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:One ONT-ULK sequencing run from the kidney of a single male CDMR (Bathyergus suillus) sample used to make the mBatSui1.1.primary genome assembly as an evolutionary comparator to our telomere-to-telomere naked mole-rat genome assembly. Specifically, we assembled a CDMR from a wild-derived sample in South African cape and sequenced in Toronto, Canada, using PacBio HiFi (89 Gb, read N50 = 18 Kb) and ONT-ULK (55 Gb, read N50 = 43 Kb) reads (contig N50 = 33 Mb, Compleasm S = 99%, QV = 71.0). This accession stores the ONT-ULK data for this assembly.
2026-08-05 | E-MTAB-17420 | biostudies-arrayexpress
Project description:One PacBio Hifi sequencing run from the kidney of a single male CDMR (Bathyergus suillus) sample used to make the mBatSui1.1.primary genome assembly as an evolutionary comparator to our telomere-to-telomere naked mole-rat genome assembly. Specifically, we assembled a CDMR from a wild-derived sample in South African cape and sequenced in Toronto, Canada, using PacBio HiFi (89 Gb, read N50 = 18 Kb) and ONT-ULK (55 Gb, read N50 = 43 Kb) reads (contig N50 = 33 Mb, Compleasm S = 99%, QV = 71.0). This accession stores the Pacbio Hifi data for this assembly.
2026-08-05 | E-MTAB-17312 | biostudies-arrayexpress