Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: ESBL Enterobacterales from Companion Animals Raw sequence reads

PROVIDER: PRJNA856883 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR20048900_1.fastq.gz	Fastqsanger.gz
	SRR20048900_2.fastq.gz	Fastqsanger.gz
	SRR20048901_1.fastq.gz	Fastqsanger.gz
	SRR20048901_2.fastq.gz	Fastqsanger.gz
	SRR20048902_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 266

Similar Datasets

Morus alba Raw protein sequence reads

Project description:Morus alba L. Raw protein sequence reads and sequence

2024-02-08 | PXD049451 |

ESBL-sharing

Project description:Healthy companion animals and owners colonisation and sharing of ESBL/AmpC-producing Enterobacterales, Portugal and United Kingdom

| PRJEB51686 | ENA

Project description:ESBL-encoding E. coli from companion animals and livestock in Tanzania

| PRJEB12335 | ENA

Enterobacterales

Project description:Enterobacterales Raw sequence reads

| PRJNA1049776 | ENA

Escherichia coli

Project description:Enterobacterales plasmids - raw sequence reads

| PRJNA877861 | ENA

Comprehensive Assessment of Initial Adaptation of ESBL Positive ST131 E. coli to Carbapenem Exposure

Project description:Background: It remains unclear how high-risk Escherichia coli lineages, like sequence type (ST) 131, initially adapt to carbapenem exposure in its progression to becoming carbapenem resistant. Methods: Carbapenem mutation frequency was measured in multiple subclades of extended-spectrum β-lactamase (ESBL) positive ST131 clinical isolates using a fluctuation assay followed by whole genome sequencing (WGS) characterization. Genomic, transcriptomic, and porin analyses of ST131 C2/H30Rx isolate, MB1860, under prolonged, increasing carbapenem exposure was performed using two distinct experimental evolutionary platforms to measure fast vs. slow adaptation. Results: All thirteen ESBL positive ST131 strains selected from a diverse (n=184) ST131 bacteremia cohort had detectable ertapenem (ETP) mutational frequencies with a statistically positive correlation between initial ESBL gene copy number and mutation frequency (r = 0.87, P<1e-5). WGS analysis of mutants showed initial response to ETP exposure resulted in significant increases in ESBL gene copy numbers or mutations in outer membrane porin (Omp) encoding genes in the absence of ESBL gene amplification with subclade specific adaptations. In both experimental evolutionary platforms, MB1860 responded to initial ETP exposure by increasing blaCTX-M-15 copy numbers via modular, insertion sequence 26 (IS26) mediated pseudocompound transposons (PCTns). Transposase activity driven by PCTn upregulation was a conserved expression signal in both experimental evolutionary platforms. Stable mutations in Omp encoding genes were detected only after prolonged increasing carbapenem exposure consistent with clinical observations. Conclusions: ESBL gene amplification is a conserved response to initial carbapenem exposure, especially within the high-risk ST131 C2 subclade. Targeting such amplification could assist with mitigating carbapenem resistance development.

2024-08-04 | GSE273456 | GEO

Project description:ESBL-EC in animals

| PRJNA1043574 | ENA

Project description:Complete genome sequence of Escherichia coli isolated from humans, companion animals, industrial animals and wild animals.

| PRJNA1087359 | ENA

Project description:ESBL Salmonella enterica Raw sequence reads

| PRJNA740259 | ENA

Quantitative profiling of differentially expressed miRNAs in siCTL- and siOASL-transfected HUVECs

Project description:Purpose: The goal of this study is to compare endothelial small RNA transcriptome to identify the target of OASL under basal or stimulated conditions by utilizing miRNA-seq. Methods: Endothelial miRNA profilies of siCTL or siOASL transfected HUVECs were generated by illumina sequencing method, in duplicate. After sequencing, the raw sequence reads are filtered based on quality. The adapter sequences are also trimmed off the raw sequence reads. rRNA removed reads are sequentially aligned to reference genome (GRCh38) and miRNA prediction is performed by miRDeep2. Results: We identified known miRNA in species (miRDeep2) in the HUVECs transfected with siCTL or siOASL. The expression profile of mature miRNA is used to analyze differentially expressed miRNA(DE miRNA). Conclusions: Our study represents the first analysis of endothelial miRNA profiles affected by OASL knockdown with biologic replicates.

2022-09-06 | GSE186354 | GEO

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