snRNA-seq

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.

Comparison of different computational frameworks for metabolic modeling from single-cell transcriptomics data in glioblastoma

The paper compares three computational methods to infer metabolism from single-cell transcriptomics data in glioblastoma, finding tumor-associated macrophages as metabolically dominant.

Comparative analysis of nuclei isolation methods for brain single-nucleus RNA sequencing

This study compares three nuclei isolation methods for brain snRNA-seq, finding protocol-dependent differences in cell type proportions, transcriptional homogeneity, and RNA contamination levels.

Comprehensive cellular analysis with single-nucleus RNA-seq of archived PAXgene whole blood samples

The paper develops a method for single-nucleus RNA-seq of archived PAXgene whole blood samples, achieving high nuclei yields and unbiased cell-type representation through optimized isolation and globin depletion.

Asynchronous Transitions from Hepatoblastoma to Carcinoma in High-Risk Pediatric Tumors

The paper characterizes hepatoblastoma with carcinoma features (HBCs) using multi-omics data, revealing their heterogeneous composition, worse outcomes, and origin from arrested HB cells due to WNT signaling.

Single-cell transcriptomics reveals the impact of sex and age in the healthy human liver

This study uses single-cell RNA sequencing to analyze how sex and age affect gene expression and cellular interactions in healthy human liver cells.

Single-nucleus transcriptional and chromatin accessibility analyses of maturing mouse Achilles tendon uncover the molecular landscape of tendon stem/progenitor cells

This study identifies CD55 and CD248 as novel surface markers for tendon stem/progenitor cells using single-cell and single-nucleus sequencing in mouse Achilles tendon.

Precision-Based Filtering Facilitates Integration of Conventional and Single-Nucleus Transcriptomes to Identify Time- and Temperature-Sensitive Cell Populations

The paper introduces a coefficient of variation-based filter for RNAseq data to retain low-variation genes, enabling better identification of cell populations in Arabidopsis snRNAseq data.

Machine Learning Identifies Distinct Treg-Mediated Remodeling in HFpEF Hearts Treated with Neonatal Mesenchymal Stem Cells and Their Secretome

This study uses machine learning to identify Treg-mediated mechanisms by which nMSCs and their secretome improve diastolic function in HFpEF.

Identification of an epigenetically and phenotypically distinct peritumoral glioblastoma cell population linked to inferior patient outcome

The paper identifies a distinct peritumoral glioblastoma cell population with unique epigenetic and phenotypic features associated with poor patient outcomes.

4D multimodal wound healing atlas reveals organ-level controls of repair phase transitions

The paper presents OWHA, a 4D multimodal atlas of wound healing in mice, revealing a conserved Basal IV/SEMA3C circuit that coordinates repair, and shows its disruption in diabetic wounds.

Ablation of Prdm16 and beige fat causes vascular remodeling and elevated blood pressure

Adipocyte-specific deletion of Prdm16 ablates beige fat identity, derepresses the secreted enzyme Qsox1, and induces vascular fibrosis, angiotensin II hyperreactivity, and elevated blood pressure in mice.

Single cell-resolved transcriptional dynamics of human subcutaneous adipose tissue during lifestyle- and bariatric surgery-induced weight loss

This study examines transcriptional changes in human adipose tissue during weight loss from lifestyle and bariatric surgery, showing significant remodeling and reduced inflammation.

Factorization of Alzheimer's disease genetic risk influences allow patient stratification, predicting disease onset, cognitive decline, and cell-type specific responses

The paper uses matrix factorization to analyze genetic risk variants in Alzheimer's disease, identifying factors that predict disease onset, cognitive decline, and cell-type specific responses.

Identification of distinct functions of GLIS3 in β-cell generation critical to prevention of neonatal diabetes

This study identifies two distinct roles of GLIS3 in β-cell development, showing its critical function in bipotent progenitor generation and preβ-to-β cell differentiation, contributing to neonatal diabetes in GLIS3-deficient mice.

Coordinated IFN-γ/TNF Axis Drives Selective Loss of Activated Enteric Glia in Inflammatory Bowel Diseases

This study identifies IBD type-associated EGC activation signatures and reveals TNF/IFN-γ-driven necroptosis of activated enteric glia in inflammatory bowel diseases.

A streamlined and comprehensive protocol for the generation and multi-omic analysis of human monocyte-derived macrophages

This paper presents a streamlined protocol for generating and multi-omic analyzing human macrophages from frozen PBMCs, showing their phenotypic stability and compatibility with snRNA-seq.

Central T3 deprivation disturbs cortical cilia formation, oligodendrocyte lineage and neuronal cell-cell-communication in a MCT8/OATP1C1 deficient Allan-Herndon-Dudley Syndrome mouse model

This study uses single nucleus RNA sequencing to analyze cortical and striatal development in a mouse model of Allan-Herndon-Dudley Syndrome, identifying disruptions in oligodendrocyte lineage, cell-cell communication, and cilia formation.

Infusible Extracellular Matrix Biomaterial Enhances Cell-Specific Pro-Repair Responses Following Acute Myocardial Infarction

This study uses snRNAseq to identify cell-specific pro-repair responses induced by an infusible ECM biomaterial after myocardial infarction.

A poly(A) isoform-aware single-cell and spatial atlas defines fibroblast niches in the human bladder

The paper creates a poly(A) isoform-aware single-cell and spatial atlas of the human bladder, identifying fibroblast niches and their spatial relationships.

Tri-AD: Hippocampal cell-type-specific responses to age, sex and APOE genotype

The paper investigates how age, sex, and APOE genotype affect hippocampal cell-type-specific gene expression and communication in mice, revealing sex-divergent effects of APOE4.

RamanOmics Decodes Spatial Vibrational-Molecular Architecture and Rewiring in Aging and Repair

RamanOmics integrates snRNA-seq, spatial transcriptomics, and Raman imaging to map spatial biochemical and molecular changes in aging and repair, identifying senescent cell signatures and their functional roles.

NVUAtlas: A Comprehensive Single-Nucleus RNA-Seq Resource for the Human Neurovascular Unit in Alzheimer's Disease

The paper constructs a comprehensive single-nucleus RNA-seq atlas of the human neurovascular unit in Alzheimer's disease, revealing sex-specific vascular dysfunctions and disrupted intercellular communication.

Single Cell Landscape of Sex-specific Drivers of Alzheimers Disease

This study identifies sex-specific gene expression associations with Alzheimer's disease neuropathology and cognitive decline using single-nucleus RNA sequencing from human brain tissue.

snRNA-seq of Huntington's disease mice reveals vulnerability profiles of cortical cell types

This study uses snRNA-seq to analyze cortical cell types in HD mice, revealing differential vulnerability and identifying ER-phagy as a protective pathway in HD.

Chrom-Sig: de-noising 1-dimensional genomic profiles by signal processing methods

Chrom-Sig de-noises 1-dimensional genomic coverage tracks using signal processing to separate signal from noise, validated across multiple datasets.

High cell-type specificity of eQTLs revealed by single-nucleus analyses of brain and blood

The paper identifies highly cell-type-specific eQTLs using snRNA-seq data from brain and blood, showing that bulk analyses overestimate eQTL agreement.

A Multi-omic Atlas of Human Choroid Plexus in Alzheimer's Disease

This study creates a multi-omic atlas of the choroid plexus in Alzheimer's disease, identifying disease-associated cell state transitions and functional impairments.

APOE E4 Alzheimer's Risk Converges on an Oligodendrocyte Subtype in the Human Entorhinal Cortex

The paper investigates how APOE genotype affects gene expression in the human entorhinal cortex, identifying an oligodendrocyte subtype as a potential mediator of Alzheimer's disease risk.

RUNX2 promotes epigenetic WNT signaling in inflamed intestinal epithelial cells

This study identifies RUNX2 as a regulator of WNT signaling in UC by analyzing snRNA-seq and snATAC-seq data from UC patient-derived colonoids.