bulk RNA-seq

Inhibiting 2-oxoglutarate dehydrogenase reveals the mechanisms and limits of metabolic plasticity in developing maize kernels

This study investigates the role of 2-oxoglutarate dehydrogenase in maize kernels by knocking it down and analyzing metabolic changes and structural impacts.

Long-term effects of the early life environment on alternative splicing

This study shows that early life environment has long-term effects on alternative splicing in pea aphids, independent of morph identity.

The role of the NLRP3 inflammasome in a CLN2 mouse model of neuroinflammation

This study investigates the role of the NLRP3 inflammasome in a CLN2 mouse model, showing that inflammasome activation occurs at 3 months and that its inhibition reduces neuroinflammation.

Chromosome 7 gain establishes a just-right WNT signaling state during colorectal tumorigenesis

This study shows that chromosome 7 gain optimizes WNT signaling in colorectal cancer by counteracting excessive stemness from APC mutations.

Subchondral bone remodeling in knee osteoarthritis is coupled to lipid mobilization from bone marrow adipocytes

This study investigates the link between lipid mobilization from bone marrow adipocytes and bone formation in knee osteoarthritis, finding that lipolysis is associated with osteogenic activity and can be pharmacologically modulated.

DiffRhyShiny: A Benchmarking-Informed Platform for Differential Rhythmicity Analysis with Dependence-Aware Evidence Integration

The paper benchmarks differential rhythmicity analysis methods and introduces a web platform for robust analysis and visualization of rhythmicity changes.

Apoptosis at the optic fissure shapes transient retinal myeloid states

The paper identifies the optic fissure as the entry site for myeloid cells into the embryonic mouse retina, showing that apoptosis and CD206 expression are linked to transient myeloid states during development.

The nuclear membrane protein Samp1 links peripheral genome organization to the myogenic transcriptional program

This study shows Samp1 is essential for myogenic differentiation by linking its role in chromatin organization at the nuclear periphery to the transcriptional program of muscle development.

MetAR: A semi-automated meta-analysis of skeletal muscle androgen receptors association with age

This study uses a novel R-based pipeline, MetAR, to analyze RNA-seq datasets and finds that androgen receptor expression declines with age in human skeletal muscle.

A Trisomy 21 Model Atlas reveals conserved dosage effects and context-specific transcriptional responses across mouse and human models of Down syndrome

The paper presents a Trisomy 21 Model Atlas comparing mouse and human models to show conserved dosage effects and context-specific transcriptional responses across tissues and developmental stages.

Preoperative thymic output and T cell repertoire diversity are associated with recurrence after nephrectomy for localized renal cell carcinoma

Evolutionary insights into β-cyclocitral signaling in Physcomitrium patens

The paper investigates how β-cyclocitral signaling evolved in the moss Physcomitrium patens, finding that while it triggers a strong transcriptional response, it impairs photosynthesis and lacks protective effects.

Non-canonical IL-2 signaling facilitates peripheral regulatory T cell differentiation

This study identifies MACS as a non-canonical IL-2 signaling pathway that promotes Treg differentiation and function through AP-1-dependent mechanisms.

Keratinocyte FABP5 mediates saturated fat-induced MAPK/CCL20 signaling in psoriatic inflammation

Reference-Gene Stability for RT-qPCR in the Medial Prefrontal Cortex and Hippocampal Subregions of the 5xFAD Mouse Brain

The paper evaluates reference gene stability for RT-qPCR in specific brain regions of 5xFAD mice and recommends gene pairs for accurate normalization.

Cirrhosis-associated immune dysfunction reflects impaired intestinal CD8ab⁺ intraepithelial lymphocyte compartmentalization

The paper investigates immune dysfunction in cirrhosis by analyzing CD8ab⁺ intraepithelial lymphocytes and identifies CCL25-CCR9 axis disruption as a key factor.

The root knot nematode effector MiEFF186 interacts with a splicing factor to reshape plant transcriptome

This study identifies MiEFF186a as a nematode effector that interacts with GDP1/CIS2 to alter plant transcriptome splicing and gene expression, affecting susceptibility to nematode infection.

In Vivo Transcriptomics-Based Framework for Systematic Indication Expansion

This paper presents a drug repurposing framework using in vivo transcriptomics to expand indications by matching drug signatures with disease signatures, successfully recovering established uses of semaglutide and proposing new ones.

Endothelial CXCL12 is dispensable for adipose tissue function

This study investigates the role of CXCL12 in adipose tissue endothelial cells and finds it dispensable for adipose tissue function under normal and cold conditions, as well as during obesity.

Temporal RNA splicing dysregulation in a human multicellular model of C9orf72 ALS

This study uses human spinal cord organoids to model C9orf72 ALS, identifying early RNA splicing dysregulation and RBP network dysfunction as key features of the disease.

Sugarcane bZIP16 regulates internode elongation by targeting gibberellic acid biosynthesis pathway

This study identifies ScbZIP16 as a regulator of internode elongation in sugarcane by modulating gibberellic acid biosynthesis.

The mitochondrial transaminase GOT2 supports Japanese encephalitis virus replication in neuronal cells

This study identifies the mitochondrial transaminase GOT2 as a metabolic dependency of JEV and a potential host-directed antiviral target through integrated transcriptomics and proteomics analyses.

Apoptotic Cells Promote Tim4+ Macrophage Differentiation Through Direct and Indirect Signaling Pathways

This study shows that apoptotic cells promote Tim4+ macrophage differentiation through both direct and indirect signaling pathways involving efferocytosis and IL-4R-STAT6 signaling.

Linking H3K36me3 to transcriptional dynamics

This study investigates the role of SETD2 and H3K36me3 in transcriptional dynamics by analyzing gene expression and splicing in murine C2C12 myoblast cells following their depletion.

An androgen-derived transcriptional state reveals signaling and mitochondrial vulnerabilities in cancer

The paper identifies an androgen-derived transcriptional state in cancer cells and links it to drug resistance and mitochondrial vulnerabilities.

Direct 3D isolation in gelatin methacryloyl microbeads versus conventional 2D isolation and culture: a trade-off between mesenchymal stromal cell purity and niche-associated transcriptional profiles

This study compares 3D GelMA microbeads with 2D culture for MSC isolation, finding 2D yields purer MSCs while 3D retains niche-associated transcriptional profiles.

Ontology-Driven Annotation of Key Events Enables Transcriptomics-Based Assessment of Adverse Outcome Pathway Networks

The paper enhances AOP networks by annotating Key Events with Gene Ontology terms, improving transcriptomics-based assessment of KE perturbation in pesticide-induced hepatotoxicity.

PIEZO1 marks a low neuroendocrine state and supports cisplatin tolerance in small cell lung cancer

This study identifies PIEZO1 as a marker of low neuroendocrine state and a contributor to cisplatin tolerance in SCLC through mechanistic and multi-omics analyses.

Lysosomal Glycosaminoglycan Catabolism Regulates Microglial Cell State in the Developing CNS

This study shows that lysosomal glycosaminoglycan catabolism in microglia regulates their cell state during CNS development, linking ECM remodeling to microglial identity.

Cyclin E/CDK2 deficiency links cell cycle control to intestinal barrier integrity and tight junction regulation

This study shows that Cyclin E/CDK2 deficiency enhances intestinal barrier integrity and tight junction expression in mice, contrary to initial hypotheses.