snRNA-seq

scCDC: a computational method for gene-specific contamination detection and correction in single-cell and single-nucleus RNA-seq data

scCDC detects and corrects contamination in scRNA-seq and snRNA-seq data by identifying contamination-causing genes, achieving better accuracy than existing methods.

A chromosome region linked to neurodevelopmental disorders acts in distinct neuronal circuits in males and females to control locomotor behavior

This study identifies sex- and cell type-specific transcriptomic and behavioral effects of 16p11.2 hemideletion in mice, revealing distinct impacts on striatal circuits and locomotor behavior.

Characterizing cell type specific transcriptional differences between the living and postmortem human brain.

The paper compares gene expression differences between living and postmortem human brain samples using snRNA-seq and develops a model to account for these differences in analysis.

Analysis of changes in inter-cellular communications during Alzheimer's Disease pathogenesis reveals conserved changes in glutamatergic transmission in mice and humans

The paper analyzes inter-cellular communication changes in Alzheimer's Disease using snRNA-seq and CellChat, finding conserved glutamatergic transmission changes in mice and humans.

Uncoupling protein 1-driven Cre (Ucp1-Cre) is expressed in the epithelial cells of mammary glands and various non-adipose tissues

This study investigates Ucp1-Cre expression in non-adipose tissues and finds it in epithelial cells during development, but not in adult mammary glands.

Single-nucleus and spatial transcriptomic profiling of human temporal cortex and white matter reveals novel associations with AD pathology

This study uses single-nucleus and spatial transcriptomics to identify cell type-specific associations with Alzheimer's disease pathology in human temporal cortex and white matter.

Chst9 Marks a Spatially and Transcriptionally Unique Population of Oprm1-Expressing Neurons in the Nucleus Accumbens

The paper identifies a novel population of Oprm1-expressing neurons in the NAc marked by Chst9 expression, showing spatial and transcriptional distinctiveness across species.

Nicheformer: a foundation model for single-cell and spatial omics

Pretrained on 57 million dissociated and 53 million spatial human and mouse cells, a 49.3M-parameter transformer predicts niche, region, neighborhood composition and density, and carries spatial labels onto scRNA-seq.

A single-nucleus RNA sequencing atlas of the postnatal retina of the shark Scyliorhinus canicula

This study presents a single-nucleus RNA-sequencing atlas of the postnatal shark retina, identifying 22 cell types and providing insights into retinal evolution.

Association of 10 VEGF Family Genes with Alzheimer's Disease Endophenotypes at Single Cell Resolution

This study investigates the role of 10 VEGF genes in Alzheimer's disease using single-nucleus RNA sequencing, finding altered expression and associations with disease endophenotypes.

Robust single nucleus RNA sequencing reveals depot-specific cell population dynamics in adipose tissue remodeling during obesity

This study develops a robust snRNA-seq method to analyze depot-specific adipose tissue remodeling during obesity, identifying distinct adipocyte subpopulations and their functional trajectories.

Identification of cell-type-specific response to silicon treatment in soybean leaves through single nucleus RNA-sequencing

This study uses snRNA-seq to identify cell-type-specific responses to silicon treatment in soybean leaves, revealing novel Si-induced cell clusters and gene expression changes related to defense mechanisms.

Cell type specificity of mosaic chromosome 1q gain resolved by snRNA-seq in a case of epilepsy with hyaline protoplasmic astrocytopathy

The paper uses snRNA-seq to analyze mosaic chromosome 1q gain in a case of epilepsy with hyaline protoplasmic astrocytopathy, finding cell-type-specific gene expression changes in neurons and astrocytes.

Intercellular Signaling Pathways as Therapeutic Targets for Vascular Dementia Repair

This study identifies intercellular signaling pathways involved in vascular dementia repair and demonstrates therapeutic potential through drug intervention.

A Cell Atlas of Thoracic Aortic Perivascular Adipose Tissue: a focus on mechanotransducers

The paper uses snRNAseq to analyze thoracic aortic perivascular adipose tissue (taPVAT) and subscapular brown adipose tissue (BAT) in rats, identifying cell-specific gene expression and highlighting PIEZO1 as a key mechanotransducer in taPVAT.

Single-Cell Atlas Uncovers Layer 4 Heterogeneity and Functional Gradients in Rhesus Macaque Visual Cortex

The paper uses snRNA-seq to analyze layer 4 heterogeneity in rhesus macaque visual cortex, identifying distinct subtypes and linking them to neurodevelopmental disorders.

Molecular mechanisms reconstruction from single-cell multi-omics data with HuMMuS

HuMMuS infers regulatory mechanisms from single-cell multi-omics data, improving predictions of TF targets, binding motifs, and regulatory regions.

A spatially-resolved transcriptional atlas of the murine dorsal pons at single-cell resolution

This study creates a spatially-resolved transcriptional atlas of the murine dorsal pons using snRNA-seq and MERFISH, identifying 120 neuronal subtypes and their spatial distribution.

Familial Parkinson's Disease Mutations Converge on Alternative Splicing Programs Linked to Lysosomal, Autophagic and Vesicle Trafficking Pathways

The paper investigates how familial Parkinson's disease mutations affect pre-mRNA splicing in dopaminergic neurons, identifying five functional classes of splicing changes and potential biomarkers and therapeutic targets.

Identification of robust cellular programs using reproducible LDA that impact sex-specific disease progression in different genotypes of a mouse model of AD

The paper introduces Topyfic, a reproducible LDA method, to identify cellular programs in single-cell data and shows sex-specific differences in microglial activation in Alzheimer's disease mouse models.

Single-cell and single-nucleus RNA-sequencing from paired normal-adenocarcinoma lung samples provide both common and discordant biological insights

This study compares scRNA-seq and snRNA-seq in lung samples, finding differences in cell type composition and biological insights between fresh and frozen tissues.

A single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pup

12.4 million single-nucleus transcriptomes from 83 staged mouse embryos (E8 to P0) yield 190 cell types, a zygote-to-pup cell-type tree, and rapid postnatal transcriptional shifts.

Single-nucleus RNA sequencing reveals cellular and molecular dynamics of white and brown adipose tissue in a mouse model of type-2 diabetes

This study uses single-nucleus RNA sequencing to analyze adipose tissue changes in a mouse model of type-2 diabetes, revealing altered cellular phenotypes and transcriptional circuits.

Differences in molecular sampling and data processing explain variation among single-cell and single-nucleus RNA-seq experiments

The paper reanalyzes RNA-seq data to show pre-mRNA levels vary across cell types, affecting gene length bias and normalization methods, and highlights the impact of bioinformatic processing over assay choice.

TrkB-dependent regulation of molecular signaling across septal cell types

This study investigates TrkB signaling in the lateral septum using RNA-seq, identifying gene expression changes linked to psychiatric and neurodegenerative disorders.

CellDemux: coherent genetic demultiplexing in single-cell and single-nuclei experiments.

CellDemux demultiplexes genetically labeled single-cell and single-nuclei libraries across modalities, achieving 88% donor assignment accuracy in benchmarking.

Selective Vulnerability of Layer 5a Corticostriatal Neurons in Huntington's Disease

The paper identifies layer 5a corticostriatal neurons as selectively vulnerable in Huntington's disease using single nucleus RNA sequencing and shows they have extensive mHTT-CAG expansions.

Mesophyll-Specific Circadian Dynamics of CAM Induction in the Ice Plant Unveiled by Single-Cell Transcriptomics

The paper uses snRNA-seq to study CAM induction in ice plant mesophyll cells, revealing circadian gene expression differences between CAM and C3 pathways.

Integrated single-cell multiomics uncovers foundational regulatory mechanisms of lens development and pathology

The paper creates a single-cell multiomic atlas of lens development, identifying regulatory mechanisms and cataract-linked networks through snRNA-seq, snATAC-seq, and CUT&RUN-seq.

Single-Nuclei RNA Sequencing Identifies Type C Low-Threshold Mechanoreceptors as Key Players in Paclitaxel-Induced Peripheral Neuropathy

This study uses snRNA-seq to identify type C low-threshold mechanoreceptors as key contributors to paclitaxel-induced neuropathic pain.