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1st ToBRFV Nextstrain update

ABSTRACT: First expansion of the public Tomato brown rugose fruit virus (ToBRFV) Nextstrain build inclusion of new genomic and epidemiological data

PROVIDER: PRJEB42296 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	ERR5032740_1.fastq.gz	Fastqsanger.gz
	ERR5032740_2.fastq.gz	Fastqsanger.gz
	ERR5032750_1.fastq.gz	Fastqsanger.gz
	ERR5032750_2.fastq.gz	Fastqsanger.gz
	ERR5032760_1.fastq.gz	Fastqsanger.gz

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Project description:EMG produced TPA metagenomics assembly of PRJEB42296 data set (First expansion of the public Tomato brown rugose fruit virus (ToBRFV) Nextstrain build inclusion of new genomic and epidemiological data).

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Project description:Real-time tracking of Tomato brown rugose fruit virus (ToBRFV) outbreaks in the Netherlands using Nextstrain.

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Atlas of ticks (Acari: Argasidae, Ixodidae) in Germany: 1st data update.

Project description:The first data update of the atlas of ticks in Germany published in 2021 is presented here. This atlas provides maps based on georeferenced tick locations of 21 species endemic in Germany as well as three tick species that are regularly imported to Germany. The data update includes the following numbers of newly georeferenced tick locations: 17 Argas reflexus, 79 Carios vespertilionis, 2 Dermacentor marginatus, 43 Dermacentor reticulatus, 4 Haemaphysalis concinna, 3 Haemaphysalis punctata, 3 Hyalomma rufipes, 3 Ixodes apronophorus, 9 Ixodes arboricola, 1 Ixodes ariadnae, 30 Ixodes canisuga, 3 Ixodes frontalis, 80 Ixodes hexagonus, 3 Ixodes lividus, 497 Ixodes ricinus/inopinatus, 1 Ixodes rugicollis, 17 Ixodes trianguliceps, 14 Ixodes vespertilionis, and 45 Rhipicephalus sanguineus sensu lato. Old and new tick findings were mapped, such as the northernmost occurrence of D. marginatus in Germany observed in 2021, but also the historical records from the first descriptions of I. apronophorus and I. arboricola, which were georeferenced here for the first time. The digital dataset of tick locations available for Germany is supplemented by 854 new tick locations. These records increase the number of tick species mapped in the federal states Bavaria, Brandenburg and Mecklenburg Western Pomerania by five each, those in Berlin and Schleswig-Holstein by four each, those in Hamburg by three, those in Baden-Wuerttemberg, Bremen, Lower Saxony, Northrhine-Westphalia, Rhineland Palatinate and Thuringia by two each, and those in Hesse, Saxony and Saxony-Anhalt by one each. Thus, the first data update of the tick atlas in Germany and the underlying digital dataset significantly improve our knowledge of the distribution of these tick species and helps to investigate the effects of climate change and habitat changes on them.

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Microbial Reference Data - 1st phase

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GNPS - Microbial Reference Data - 1st phase

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Project description:State-Wide Genomic and Epidemiological Analyses of VREfm in Tasmania's Public Hospitals

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Contradictory of gene expression signatures for clinical prognostic prediction caused by update of reference genome and annotation

Project description:Gene expression estimates detected by RNA-sequencing technology vary with the updates of reference genome and gene annotation, which might confound existing expression-based prognostic signatures, making them inapplicable to clinical practice. In this study, we proposed a method to decrease these effects and developed a qualitative signature for stage I lung adenocarcinoma, whose classification was based on within-sample relative expression orderings (REOs) of gene pairs. The signature was validated in 471 stage I samples derived from public RNA-sequencing and microarray data (both log-rank p < 0.001). Notably, our signature could effectively predict prognosis for 30 stage I patients with severely degraded FFPE tissues (log-rank p = 0.0177). More important, the risk classification was stable in the latest annotation. In summary, our signature would be a promising signature for clinical individualized application because of its excellent prognostic performance and classification robustness.

2020-01-13 | GSE143486 | GEO

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