snRNA-seq

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.

Disagreement between demultiplexing methods reveals structured cell quality gradients in multiplexed single-cell data

This paper introduces Split-flow, a pipeline that uses concordance between demultiplexing methods to classify cell quality in multiplexed single-cell data, revealing structured quality gradients.

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.

Gene regulatory networks define human airway epithelial cell types and their distinct responses to type I interferon

The paper characterizes gene regulatory networks in human airway epithelial cells and identifies cell type-specific responses to type I interferon.

Dogcatcher2: Improved statistical detection of transcriptional readthrough and repetitive element analysis across sequencing platforms

Dogcatcher2 improves detection of transcriptional readthrough and identifies Alu element enrichment in DoG regions across sequencing platforms.

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.

Single nucleus transcriptome analysis of Arabidopsis thaliana roots infected with Phytophthora. capsici

The paper uses snRNA-seq to analyze Arabidopsis root cell responses to P. capsici infection, identifying transcriptional changes and hormone-related pathways in different cell types.

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.

Leaves in Transition: Single nuclei RNA sequencing provides insights into sorghums juvenile and adult phases

This study uses snRNA-seq to analyze sorghum leaf development, revealing that trichomes and bulliform cells exist in both juvenile and adult stages with stage-specific gene expression patterns.

An integrated single cell and spatial omics atlas of human prenatal development

Human Developmental Cell Atlas integrates ~4.6 million cells/nuclei from 4-22 post-conception weeks into 454 refined cell types and maps 114 spatial niches across 6PCW whole-embryo sections.

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.

Rapid Remodeling of Human White Adipose Tissue Following Bariatric Surgery

This study identifies rapid remodeling of human subcutaneous white adipose tissue within one month after bariatric surgery using snRNA-seq, revealing changes in adipocyte populations and transcriptional dynamics.

The Alzheimer's disease neurodegenerative cascade reconstructed in human L2/3 excitatory neurons

The paper reconstructs the Alzheimer's disease neurodegenerative cascade in human L2/3 excitatory neurons using single-nucleus RNA sequencing data from multiple datasets.

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.

Experimental and Computational Methods for Allelic Imbalance Analysis from Single-Nucleus RNA-seq Data

This paper develops computational tools for allelic imbalance analysis using single-nucleus RNA-seq and demonstrates their application in a Parkinson's disease cohort.

A region-delineated snRNA-seq atlas of mouse spinal cord across lifespan resolves the interaction of normative aging programs with SOD1-G93A ALS

This study creates a lifespan snRNA-seq atlas of mouse spinal cord, revealing how aging and SOD1-G93A ALS interact regionally and cell-type specifically.

Benchmarking ambient RNA removal across droplet and well-plate platforms reveals artificial count generation as a critical failure mode of scAR and CellClear

The paper benchmarks ambient RNA removal tools across different platforms, finding that scAR and CellClear generate artificial counts and cell types, while CellBender and SoupX perform reliably.

Cell-type-resolved transcriptional reprogramming in resistant soybean roots reveals cambial activation and early syncytium initiation upon nematode infection

This paper uses snRNA-seq to analyze soybean root responses to nematode infection, identifying vascular cambium as the origin of syncytia and revealing coordinated cell-type-specific defense mechanisms.

Identification and Characterization of Neoplastic Cells in Keratin-Positive Giant Cell-Rich Tumors

This paper uses single-nuclei RNA sequencing and spatial transcriptomics to characterize KPGCT, showing neoplastic cells express HMGA2::NCOR2 fusions and activate the hippo pathway, driving CSF1 production and macrophage recruitment.

Integrated single-cell and spatial multiomic analysis reveals widespread reactivation of developmental programs in diseased human hearts

The paper integrates single-cell and spatial multiomic data to show widespread reactivation of developmental programs in diseased human hearts, with insights into transcriptional factors and localized fetal reactivation.

Single-Nuclei Transcriptomic Characterization of APOE4-Associated Alzheimer's Disease

This study characterizes cell-type-specific transcriptomes across APOE genotypes in Alzheimer's disease using single-nuclei RNA sequencing, revealing APOE4-associated changes in excitatory neurons and microglia.

Spatial multi-omics unveils the monoclonal origin, neuroendocrine plasticity, and microenvironment niches in combined small cell lung cancer

This study uses spatial multi-omics to show cSCLC has a monoclonal origin, lineage plasticity, and distinct microenvironment niches, leading to a new diagnostic assay.

Integrating single-cell and single-nucleus datasets improves bulk RNA-seq deconvolution

This study improves bulk RNA-seq deconvolution by integrating single-cell and single-nucleus datasets through filtering and transformation strategies, achieving near-scRNA-seq accuracy.

Low Transcriptional Complexity Cells Represent a Conserved, Aging-Relevant Maintenance State Overlooked by Single-Cell Transcriptomics

The paper identifies a previously unrecognized cellular state with low transcriptomic complexity in mature tissues, linked to aging and cellular maintenance.

Advancing Nuclei Isolation from Frozen Human Heart for Single-Nucleus RNA Sequencing Applications

This paper presents a standardized nuclei isolation protocol for frozen human heart tissue and a downstream snRNA-seq analysis pipeline, improving yield and consistency in cardiac single-nucleus transcriptomic studies.

SingleBrain: A Meta-Analysis of Single-Nucleus eQTLs Linking Genetic Risk to Brain Disorders

SingleBrain integrates snRNA-seq and genotype data to map cis-eQTLs across brain cell types, identifying novel disease-associated genes and causal variants.

Single Cell Transcriptomics of Refractory Epilepsy patients in Colombia

This study analyzes single-cell transcriptomics data from five pediatric refractory epilepsy patients in Colombia, identifying glia-driven dysregulation and neuroinflammatory processes.

Multimodality Molecular Profiling Nominates Targetable Mechanisms in Progressive RV Dysfunction

This study uses multi-omics profiling to identify molecular mechanisms contributing to progressive right ventricular dysfunction in pigs.

Fixative eXchange (FX)-seq: Scalable Single-nucleus RNA Sequencing Analysis of PFA-fixed or FFPE Tissue

FX-seq improves snRNA-seq from FFPE and PFA-fixed tissues by removing crosslinks and preventing RNA leakage, enabling analysis of 321,710 nuclei from mouse and human samples.