snRNA-seq

This paper uses single-nucleus RNA-seq to map transcriptional changes in 5xFAD mouse brains, identifying VIP interneurons as the most vulnerable and showing rolipram's preferential rescue effect through Pde7b/CREB1 signaling.

This study shows that loss of stromal VEGFR2 protects against ischemic AKI by preserving the renal microvasculature through enhanced endothelial function and communication.

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.

The paper identifies age-dependent senescent endothelial cells in adipose tissue using snRNA-Seq and finds ion channel genes as predictive biomarkers.

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.

The paper constructs a multi-scale atlas of cardiomyocyte changes in infarcted hearts, showing partial identity loss without regenerative proliferation and altered intercellular communication.

This study shows that Ctcf deficiency in myofibers leads to genome reprogramming and myopathy by disrupting 3D genome structure and gene regulation.

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 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.

AmbiDose removes ambient RNA contamination in single-cell RNA sequencing by using cell-specific removal budgets and ambient profiles, achieving high specificity for same-species UMIs.

A marker audit finds 97.9% of CEREBRI's 45,051 official 'glutamatergic neuron' cells are not glutamatergic (four-check composite 82.6%), creating false ion-channel and OXPHOS signals; true neurons show acute KCNC3 up-regulation.

The paper shows TFE3 fusions upregulate CD44 and SPP1 in tRCC, with potential therapeutic implications.

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

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.

FORGE is a configurable Nextflow pipeline for snMultiome analysis that integrates snRNA-seq and snATAC-seq data through latent-variable models and enables regulatory network inference and differential testing.

This study uses snRNA-seq to analyze bleomycin-induced lung injury in mice, identifying dynamic changes and rare cell types not well captured by scRNA-seq.

Single-nucleus RNA+ATAC profiling of 32 mice shows asymmetric PRDM9 binding drives asynapsis, pachytene cell loss, aneuploidy and multi-megabase crossover redistribution, tuned by a chromosome 15 locus.

This study creates a transcriptomic atlas of the Syrian hamster preoptic area using snRNA-seq and spatial transcriptomics, comparing seasonal and hibernation states.

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

The paper identifies a conserved molecular marker in the dLGN that correlates with SC connections in mice and tree shrews, and confirms its presence in humans.

The paper shows that CASIN inhibits CDC42, reversing PD-related transcriptional changes and affecting MAPK and PI3K/AKT pathways in an aging mouse model.

This study shows that cellular senescence disrupts liver zonation and hepatocyte function with age by altering gene expression and cell signaling.

The paper describes an optimized nuclei isolation protocol for mouse brain tissues using benchtop centrifugation and magnetic enrichment to improve quality for snRNA-seq.

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

In mice 4 days after kainate-induced status epilepticus, H3K27me3 gains coincide with repression of excitability genes; EZH2 inhibition with UNC1999 lowers seizure threshold acutely and increases chronic seizure frequency.

The paper modifies single-nucleus RNA sequencing protocols to study gene expression in small brain circuits, focusing on the dentate gyrus in a mouse Alzheimer's disease model.

This paper introduces UURNA-seq, a high-throughput single-nucleus RNA sequencing method, and constructs a comprehensive obesity atlas revealing transcriptional changes and metabolic pathway dysregulation.

Reprocessing nine human brain datasets (2,157,582 cells, 156 donors, GW6 to adulthood) under one marker-based taxonomy yields 35 replicable cell types with cell type-specific timing of adult-like maturation.

This study identifies a cardio-intestinal innate immune circuit driven by tricuspid valve regurgitation that promotes heart failure through IL-6-mediated myocardial fibrosis and dysfunction.

The paper uses snRNA-seq to analyze mPOA neurons in dominant and subordinate mice, revealing sex-dependent transcriptomic changes linked to social dominance.