snRNA-seq

QClus: A droplet-filtering algorithm for enhanced snRNA-seq data quality in challenging samples

QClus improves snRNA-seq data quality by filtering droplets in challenging samples, achieving high quality across multiple datasets and metrics.

Integrated Spatial and Single-Nuclei Transcriptomic Analysis of Long Non-Coding RNAs in Alzheimer's Disease

The paper identifies AD-associated lncRNAs with spatial and cell-type-specific expression patterns and shows OIP5-AS1 contributes to microglial activation in AD.

Functional diversities within neurons and astrocytes in the adult rat auditory cortex revealed by single-nucleus RNA sequencing.

The paper uses snRNA-seq to identify diverse neuron and astrocyte subtypes in the adult rat auditory cortex, revealing functional diversity in these cell types.

Overloading And unpacKing (OAK) - droplet-based combinatorial indexing for ultra-high throughput single-cell multiomic profiling

OAK enables ultra-high throughput single-cell multiomic profiling with high sensitivity and reduced labor, demonstrating its utility in detecting rare resistant cell populations.

Mapping the glial transcriptome in Huntington's disease using snRNAseq: Selective disruption of glial signatures across brain regions

This study uses snRNAseq to analyze glial cell heterogeneity in Huntington's disease across brain regions, identifying subtype-specific changes and potential mechanisms of glial dysfunction.

Transcriptomic profiling of Schlemm's canal cells reveals a lymphatic-biased identity and three major cell states

The paper performs transcriptomic analyses of Schlemm's canal endothelial cells to reveal their lymphatic identity, three major cell states, and interactions with trabecular meshwork cells.

A Reproducibility Focused Meta-Analysis Method for Single-Cell Transcriptomic Case-Control Studies Uncovers Robust Differentially Expressed Genes

The paper develops a meta-analysis method to identify reproducible differentially expressed genes across single-cell transcriptomic case-control studies and finds shared genes across neurodegenerative diseases.

kallisto, bustools, and kb-python for quantifying bulk, single-cell, and single-nucleus RNA-seq

The paper describes using kallisto, bustools, and kb-python to quantify RNA-seq data from bulk, single-cell, and single-nucleus samples.

CREB3 gain of function variants protect against ALS

The paper identifies a protective variant CREB3R119G that reduces ALS risk and progression by modulating CREB3 activity in vulnerable neurons.

Sex-specific single cell-level transcriptomic signatures of Rett syndrome disease progression

The paper identifies sex-specific transcriptomic changes in a mouse model of Rett syndrome, showing more differentially expressed genes in females and non-cell-autonomous effects.

High-Complexity Barcoded Rabies Virus for Scalable Circuit Mapping Using Single-Cell and Single-Nucleus Sequencing

The paper introduces a method to map neuronal circuits using barcoded rabies virus and single-nucleus RNA sequencing, revealing cell-type-specific circuit motifs in developing human cerebral cortex.

Single-cell X-chromosome inactivation analysis links biased chimerism to differential gene expression and epigenetic erosion

The paper introduces a computational method to analyze X-chromosome inactivation at the single-cell level using sc/snRNA-Seq data and shows its application in identifying biased inactivation and its association with gene expression and epigenetic changes.

Inflammatory Signatures of Microglia in the Mouse Model of Corticosterone-Induced Depression

The paper identifies inflammatory microglia signatures in a mouse model of corticosterone-induced depression using bulk and single-cell RNA sequencing.

Transcriptomic changes in oligodendrocytes and precursor cells predicts clinical outcomes of Parkinsons disease

The paper identifies transcriptomic changes in oligodendrocytes and precursor cells linked to Parkinson's disease outcomes and shows their predictive value for cognitive and depressive symptoms.

Expression quantitative trait locus mapping in recombinant gametes using single nucleus RNA sequencing

This paper develops a method to map eQTLs using snRNA-seq of gametes from a small number of heterozygous individuals, uncovering cis- and trans-eQTLs in Arabidopsis pollen nuclei.

Interneuron diversity in the human dorsal striatum

The paper uses snRNA-seq to identify eight interneuron classes in the human dorsal striatum, validates markers with in situ hybridization, and compares them to mouse interneurons.

Transcriptional dynamics orchestrating the development and integration of neurons born in the adult hippocampus

This study uses snRNA-seq to track the transcriptional changes in adult hippocampal neurons from birth to maturity, identifying key transcription factors and molecular switches involved in their differentiation.

Single-nucleus transcriptomics reveal the cytological mechanism of conjugated linoleic acids in regulating intramuscular fat deposition

This study uses snRNA-seq in pigs to reveal CLAs promote fat infiltration by altering myofiber types and adipocyte differentiation through JNK pathway inhibition.

A public resource of single cell transcriptomes and multiscale networks from persons with and without Alzheimer's disease

The paper provides a public resource of single nucleus RNA sequencing data and multiscale networks from Alzheimer's disease and non-disease individuals, linking genetic variants to molecular features and revealing novel disease biology.

Multiplatform molecular profiling and functional genomic screens identify prognostic signatures and mechanisms underlying MEK inhibitor response in somatic NF1 mutant glioblastoma

Comparative analysis of the syncytiotrophoblast in placenta tissue and trophoblast organoids using snRNA sequencing

This study compares syncytiotrophoblast gene expression in placental tissue and trophoblast organoids using snRNA-seq, identifying distinct nuclear subtypes and environmental influences on STB gene expression.

Pathogenic variants associated with speech/cognitive delay and seizures affect genes with expression biases in excitatory neurons and microglia in developing human cortex

The paper identifies cell-specific gene expression biases in excitatory neurons and microglia for pathogenic variants linked to speech/cognitive delay and seizures using single-nucleus RNA-seq data.

Cell-type-specific alternative splicing in the cerebral cortex and kidney of a Setbp1S858R Schinzel-Giedion Syndrome patient variant mouse

The paper identifies cell-type-specific alternative splicing changes in the cerebral cortex and kidney of Setbp1S858R mice, with implications for Schinzel-Giedion Syndrome.

sNucConv: A bulk RNA-seq deconvolution method trained on single-nucleus RNA-seq data to estimate cell-type composition of human subcutaneous and visceral adipose tissues

Border-forming wound repair astrocytes

The paper identifies the cellular origins and functional changes of astrocytes forming protective borders around CNS injuries, showing their role in neuroprotection.

Opto-seq reveals input-specific immediate early gene induction in ventral tegmental area cell types

The paper uses optogenetic stimulation and single-nucleus RNA sequencing to identify input-specific activation patterns of VTA neuronal subpopulations and their immediate early gene programs.

Transcriptome Analysis Identifies An ASD-Like Phenotype In Oligodendrocytes And Microglia From C58/J Amygdala That Is Dependent On Sex and Sociability

This study identifies ASD-like transcriptomic changes in oligodendrocytes and microglia of C58/J mice amygdala, dependent on sex and sociability, using bulk RNA-Seq and snRNA-Seq.

DCX knockout ferret reveals a neurogenic mechanism in cortical development

This study examines DCX knockout ferrets to understand neurogenic mechanisms in cortical development and reveals phenotypes resembling human lissencephaly.

Altered Glia-Neuron Communication in Alzheimer's Disease Affects WNT, p53, and NFkB Signaling Determined by snRNA-seq

The paper identifies altered glia-neuron communication in Alzheimer's disease using snRNA-seq, revealing dysregulation of WNT, p53, and NFkB signaling in inhibitory neurons.

A Single-cell and Spatial RNA-seq Database for Alzheimer's Disease (ssREAD)

ssREAD is a database that compiles single-cell and spatial RNA-seq data for Alzheimer's Disease, offering analysis tools for integrative studies.