Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Salmonella enterica subsp. enterica

ABSTRACT: Evaluation of commercial DNA extraction kits for implementation of rapid Nanopore sequencing for routine diagnostic laboratories

PROVIDER: PRJNA768992 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR16525216_1.fastq.gz	Fastqsanger.gz
	SRR16525217_1.fastq.gz	Fastqsanger.gz
	SRR16525218_1.fastq.gz	Fastqsanger.gz
	SRR16525219_1.fastq.gz	Fastqsanger.gz
	SRR16525220_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 60

Similar Datasets

Project description:Evaluation of Commercial RNA Extraction Kits for Long-Read Metatranscriptomics in Soil

| PRJNA1079547 | ENA

Project description:Evaluation of commercial DNA extraction kits for analysing microbial diversity in the pig gastrointestinal tract

| PRJEB9411 | ENA

Comparison of RNA Isolation Methods in Yeast on RNA-Seq: Implications for Differential Expression and Meta-Analyses

Project description:Based on the different chemistries of phenol extraction of RNA versus commercial kits, we hypothesized that certain species of mRNA may be preferentially extracted depending upon method, which could masquerade as differential expression in downstream RNA-seq experiments. We tested this using Saccharomyces cerevisiae samples that only differ in the RNA isolation method: a "standard" hot phenol extraction, versus two different commercial RNA isolation kits. While the kits had comparable relative mRNA abundances, samples isolated with hot phenol had higher relative abundance of mRNAs encoding membrane proteins. We hypothesize that hot phenol better solubilizes mRNAs associated with cellular membranes. We then compared the effects of each RNA isolation method on the ability to identify differentially expressed transcripts, using the yeast heat shock response a test case. The method of RNA isolation had little effect on the ability to identify differentially expressed transcripts. Thus, experiments within a single lab are unlikely to be affected by the choice of RNA isolation method as long as the same method is used throughout an experiment. For meta-analyses however, researchers should be cautious if trying to compare experiments where the RNA isolation methods differ.

2019-08-07 | GSE135430 | GEO

Extraction of Entamoeba histolytica membrane proteins using three extraction methods

Project description:Entamoeba histolytica membrane proteins are important players in the parasite’s pathogenicity. However, most of the proteins have not been identified. This study reports the membrane proteins extracted using three extractions methods: two commercial kits (ProteoExtract® from Calbiochem and ProteoPrep® from Sigma), and a conventional laboratory method. The resulting membrane fractions (MF) and cytosolic fractions (CF)were analysed using LC-ESI-MS/MS. The proteins identified in at least two out of three biological replicates revealed a total of 490, 492, and 587 MF proteins extracted using the ProteoExtract® kit, ProteoPrep® kit and conventional method, respectively. Meanwhile, 487, 611 and 343 proteins were identified in the CF extracted using the ProteoExtract® kit, ProteoPrep® kit and conventional method, respectively. Analysis of the identified MF and CF proteins extracted by the respective extraction kits suggests that the ProteoPrep® extraction kit was the most selective in separating MF and CF among the three extraction methods.

2018-10-16 | PXD010171 | Pride

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

Bacteria and eukaryotes

Project description:The study of DNA extraction kits

| PRJNA474064 | ENA

Diagnosis of Taenia solium infections based on “mail order” RNA-sequencing of single tapeworm egg isolates from stool samples

Project description:Combined community health programs aiming at health education, preventive antiparasitic chemotherapy, and vaccination of pigs have proven their potential to regionally reduce and even eliminate Taenia solium infections that are associated with a high risk of neurological disease through ingestion of T. solium eggs. Yet it remains challenging to target T. solium endemic regions precisely or to make exact diagnoses in individual patients. One major reason is that the widely available stool microscopy may identify Taenia ssp. eggs in stool samples as such, but fails to distinguish between invasive (T. solium) and less invasive Taenia (T. saginata, T. asiatica, and T. hydatigena) species. The identification of Taenia ssp. eggs in routine stool samples often prompts a time-consuming and frequently unsuccessful epidemiologic workup in remote villages far away from a diagnostic laboratory. Here we present “mail order” single egg RNA-sequencing, a new method allowing the identification of the exact Taenia ssp. based on a few eggs found in routine diagnostic stool samples. We provide first T. solium transcriptome data, which show extremely high mitochondrial DNA (mtDNA) transcript counts that can be used for subspecies identification. “Mail order” RNA-sequencing can be administered by health personnel equipped with basic laboratory tools such as a microscope, a Bunsen burner, and access to an international post office for shipment of samples to a next generation sequencing facility. Our suggested workflow combines traditional stool microscopy, RNA-extraction from single Taenia eggs with mitochondrial RNA-sequencing, followed by bioinformatic processing with a basic laptop computer. The workflow could help to better target preventive healthcare measures and improve diagnostic specificity in individual patients based on incidental findings of Taenia ssp. eggs in diagnostic laboratories with limited resources.

2021-11-06 | GSE175668 | GEO

Mock communities - ONT

Project description:Evaluation of DNA extraction kits for long-read shotgun metagenomics using Oxford Nanopore sequencing for rapid taxonomic and antimicrobial resistance detection

| PRJEB75510 | ENA

Nassar2022 - Microbome nucleic acid extraction kit NER model

Project description:Microbiome nucleic acid extraction kit model is a Named Entity Recognition (NER) model that identifies and annotates the name of the kits used in extracting microbiome nucleic acids in texts. This is the final model version used to annotate metagenomics publications in Europe PMC and enrich metagenomics studies in MGnify with kits metadata from literature. For more information, please refer to the following blogs: http://blog.europepmc.org/2020/11/europe-pmc-publications-metagenomics-annotations.html https://www.ebi.ac.uk/about/news/service-news/enriched-metadata-fields-mgnify-based-text-mining-associated-publications

2022-02-21 | MODEL2202170007 | BioModels

syrian hamster plasma FPLC data

Project description:Plasma lipoprotein profiles were analyzed by FPLC.The TC and TG levels were determined using the same commercial kits for TC and TG.

2022-10-13 | PXD036331 | Pride

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