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Integrative analysis of left ventricle and epicardial adipose tissue identifies SDHA and OGDH as candidate targets for ischemic heart disease
Ischemic heart disease (IHD) involves coordinated molecular changes across heart; yet, their interplay remains poorly understood. Here, we investigated transcriptomic alterations in two heart tissue subtypes, left ventricle (LV) and epicardial adipose tissue (EAT), from …
Read PDFOptimal gene panel selection for targeted spatial transcriptomics experiments
Spatial transcriptomics analysis is a powerful approach for dissecting the structure of tissue microenvironment and uncovering the mechanism of cell-cell communications. However, existing technologies are limited by either spatial resolution or gene coverage. Most single-cell-resolution …
Read PDFSingle-cell Technologies in Atherosclerosis: Uncovering Cellular Heterogeneity, Mechanisms, and Therapeutic Opportunities
<h4>Purpose of review</h4>This review highlights recent advances in single-cell analysis technologies and their application in clarifying the cellular and molecular complexity of atherosclerosis, redefining our understanding of vascular biology and immune cell functioning within the …
Read PDFMulti-Dimensional Transcriptomics Reveals the Prominent Role of Neuroinflammation in Alzheimer's Disease
Alzheimer's Disease (AD), the most common form of dementia, is pathologically defined by extracellular beta-amyloid (Aβ) plaques and intraneuronal neurofibrillary tangles (NFTs), accompanied by chronic neuroinflammation. Recent advances in single-cell RNA sequencing (scRNA-seq/snRNA-seq) and spatial …
Read PDFTranscriptomic Insights Into the Evolution of Snake Venom: Mechanisms, Diversity, and Adaptation
Snake venoms are evolutionarily refined biochemical arsenals composed of diverse toxins with complex functional roles in predation, defense, and competition. Over the past 2 decades, transcriptomic approaches have transformed venom research by enabling high-resolution insights …
Read PDFCorrection: Detection of differentially expressed genes in spatial transcriptomics data by spatial analysis of spatial transcriptomics: A novel method based on spatial statistics
[This corrects the article DOI: 10.3389/fnins.2022.1086168.].
Read PDFImaging-Based Spatial Transcriptomics: Data Interpretation Methods and Biomedical Applications
Imaging-based spatial transcriptomics has advanced from low-plex single-molecule fluorescence in situ hybridization to a diverse set of highly multiplexed platforms, with recent multimodal and pathology-compatible capabilities. Despite major differences in chemistry, coding, and imaging strategies …
Read PDFSpatial transcriptomics in Alzheimer's disease: technologies, challenges and discoveries
Alzheimer's disease (AD) is a complex neurodegenerative disorder that is associated with cognitive decline in the elderly. While β-amyloid (Aβ) plaques and neurofibrillary tau tangles have been used to define and stage AD onset in …
Read PDFMultiomics insights into rumen microbiome and function in grazing lambs: implications for nutrient absorption and grassland sustainability
<h4>Background</h4>The center of sustainable development of grassland husbandry is the balance between forage intake and growth characteristics of animals, and one of the keys to restricting the conversion efficiency of forage intake is the digestibility …
Read PDFRhizosphere Microbiome Engineering for Climate-Smart Agriculture: From Synthetic Consortia to Precision Decision Support
Rhizosphere microbiome engineering is a promising approach that can enhance crop resilience and input use efficiency by redirecting plant-microbe-soil interactions toward predictable functions. Here, we review the mechanistic bases underlying rhizosphere assembly and stability, including …
Read PDFBeyond counting: how single-cell long-read sequencing turns transcriptome complexity into precision targets
Single-cell RNA sequencing (scRNA-seq) has emerged as a critical tool in oncology research, revealing key aspects of immune infiltration, tumor heterogeneity, and the tumor microenvironment. However, most scRNA-seq experiments capture only a portion of the …
Read PDFDirect RNA Sequencing Reveals Sex-Biased Transcriptomic and Epitranscriptomic Regulation in <i>Procambarus clarkii</i>
The red swamp crayfish (<i>Procambarus clarkii</i>) is a globally important freshwater crustacean that exhibits pronounced sexual dimorphism, with males growing faster than females. However, the molecular mechanisms underlying sex differentiation in crustaceans remain poorly understood. …
Read PDFFull-length transcriptome of <i>Camellia perpetua</i> reveals candidate <i>SCPL</i>1<i>A</i> gene family members involved in galloylated catechins biosynthesis
Catechins includ galloylated catechins and non-galloylated catechins, among which galloylated catechins exhibit stronger antioxidant, anti-inflammatory and anti-cancer activities. Section <i>Chrysantha</i> Chang, the only group of yellow <i>Camellia</i> with rich catechins in their flowers, is a …
Read PDFDirect RNA sequencing reveals multilayered epitranscriptomic remodeling in macrophages upon Mtb infection
Understanding the host transcriptional and epitranscriptomic response to <i>Mycobacterium tuberculosis</i> (Mtb) infection is vital for decoding mechanisms of immune evasion and persistence. Here, we employed Oxford Nanopore Technologies (ONT)-based direct RNA sequencing (DRS) on human …
Read PDFComprehensive analysis of alternative splicing and transcriptome diversity in apple using long-read sequencing
<h4>Introduction</h4>Alternative splicing (AS) is a major source of transcriptome diversity in plants, but short-read RNA sequencing (RNA-seq) has limited power for resolving full-length transcripts and complex AS patterns, particularly in perennial crops.<h4>Methods</h4>We integrated Oxford Nanopore …
Read PDFLong-read sequencing transcriptome quantification with lr-kallisto
RNA abundance quantification has become routine and affordable thanks to high-throughput "short-read" technologies that provide accurate molecule counts at the gene level. Similarly accurate and affordable quantification of definitive full-length, transcript isoforms has remained a …
Read PDFProtocol for generating native and unmodified bacterial RNA for nanopore direct RNA sequencing and downstream analysis
Nanopore direct RNA sequencing (DRS) relies on adapter ligation to poly(A) tails, posing challenges for bacterial mRNAs, which naturally lack these structures. Here, we present a protocol for generating native and unmodified bacterial RNA for …
Read PDFAdvances in Detecting RNA Modifications Using Direct RNA Nanopore Sequencing
RNA modifications add a dynamic and versatile regulatory layer to gene expression, influencing RNA stability, splicing, translation, and cellular responses. Despite their importance, traditional detection methods-such as antibody-based enrichment, chemical labeling, or indirect sequencing approaches-often …
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