronal subtypes of the prefrontal cortex.

Single-nucleus RNA sequencing reveals cell type-specific responses to heat stress in bovine mammary gland

This study uses single-nucleus RNA-seq to analyze cell type-specific responses to heat stress in bovine mammary glands, identifying changes in gene expression, proteostasis, and intercellular communication.

Single nuclear RNA sequencing shows altered microglial and astrocytic functions in post-mortem Parkinson's disease tissue

This study uses snRNA-seq data from post-mortem Parkinson's disease tissue to identify altered molecular pathways in microglia and astrocytes, showing upregulated protein misfolding responses and downregulated inflammation-related genes.

Comparative evaluation of reference genomes and cell-type annotation frameworks for single-nucleus transcriptomic analysis in apple

The paper evaluates reference genomes and cell-type annotation frameworks for snRNA-seq in apple, finding that GDDH13 provides the best mapping and annotation performance, and that combining marker genes with cross-species frameworks improves cell-type identification.

Decoding Lymphangioleiomyomatosis (LAM) Niche Environment via Integrative Analysis of Single Cell Multiomics and Spatial Transcriptomics

This study identifies two distinct LAM subtypes and their microenvironmental interactions using multi-omics and spatial transcriptomics, revealing key regulatory networks and potential therapeutic targets.

Cluster replicability in single-cell and single-nucleus atlases of the mouse brain

The paper evaluates cluster replicability across two mouse brain atlases using single-cell and single-nucleus RNA sequencing, identifying 2009 reciprocally matched clusters with consistent spatial and gene expression patterns.

Decoding stage-specific symbiotic programs in the Rhizophagus irregularis-tomato interaction using single-nucleus transcriptomics

This study uses single-nucleus transcriptomics to identify stage-specific transcriptional programs in tomato roots colonized by Rhizophagus irregularis, revealing key regulatory factors and cellular responses during arbuscular mycorrhizal symbiosis.

Single-cell map of the healthy human immune system across the lifespan reveals unique infant immune signatures

The paper maps the human immune system across the lifespan using scRNA-seq and snATAC-seq, revealing unique infant immune signatures and age-related changes in immune cell populations.

Multimodal analysis identifies pericyte-centered signaling programs altered by sex and brain region in Alzheimer's Disease

The paper identifies sex- and brain region-specific pericyte signaling changes in Alzheimer's Disease using single-nucleus RNA sequencing and spatial transcriptomics.

Social Processing in the Amygdala: Single-Nucleus RNA-Sequencing Reveals Distinct Neuronal Responses to Dominant and Subordinate Cues

This study uses snRNA-seq to identify distinct neuronal responses in the amygdala to dominant and subordinate olfactory cues, revealing specialized glutamatergic and GABAergic populations.

Tracing the stemness and malignant transition in a heritable colorectal cancer Lynch Syndrome by single-cell RNA-seq analysis

This paper uses single-cell RNA sequencing to analyze cellular changes in Lynch Syndrome colorectal cancer, identifying cancer stem cells, immune infiltration, and mutation burden during malignant transition.

Region-Specific Transcriptional Signatures of Brain Aging in the Absence of Neuropathology at the Single-cell Level

This study uses snRNA-seq to analyze age-related transcriptional changes in four brain regions across young and aged individuals, identifying region-specific age-associated genes and biological processes.

Persistent viral infection in the Drosophila fat body is associated with immune activation at the single-cell level

The paper examines transcriptional changes in Drosophila fat body cells during persistent viral infections using snRNA-seq data, revealing immune pathway activation and transposable element dysregulation.

Interleukin-1β Drives Disease Progression in Arrhythmogenic Cardiomyopathy

Human arrhythmogenic cardiomyopathy hearts harbor a lesion niche of POSTN fibroblasts and NLRP3+ inflammatory macrophages; IL-1β neutralization in Dsg2-mutant mice reduced fibrosis, dysfunction, and ventricular ectopy.

Semi-parametric Empirical Bayes Method for Multiplet Detection in snATAC-seq with Probabilistic Multi-omic Integration

SEBULA detects multiplets in snATAC-seq using a semi-parametric empirical Bayes model and integrates with scRNA-seq data, showing superior performance on benchmark datasets.

Multi-omic mapping of Drosophila protein secretomes reveals tissue-specific origins and inter-organ trafficking

The paper maps the Drosophila secretome to identify tissue-specific origins and inter-organ trafficking of 535 blood plasma proteins.

An snRNA-seq aging clock for the fruit fly head sheds light on sex-biased aging

The paper introduces TimeFlies, an snRNA-seq aging clock for Drosophila heads, identifies key lncRNAs as biomarkers, and shows sex-specific aging pathways.