snRNA-seq

An Integrated Atlas of the Human Kidney Spanning Health and Diseases

The paper integrates multiple single-cell and single-nucleus RNA-sequencing datasets to create a comprehensive Human Kidney Cell Atlas, identifying cell types, states, and disease-associated populations.

TFE3 fusions drive expression of CD44 and SPP1 in Translocation Renal Cell Carcinoma

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

INTACT-olotl: A simplified system for rapid cell type-specific profiling during axolotl limb regeneration

The paper introduces INTACT-olotl, a method to isolate cell type-specific nuclei from axolotl limb regenerating tissues, enabling efficient snRNA-seq profiling and revealing TGFβ signaling's role in regeneration.

Analysis of Rare Coding Variation Identifies New Genetic Contributors to Schizophrenia

Ultra-rare damaging coding variants in 87,959 schizophrenia cases and 150,587 controls implicate 40 genes (16 exome-wide, 24 at 5% FDR), half overlapping autism, developmental delay or bipolar genes.

Pirfenidone treatment attenuates fibrosis in autosomal dominant polycystic kidney disease

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

Incomplete references leave bulk deconvolution targets non-identifiable, but identification has a computable precision price

With an incomplete deconvolution reference, operator history changes estimates and associations, and the target is not point-identified; fitdrop scores remedies on shrinkage, coverage, certification and false certification, and prices measurements.

The Unreasonable Effectiveness of Cell Types in Describing Neuronal Physiological Features

On 495 human Patch-seq neurons, cell type means predicted electrophysiology better than neural networks on scGPT embeddings or gene panels; fusing scGPT embeddings with cell type labels predicted best.

Maternal-fetal immune conflict contributes to male-specific impairments in a mouse model of neurodevelopmental disorders

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.

Flow Orchestrated Regulatory Genomics Engine (FORGE): A Configurable Nextflow Pipeline for End-to-End snMultiome Analysis

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.

Dynamics of bleomycin-induced lung injury at single-nucleus resolution

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.

Mammalian spermatogenesis at single-cell resolution downstream of genetic perturbations in meiotic double-strand break repair

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.

SPP1+ Microglia Are Associated with Neuroimmune Rewiring and Glutamatergic Neuronal Injury in ART-Suppressed People Living with HIV

In ART-suppressed human brain, an SPP1+ activated microglial subset holds most detected HIV RNA and shows chronic interferon-I and MHC-I signatures, alongside complement signaling and neuronal loss.

A single-nucleus and spatial transcriptomic atlas of the Syrian hamster preoptic area across hibernation states

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

Cell-type-specific circadian and light-responsive transcriptional dynamics in adult Drosophila neurons

The paper profiles circadian neuron transcriptomes across timepoints under different light conditions to reveal transcriptional and light-dependent gene regulation in Drosophila.

Single-Cell Indel Detection Enhances Genetic Ancestry and Cellular Lineage Analysis

Monopogen-Indel calls germline indels from single-cell and single-nucleus RNA data at 73.0% (retina) and ~87% (ovarian cancer) WGS-validated precision, though no single-cell somatic indel matched a WGS somatic indel.

Amygdalostriatal transition zone neurons encode sustained cue responses to guide defensive behaviors

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

Conserved Neuronal-like and Secretory Programs Define the Spatial Architecture of Gastroenteropancreatic Neuroendocrine Tumors

This study identifies conserved neuronal-like and secretory programs in GEP-NETs and links them to spatial microenvironmental niches and metastatic potential.

Coordinated dysregulation of modular gene activity in human neuropathologies

The paper introduces CoPA, a method to identify dysregulated gene coexpression modules in specific cell types across neuropathologies, finding reproducible dysregulation in Alzheimers and schizophrenia.

Single-Nuclear RNA Sequencing Reveals Regional Specialization and Cellular Interactions in Epicardial and Perivascular Adipose Tissue

This study uses snRNA-seq to analyze human adipose tissue depots, identifying distinct adipocyte and progenitor subpopulations and depot-specific intercellular communication networks, with changes observed in disease states.

The Drosophila Secretome

A tiered catalogue of 5,280 Drosophila genes encoding putative secreted proteins (1,802 high-confidence) with a web portal; these genes are less conserved, more tissue-restricted and disproportionately down-regulated with age.

Mapping Alzheimer's neuropathology signatures to the whole brain transcriptome using machine learning data fusion

Cell type-specific logistic regression estimators trained on 427 ROSMAP prefrontal donors project Braak- and β-amyloid-like transcriptomic signatures onto the 108-region Siletti atlas, flagging brainstem, hypothalamic and rostral hippocampal regions.

A conserved molecular marker for connections between two evolutionarily distinct visual centers

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.

Mapping tumor microenvironment heterogeneity of human melanoma metastases across distant organs

This study maps the heterogeneity of human melanoma metastases across brain, liver, and lung using single-nucleus RNA sequencing, revealing organ-specific immune and stromal adaptations.

Pathology-defined cell states reveal reproducible transcriptomic signatures across ALS cortical single-nucleus RNA-seq studies

The paper shows that using pathology-defined cell states improves reproducibility of transcriptomic signatures in ALS snRNA-seq studies compared to conventional case-control analyses.

The extreme diversity of retinal amacrine cells has deep evolutionary roots

The paper reconstructs the evolutionary origins of retinal amacrine cell diversity using transcriptomic data from 24 vertebrate species, identifying 42 orthologous cell types and suggesting a hybrid precursor origin.

Targeting CDC42 with CASIN Reprograms Cell-Type-Specific Transcriptomes and MAPK-Driven Transcription Factor Networks in the Aging Brain

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

Cellular senescence is associated with age-related loss of liver zonation and hepatocyte function

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

Myelin-Free Nuclei Isolation from Mouse Hippocampus and Cerebellum for snRNA-Seq with Benchtop Gradient Centrifugation

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

Single-nucleus transcriptome analysis provides new insights into B chromosome elimination in sorghum

The paper uses snRNA-seq to study B chromosome elimination in sorghum embryos, identifying two subpopulations of B-containing nuclei with distinct transcriptional profiles.

Invasion status stratifies the composition of the human pancreatic cancer perineural niche

Xenium and single-nucleus profiling of 14 human pancreatic tumors shows invaded nerve neighborhoods enriched for classical cancer cells, myCAFs and lipid-handling macrophages but depleted of lymphocytes.