Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Swine wastewater

ABSTRACT: swine wastewater Genome sequencing and assembly

PROVIDER: PRJNA1212861 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR32367546_1.fastq.gz	Fastqsanger.gz
	SRR32367546_2.fastq.gz	Fastqsanger.gz
	SRR32367547_1.fastq.gz	Fastqsanger.gz
	SRR32367547_2.fastq.gz	Fastqsanger.gz
	SRR32367548_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 20

Similar Datasets

swine wastewater

Project description:swine wastewater Metagenome

| PRJNA1050755 | ENA

Metagenomic samples of swine wastewater

Project description:Metagenomic samples of swine wastewater

| PRJNA1000773 | ENA

Large-scale swine wastewater

Project description:Large-scale swine wastewater Raw sequence reads

| PRJNA1152766 | ENA

Wastewater treatment and land application of swine wastewater

Project description:Wastewater treatment and land application of swine wastewater Raw sequence reads

| PRJNA591725 | ENA

Wastewater from anoxic-oxic processes for swine wastewater treatment

Project description:Wastewater from anoxic-oxic processes for swine wastewater treatment Metagenome

| PRJNA1176330 | ENA

Effective Inhibitor Removal from Wastewater Samples Increases Sensitivity of RT-dPCR and Sequencing Analyses and Enhances the Stability of Wastewater-Based Surveillance

Project description:Wastewater-based surveillance (WBS) is a proven tool for monitoring population-level infection events. Wastewater contains high concentrations of inhibitors, which contaminate total nucleic acids (TNA) extracted from these samples. We found that TNA extracts from raw influent of Berlin wastewater treatment plants contained highly variable amounts of inhibitors that impaired molecular analyses like dPCR and next-generation sequencing (NGS). By using dilutions, we were able to detect inhibitory effects. To enhance WBS sensitivity and stability, we applied a combination of PCR inhibitor removal and TNA dilution (PIR+D). This approach led to a 26-fold increase in measured SARS-CoV-2 concentrations, practically reducing the detection limit. Additionally, we observed a substantial increase in stability of the time series. We define suitable stability as a mean absolute error (MAE) below 0.1 log10 copies/l and a geometric mean relative absolute error (GMRAE) below 26%. Using PIR+D, the MAE could be reduced from 0.219 to 0.097 and the GMRAE from 65.5% to 26.0% and even further in real-world WBS. Furthermore, PIR+D improved SARS-CoV-2 genome alignment and coverage in amplicon-based NGS for low to medium concentrations. In conclusion, we strongly recommend both the monitoring and removal of inhibitors from samples for WBS.

2024-11-27 | GSE283001 | GEO

pigs farm wastewater

Project description:swine wastewater Raw sequence reads

| PRJNA1093017 | ENA

African swine fever virus tropism for different organ tissues and host transcriptomic responses in experimentally infected pigs

Project description:Purpose: This goal of this study was to explore the host transcriptomic responses in African swine fever virus experimentally infected pigs using RNA-Sequencing. Methods: RNAs acquired from ten different organ tissue samples were sequenced. Sequencing reads were preprocessed, aligned with the reference genome, assembled and expressions were estimated through bioinformatics approaches. Result: Several uprugulated DEGs were identified. Conclusion: We found important candidate genes and pathways for further testing in African swine fever virus infection in pig.

2023-04-23 | GSE230340 | GEO

African swine fever virus

Project description:African swine fever virus Genome sequencing and assembly

| PRJNA647921 | ENA

African swine fever virus

Project description:African swine fever virus Genome sequencing and assembly

| PRJNA559072 | ENA