Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1054055 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Genome sequencing of veterinary and human pathogens
| PRJNA601973 | ENA
Project description:Vet-LIRN Other Veterinary Pathogens Sequencing Project
| PRJNA481349 | ENA
Project description:Zoonoses pose substantial global health risks, highlighting the need to better understand animal-to-human transmission. Reptiles are increasingly recognized as hosts of diverse pathogens, including many viruses. Despite this, reptile pathogens remain poorly understood in terms of their diversity, prevalence, and potential risk to humans. Yet human–reptile contact is increasing, driven in part by the global wildlife trade and pet industry. This underscores the need to better understand reptile-associated pathogens; however, models to study reptile viruses remain scarce. Here, we establish and characterize airway organoids derived from Python regius, providing an in vitro model of the reptile airway. Through de novo assembly of a Python regius reference genome, we characterized airway organoids at single-cell resolution, revealing diverse cell populations including ionocytes, ciliated, goblet, club, endocrine, tuft, and basal cells. The organoids supported productive infection with ball python nidovirus (BPNV) and mounted a robust epithelial antiviral response through induction of interferon-stimulated genes, cytokines and genes involved in chemical defense. As a proof-of-concept, antiviral drug treatment reduced BPNV levels, highlighting the model's utility for drug testing. By providing a reductionist system of the serpentine airway, these organoids constitute a physiologically relevant in vitro model to study reptile viruses and host–pathogen interactions in the native host. This system has potential veterinary applications, ecology of serpentes, and zoonotic disease research.
2026-06-17 | GSE313817 | GEO
Project description:Zoonoses pose substantial global health risks, highlighting the need to better understand animal-to-human transmission. Reptiles are increasingly recognized as hosts of diverse pathogens, including many viruses. Despite this, reptile pathogens remain poorly understood in terms of their diversity, prevalence, and potential risk to humans. Yet human–reptile contact is increasing, driven in part by the global wildlife trade and pet industry. This underscores the need to better understand reptile-associated pathogens; however, models to study reptile viruses remain scarce. Here, we establish and characterize airway organoids derived from Python regius, providing an in vitro model of the reptile airway. Through de novo assembly of a Python regius reference genome, we characterized airway organoids at single-cell resolution, revealing diverse cell populations including ionocytes, ciliated, goblet, club, endocrine, tuft, and basal cells. The organoids supported productive infection with ball python nidovirus (BPNV) and mounted a robust epithelial antiviral response through induction of interferon-stimulated genes, cytokines and genes involved in chemical defense. As a proof-of-concept, antiviral drug treatment reduced BPNV levels, highlighting the model's utility for drug testing. By providing a reductionist system of the serpentine airway, these organoids constitute a physiologically relevant in vitro model to study reptile viruses and host–pathogen interactions in the native host. This system has potential veterinary applications, ecology of serpentes, and zoonotic disease research.
2026-06-17 | GSE313816 | GEO
Project description:Puccinia graminis f.sp. tritici (Pgt), the causal agent of stem rust disease in wheat, is one of the most destructive pathogens and can cause severe yield losses. Here, we utilize Hi-C sequencing technology to scaffold and phase the haplotypes for the genome assembly of a US Pgt isolate 99KS76A-1.
2022-10-01 | GSE210552 | GEO
Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
| 2533916 | ecrin-mdr-crc
Project description:Neonatal Pathogens genome sequencing and assembly
| PRJNA299115 | ENA
Project description:The naked mole-rat (NMR; Heterocephalus glaber) has recently gained considerable attention in the scientific community for its unique potential to unveil novel insights in the fields of medicine, biochemistry, and evolution. NMRs exhibit unique adaptations that include protracted fertility, cancer resistance, eusociality, and anoxia. This suite of adaptations is not found in other rodent species, suggesting that interrogating conserved and accelerated regions in the NMR genome will find regions of the NMR genome fundamental to their unique adaptations. However, the current NMR genome assembly has limits that make studying structural variations, heterozygosity, and non-coding adaptations challenging. We present a complete diploid naked-mole rat genome assembly by integrating long-read and 10X-linked read genome sequencing of a male NMR and its parents, and Hi-C sequencing in the NMR hypothalamus (N=2). Reads were identified as maternal, paternal or ambiguous (TrioCanu). We then polished genomes with Flye, Racon and Medaka. Assemblies were then scaffolded using the following tools in order: Scaff10X, Salsa2, 3d-DNA, Minimap2-alignment between assemblies, and the Juicebox Assembly Tools. We then subjected the assemblies to another round of polishing, including short-read polishing with Freebayes. We assembled the NMR mitochondrial genome with mitoVGP. Y chromosome contigs were identified by aligning male and female 10X linked reads to the paternal genome and finding male-biased contigs not present in the maternal genome. Contigs were assembled with publicly available male NMR Fibroblast Hi-C-seq data (SRR820318). Both assemblies have their sex chromosome haplotypes merged so that both assemblies have a high-quality X and Y chromosome. Finally, assemblies were evaluated with Quast, BUSCO, and Merqury, which all reported the base-pair quality and contiguity of both assemblies as high-quality. The assembly will next be annotated by Ensembl using public RNA-seq data from multiple tissues (SRP061363). Together, this assembly will provide a high-quality resource to the NMR and comparative genomics communities.
2022-06-27 | E-MTAB-11831 | biostudies-arrayexpress