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Protocol for transcriptomic and epigenomic analyses of tip-like endothelial cells using scRNA-seq and ChIP-seq.
STAR Protoc
January 2025
Divison of Molecular and Vascular Biology, IRDA, Kumamoto University, Kumamoto 860-0811, Japan. Electronic address:
Angiogenesis begins as endothelial cells migrate, forming a sprouting tip and subsequent growth-rich stalk cells. Here, we present a protocol for transcriptomic and epigenomic analyses of tip-like cells in cultured endothelial cells. We describe steps for stimulating human umbilical vein endothelial cells (HUVECs) with vascular endothelial cell growth factor (VEGF) to generate tip-like cells.
View Article and Find Full Text PDFPrevalence of chronic kidney disease and anemia in Hirakud Command Area, Odisha, India: unveiling the role of environmental toxicants.
J Nephrol
January 2025
Laboratory of Renal Toxicopathology & Medicine, P.G. Department of Environmental Sciences, Sambalpur University, Burla, Odisha, 768019, India.
Background: The present community-based study assessed the prevalence of chronic kidney disease (CKD)/chronic kidney disease of unknown origin (CKDu) as well as anemia in some intense agricultural zones under Hirakud Command Area and evaluated their association with pesticides and heavy metal exposure.
Methods: Random cluster sampling method was used to assess the prevalence of CKD and anemia. Hematological analysis was carried out using autoanalyzer.
Funmap: integrating high-dimensional functional annotations to improve fine-mapping.
Bioinformatics
January 2025
Department of Biostatistics, City University of Hong Kong, 83 Tat Chee Avenue, Hong Kong, China.
Motivation: Fine-mapping aims to prioritize causal variants underlying complex traits by accounting for the linkage disequilibrium of GWAS risk locus. The expanding resources of functional annotations serve as auxiliary evidence to improve the power of fine-mapping. However, existing fine-mapping methods tend to generate many false positive results when integrating a large number of annotations.
View Article and Find Full Text PDFnipalsMCIA: Flexible Multi-Block Dimensionality Reduction in R via Nonlinear Iterative Partial Least Squares.
Bioinformatics
January 2025
Department of Pathology and Department of Immunobiology, Yale School of Medicine.
Summary: With the increased reliance on multi-omics data for bulk and single cell analyses, the availability of robust approaches to perform unsupervised learning for clustering, visualization, and feature selection is imperative. We introduce nipalsMCIA, an implementation of multiple co-inertia analysis (MCIA) for joint dimensionality reduction that solves the objective function using an extension to Non-linear Iterative Partial Least Squares (NIPALS). We applied nipalsMCIA to both bulk and single cell datasets and observed significant speed-up over other implementations for data with a large sample size and/or feature dimension.
View Article and Find Full Text PDFFunctional analysis of the PIP5K1A gene in Liaoning Cashmere goats: an investigation based on bioinformatics, tissue localization, and biological functions.
Cell Mol Biol (Noisy-le-grand)
January 2025
College of Life Sciences, Liaoning Normal University, Dalian 116000, Liaoning Province, China.
Liaoning cashmere goat is an outstanding breed in China primarily for cashmere production, with strict controls against genetic outflow. Melatonin(MT) is a key factor affecting cashmere growth, and preliminary transcriptome sequencing indicated that melatonin upregulates the expression of the PIP5K1A gene in skin fibroblasts. To predict the physicochemical properties of PIP5K1A in Liaoning cashmere goats, ascertain the tissue localization of PIP5K1A in their skin, and explore the role and mechanism of PIP5K1A in the proliferation of skin fibroblasts.
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