Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Metagenomics: a new frontier for routine pathology testing of gastrointestinal pathogens

PROVIDER: PRJNA1156595 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR30543600_1.fastq.gz	Fastqsanger.gz
	SRR30543600_2.fastq.gz	Fastqsanger.gz
	SRR30543700_1.fastq.gz	Fastqsanger.gz
	SRR30543700_2.fastq.gz	Fastqsanger.gz
	SRR30543800_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 660

Similar Datasets

NGS of virus derived small RNAs as a diagnostics method used to determine viromes of Hungarian vineyards

Project description:As virus diseases cannot be controlled by traditional plant protection methods the risk of their spread have to be minimized on vegetatively propagated plants, such as grapevine. Metagenomics approaches used for virus diagnostics, offer a unique opportunity to reveal the presence of all viral pathogens in the investigated plant, why their usage can reduce the risk of using infected material for a new plantation. Here we used a special field, deep sequencing of virus derived small RNAs, of this high throughput method for virus diagnostics and determined viromes of vineyards in Hungary. With NGS of virus derived small RNAs we could detect not only the viruses tested routinely, but also new ones, which have never been described in Hungary before. Virus presence didn’t correlated with the age of the plantation, moreover phylogenetic analysis of the identified virus isolates suggests that infections mostly caused by the usage of infected propagating material. Our results, validated by other molecular methods, highlighted further questions to be answered before these method can be introduced as a routine, reliable test for grapevine virus diagnostics.

2018-04-05 | GSE106240 | GEO

Rapid Identification of Bacterial Pathogens using a PCR- and Microarray-Based Assay

Project description:A method based on a modified broad-range PCR and an oligonucleotide microarray for the simultaneous detection and identification of 12 bacterial pathogens at the species level. The feasibility of this assay in routine diagnostic testing was evaluated using 146 blood culture positive and 40 blood culture negative samples. The processed data are composed of ORGANISM NAME or NEGATIVE answer depending if the pathogen is detected in the sample or not. See supplementary file linked below.

2010-06-24 | E-GEOD-17221 | biostudies-arrayexpress

CGH profiles of primary breast carcinomas from HBOC (Hereditary Breast and Ovarian Cancer) families

2010-07-05 | GSE22481 | GEO

Fecal Metagenomics and Metabolomics Analyses to Identify Potential Screening Biomarkers for Colorectal Polyps and Cancer in Chinese Population

Project description:Many previous studies had revealed that gastrointestinal microbiome is changed compositionally and ecologically in patients with colorectal cancer comparing with healthy population. These finding provide us with a new sight to take advantage of gut microbiota. The current study aims to explore new potential biomarkers for early screening and prognostic prediction of colorectal cancer and colorectal polyps by analyzing metagenomics and metabolomics of gut microbiota.

| 2382228 | ecrin-mdr-crc

Whole genome sequencing in cohort of probands with isolated cleft palate

Project description:The identification of the genetic risk factors in patients with isolated cleft palate by whole genome sequencing analysis. Pathogenic or likely pathogenic variants were discovered in genes associated with CP (TBX22, COL2A1, FBN1, PCGF2, and KMT2D) in five patients; hence, rare disease variants were identified in 17% of patients with non-syndromic isolated CP. Our results are relevant to routine genetic counselling practice and genetic testing recommendations.

2022-03-30 | E-MTAB-11360 | biostudies-arrayexpress

Giardia lamblia miRNAs as a new diagnostic tool for human giardiasis

Project description:Giardia lamblia is one of most common agents causing persistent abdominal symptoms in developed and developing countries. There are several diagnostic methods for Giardia infection, but none are optimal. In this study our aim was to find a new method based on Giardia microRNA (miRNA) that would contribute to the currently available diagnostic methods of giardiasis. Profiling Giardia small RNAs by deep sequencing revealed that the previously reported putative miR5 and miR6 are expressed in several G. lamblia isolates. These miRNAs were later tested by PCR in duodenal biopsies from 8 patients with positive pathology for giardiasis, while gastric biopsies served as matched negative controls. Additionally, these miRNAs were evaluated in stool samples of patients with proven giardiasis. All 8 duodenal samples of patients with histologically proven G. lamblia infection were positive for Giardia miR5 with a mean Ct of 23.7. These results were superior to Ct levels of G. lamblia DNA, which were 26.3 (p=0.004). The miR6 results were close to negative. All 10 gastric biopsies were negative for miR5. Stool studies showed 90% specificity but only 50% sensitivity in diagnosing giardiasis using miR6. The results of miR5 in stool were even less accurate. In conclusion, miR5 testing for Giardia infection in duodenal biopsies, may be a breakthrough method for diagnosis of giardiasis. It seems to be superior to G. lamblia DNA in duodenal biopsies. It would be important to investigate the contribution of routine Giardia miRNA testing in duodenal biopsies and duodenal aspirates from patients with persistent abdominal symptoms.

2019-05-09 | GSE116101 | GEO

Project description:Gastrointestinal metagenomics of sika deer

| PRJNA866670 | ENA

Project description:New York City Routine Pathogen Surveillance Sequencing Data

| PRJNA1020074 | ENA

diagnostic metagenomics proficiency test dataset

Project description:Proficiency testing of metagenomics-based detection of food-borne pathogens using a complex artificial sequencing dataset

| PRJEB37463 | ENA

CGH profiles of primary breast carcinomas from HBOC (Hereditary Breast and Ovarian Cancer) families

Project description:89 tumors from women that were eligible for, and subjected to, routine diagnostic testing according to the HBOC criteria but were negative for pathogenic BRCA1/2-mutations or carried an UV in either BRCA1/2 A BRCA2-classifier was built using array-CGH profiles of 28 BRCA2-mutated and 28 sporadic breast tumors. The classifier was validated on an independent group of 19 BRCA2-mutated and 19 sporadic breast tumors. Subsequently, we tested 89 breast tumors from suspected hereditary breast (and ovarian) cancer (HBOC) families, in which either no BRCA1/2 mutation or an UV had been found by routine diagnostics.

2010-07-05 | E-GEOD-22481 | 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