Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: EMG produced TPA metagenomics assembly of PRJNA791897 data set (Systematic comparison of nanopore sequencing and Illumina sequencing for the detection of plant viruses and viroids using total RNA sequencing approach).

PROVIDER: PRJEB55543 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR17660995.fasta.gz	Fasta.gz
	SRR17319908.fasta.gz	Fasta.gz
	SRR17660993.fasta.gz	Fasta.gz
	SRR17660996.fasta.gz	Fasta.gz
	SRR17660994.fasta.gz	Fasta.gz

Items per page:

1 - 5 of 13

Similar Datasets

Project description:Systematic comparison of nanopore sequencing and Illumina sequencing for the detection of plant viruses and viroids using total RNA sequencing approach

| PRJNA791897 | ENA

Project description:EMG produced TPA metagenomics assembly of PRJNA479723 data set (Nanopore metagenomics).

| PRJEB42552 | ENA

HTS based monitoring of the efficiency of somatic embryogenesis and meristem culture as a method used for virus elimination in grapevine

Project description:Meristem culture and somatic embryogenesis is an effective tool for virus elimination of vegetatively propagated crops including grapevine. While they both are proved to be useful to eliminate the main grapevine viruses their efficiency differs according to the virus and the variety. In our work we investigated their efficiency using small RNA high-throughput sequencing as virus diagnostic method. Field grown mother plants of four clones representing three cultivars, infected with different viruses and viroids were selected for sanitation via somatic embryogenesis and meristem culture. Our results show that the sanitation with SE was efficient against all of the presenting viruses, including grapevine Pinot gris virus, grapevine rupestris vein feathering virus and grapevine Syrah virus 1, having no data using somatic embryogenesis for their elimination. In case of other viruses and viroids such as GFkV, GRSPaV, GYSVd-1, HSVd this study confirms the findings of earlier researches, that SE is a possible way for elimination. While the efficiency of the elimination of different viruses was high, in case of viroids this ratio was lower. Our work demonstrated that efficiency of SE is comparable to the technically difficult meristem culture technique, and show promising way for the high demand of the production of virus-free grapevine in the future.

2020-12-31 | GSE159758 | GEO

New approaches to the production of certified varieties of apple trees using NGS diagnostics of pathogens

Project description:Implementation and evaluation of tests (PCR, ELISA, NGS) for the presence of viruses, viroids and phytoplasma in propagation materials of apple. Research and application of new sanitation techniques using promising antiviral substances, or cryo-knife. Confirmation of health status of sanitated cultivars including use of modern diagnostic methods such as high-throughput sequencing (NGS).

2022-12-09 | GSE205183 | GEO

Project description:EMG produced TPA metagenomics assembly of the PRJNA288501 data set (Freshwater Viruses Metagenomic assembly).

| PRJEB31431 | ENA

Project description:Viruses and viroids in opuntia spp.

| PRJNA1096702 | ENA

Project description:EMG produced TPA metagenomics assembly of PRJNA343503 data set (fruitshake sequence reads using Oxford Nanopore MinION).

| PRJEB44280 | ENA

Large scale sequencing of viroid derived small RNA in Potato spindle tuber viroid infected tomato plants

Project description:In order to analyze the production of small RNA (sRNA) by viroids upon infecting the plants, the tomato plants (Lycopersicum esculentum cv. Rutgers) were inoculated with the variants of Potato spindle tuber viroid (PSTVd). After 21-days of post inoculation, total RNA was extracted and subjected for deep-sequencing using Illumina platform. The primers were trimmed and only 21- to 24-nt long small RNAs were filtered after quality check of the raw data. The filtered 21- to 24-nt was mapped against the genomic and antigenomic strands of the respective PSTVd variants using standard pattern matching algorithm. The profiling of viroid derived sRNA (vd-sRNA) revealed that the viroids are susceptible to host RNA silencing mechanism. Evaluation of the vd-sRNA production in PSTVd infected tomato plants by high-throughput sequencing of small RNAs.

2015-05-27 | E-GEOD-69225 | biostudies-arrayexpress

Project description:EMG produced TPA metagenomics assembly of PRJNA785116 data set (Metagenomic sequencing).

| PRJEB56770 | ENA

Nanopore sequencing of B. thetaiotaomicron hankyphages

Project description:We identified hankyphage prophages within B. thetaiotaomicron isolates gathered from French hospitals. We extracted genomic DNA from an overnight culture from a single colony of each strain and sequenced them using Nanopore sequencing using the Plasmidsaurus platform. This long-read approach helped the assembly of the phages and determination of the hankyphage ends. We also improved the annotation of the reference hankyphage (hankyphage p00 from P. dorei HM719) using a structural prediction approach and annotated our B. thetaiotaomicron hankyphages using this new annotation. In this project we upload the genomic raw reads of nanopore sequencing of our hankyphage-bearing B. thetaiotaomicron collection (jmh strains) and the processed assembled hankyphages.

2025-01-24 | E-MTAB-14724 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data