Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Diagnostic metagenomics proficiency test dataset

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

PROVIDER: PRJEB37463 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR4298353.fastq.gz	Fastqsanger.gz

Items per page:

1 - 1 of 1

Similar Datasets

GMI Proficiency Test

Project description:Global Microbial Identifier Proficiency Test

| PRJEB21132 | ENA

Proficiency testing of metagenomics

Project description:A proficiency testing of metagenomics as a diagnostic tool for the detection of RNA viruses in swine fecal material

| PRJEB44508 | ENA

DTU Genomic Proficiency Test 2020

Project description:Evaluating EURL Reference Laboratories performance in bacterial sequencing in the 2020 DTU Genomic Proficiency Test.

| PRJEB58706 | ENA

Transcription profiling of rat mixed-tissue RNA samples in different laboratories to monitor proficiency

Project description:A pilot program for monitoring proficiency in microarray facilities using three replicates of two different RNA sources. Participating laboratories prepared and hybridized targets from the six RNA samples using their own protocols. The entire process was repeated three times over a nine-month period and included approximately fifteen distinct laboratories in each testing round.

2008-09-12 | E-MEXP-1568 | biostudies-arrayexpress

The DTU Genomic Proficiency Test 2022

Project description:The 2022 DTU genomic proficiency test for the network of EU reference laboratory for antimicrobial resistance

| PRJEB65175 | ENA

The DTU Genomic Proficiency Test 2021

Project description:The 2021 DTU genomic proficiency test for the network of EU reference laboratory for antimicrobial resistance

| PRJEB65174 | ENA

Mre11 suppresses replication stress and gene amplification proficiency

Project description:Gene amplification, copy-number increases of particular genes and surrounding genomic segments, promotes cancer progression and acquired therapy resistance. Thus, understanding genetic traits that confer gene amplification proficiency is important. The primary step for gene amplification is spontaneous DNA rearrangements initiated by DNA breaks. Here we show that mammalian cells became gene amplification-proficient when we knocked down Mre11/Rad50/Nbs1 (MRN) complex, a multifunctional complex that guards the genome from DNA breaks. Cells with reduced Mre11 experienced severe replication stress, with marked increases of single-stranded breaks followed by double-stranded breaks during DNA replication. Such breaks underlay for the increase in spontaneous gene amplification. Other traits associated with replication stress, such as impaired intra-S phase checkpoint and global transcriptional changes in DNA metabolism genes also contributed to gene amplification proficiency. Our results define Mre11 deficiency as a cause of replication stress and gene amplification proficiency and provide a candidate marker for aggressive cancer phenotypes.

2015-03-05 | GSE59487 | GEO

Mre11 suppresses replication stress and gene amplification proficiency

2015-03-05 | E-GEOD-59487 | biostudies-arrayexpress

Metagenomics-Based Proficiency Test of Smoked Salmon Spiked with a Mock Community.

Project description:An inter-laboratory proficiency test was organized to assess the ability of participants to perform shotgun metagenomic sequencing of cold smoked salmon, experimentally spiked with a mock community composed of six bacteria, one parasite, one yeast, one DNA, and two RNA viruses. Each participant applied its in-house wet-lab workflow(s) to obtain the metagenomic dataset(s), which were then collected and analyzed using MG-RAST. A total of 27 datasets were analyzed. Sample pre-processing, DNA extraction protocol, library preparation kit, and sequencing platform, influenced the abundance of specific microorganisms of the mock community. Our results highlight that despite differences in wet-lab protocols, the reads corresponding to the mock community members spiked in the cold smoked salmon, were both detected and quantified in terms of relative abundance, in the metagenomic datasets, proving the suitability of shotgun metagenomic sequencing as a genomic tool to detect microorganisms belonging to different domains in the same food matrix. The implementation of standardized wet-lab protocols would highly facilitate the comparability of shotgun metagenomic sequencing dataset across laboratories and sectors. Moreover, there is a need for clearly defining a sequencing reads threshold, to consider pathogens as detected or undetected in a food sample.

| S-EPMC7760972 | biostudies-literature

Lake Cadagno Chemocline Metagenomics Dataset

Project description:Lake Cadagno Chemocline Metagenomics Dataset

| PRJNA863637 | ENA