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3' single-cell RNA sequencing (scRNA-seq) captures polyadenylation (poly(A)) sites, enabling quantification of site usage per gene and cell. Here, we present scPASU (single-cell poly(A) site usage), a Snakemake workflow for quantifying poly(A) site usage and …
Read PDF<h4>Background</h4>Small Nuclear Ribonucleoprotein Polypeptide A (SNRPA), an RNA-binding protein associated with HCC survival, emerges as a key regulator requiring mechanistic study.<h4>Methods</h4>To delineate SNRPA's functions, we generated SNRPA-overexpressing HepG2 cells and performed RNA-seq to identify SNRPA-regulated …
Read PDF<i>Brassica napus</i> a cool-season oilseed crop, is an important source of edible oil and biofuel. Heat stress during the reproductive stage poses a serious threat to its productivity, but little is known about the gene …
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Read PDFCancer immunotherapy aims to boost T cell responses against tumor cells. However, a large fraction of patients with cancer exhibit intrinsic or acquired resistance to immunotherapy. To better understand resistance mechanisms in tumor cells, we …
Read PDFPatients diagnosed with cancer of unknown primary (CUP) have poor prognoses, highlighting the need to identify primary sites for targeted therapeutic intervention. Here, we present a protocol to predict the primary sites of CUP based …
Read PDFBovine paratuberculosis (PTB), caused by <i>Mycobacterium avium</i> subsp. <i>paratuberculosis</i> (MAP), is a chronic granulomatous intestinal disease that leads to substantial economic losses in the global dairy industry. Current diagnostic tests have limited sensitivity, as they …
Read PDFA complex structural variation on chicken chromosome 27 is the causal mutation for the muffs and beard (Mb) phenotype. The Mb variant region contains copy number variations in several genes important for nervous system development, …
Read PDFHistone methylation plays a pivotal role in the epigenetic regulation of fungal development. In this study, we characterise FgJhd2, a homologue of the histone demethylase Jhd2 from the JARID family, in the plant pathogenic fungus …
Read PDFExposure to hypoxia is linked to increased cellular plasticity and enhanced metastasis, effects that are primarily attributed to the transcriptional activation of large gene programs downstream of hypoxia-inducible factors (HIFs). However, translational effects in hypoxia, …
Read PDFItaconate is produced by inflammatory macrophages and promotes negative feedback on inflammation. It is synthesized by aconitate decarboxylase 1 (ACOD1) from cis-aconitate, a metabolite of the tricarboxylic acid cycle. Here, we focused on the role …
Read PDF<h4>Background</h4>Endothelial cells (ECs) orchestrate vascular homeostasis and resilience but can undergo reprogramming into a mesenchymal-like phenotype through an endothelial-to-mesenchymal transition (EndMT). Crucially, EndMT is a linchpin underlying several cardiometabolic diseases, but is almost universally studied …
Read PDFBACKGROUND: FLASH radiotherapy, characterized by ultra-high dose rates (> 40 Gy/s), potentially spares normal tissues while maintaining antitumor efficacy (the FLASH effect). While electron and proton FLASH are explored, pulsed X-ray sources like plasma focus …
Read PDFHypertrophic cardiomyopathy (HCM) is a common genetic heart disease, with macrophages playing a critical role in its pathological remodeling. Our study aims to investigate the molecular basis of HCM by analyzing macrophage-related gene expression at …
Read PDF<h4>Background</h4>Osteoarthritis (OA) is characterized by chronic inflammation, cellular senescence, and progressive cartilage remodeling, yet effective disease-modifying therapeutic targets remain limited. Caspase-8 has classically been regarded as a key initiator of the extrinsic apoptotic pathway; however, …
Read PDF<h4>Background</h4>Inflammatory response plays a pivotal role in myocardial injury and post-infarction remodeling after acute myocardial infarction (AMI). Mechanical unloading (UL) of the left ventricle (LV) has been proposed as a potential therapeutic strategy to preserve …
Read PDFBACKGROUND: Mammary gland development and lactation are dynamic biological processes governed by coordinated changes in chromatin accessibility and gene expression. RESULTS: We performed paired ATAC-seq and RNA-seq profiling to characterize stage-associated chromatin accessibility and transcriptional …
Read PDFBody axis patterning in vertebrates is controlled by HOX genes during embryogenesis, with their expression gradients defining spatial identity along the anterior-posterior axis. While the developmental roles of HOX genes in axial patterning are well …
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