Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Whole-genome sequencing of Gram-negative bacterial strains

PROVIDER: PRJNA1247368 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR32999530_1.fastq.gz	Fastqsanger.gz
	SRR32999530_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 2 of 2

Similar Datasets

Bottom-up MS of soluble MAC released from bacteria

Project description:Human serum was treated with different Gram-positive and Gram-negative bacterial strains. The whole serum or sMAC isolated from serum were then separated by size-exclusion chromatography (SEC) and the fractions were analyzed by Bottom-up MS.

2021-12-14 | MSV000088560 | MassIVE

Profiling the circulating miRNAs in mice exposed to gram-positive and gram-negative bacteria by Illumina small RNA deep sequencing

Project description:We profiled the expression of circulating microRNAs (miRNAs) in mice exposed to gram-positive and gram-negative bacteria using Illumina small RNA deep sequencing. Recombinant-specific gram-negative pathogen Escherichia coli (Xen14) and gram-positive pathogen Staphylococcus aureus (Xen29) were used to induce bacterial infection in mice at a concentration of 1 × 108 bacteria/100 μL of phosphate buffered saline (PBS). Small RNA libraries generated from the serum of mice after exposure to PBS, Xen14, Xen29, and Xen14+Xen29 via the routes of subcutaneous injection (I), cut wound (C), or under grafted skin (S) were analyzed using an Illumina HiSeq2000 Sequencer. Following exposure to gram-negative bacteria alone, no differentially expressed miRNA was found in the injection, cut, or skin graft models. Exposure to mixed bacteria induced a similar expression pattern of the circulating miRNAs to that induced by gram-positive bacterial infection. Upon gram-positive bacterial infection, 9 miRNAs (mir-193b-3p, mir-133a-1-3p, mir-133a-2-3p, mir-133a-1-5p, mir-133b-3p, mir-434-3p, mir-127-3p, mir-676-3p, mir-215-5p) showed upregulation greater than 4-fold with a p-value < 0.01. Among them, mir-193b-3p, mir-133a-1-3p, and mir-133a-2-3p presented the most common miRNA targets expressed in the mice exposed to gram-positive bacterial infection.

2014-08-19 | GSE60492 | GEO

Project description:Whole genome sequencing of Gram-negative bacteria

| PRJNA871949 | ENA

Pathogen Class-specific Transcriptional Responses Derived from PBMCs Accurately Discriminate Between Fungal, Bacterial, and Viral Infections [DiscoveryCohort]

Project description:Host gene expression responses can be used to determine the etiology of acute infection. PBMCs were stimulated with bacterial, viral, and fungal stimuli and then analyzed for differential gene expression utilizing microarrays to derive pathogen class-specific gene expression classifiers of infection. Discovery Cohort: In vitro human PBMC challenges were performed with bacteria (gram postive and gram negative), viruses (4 strains of influenza), and fungi (Cryptococcus and Candida)

2024-09-28 | GSE277848 | GEO

A multicenter translational biomarker phase II trial of regorafenib in patients with non-resectable pretreated colorectal cancer.

Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS). Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).

| 2533916 | ecrin-mdr-crc

A cell-free pipeline for recreating methylation patterns radically enhances DNA transformation in bacteria

Project description:The bacterial world offers diverse strains for understanding medical and environmental processes and for engineering synthetic-biology chasses. However, genetically manipulating these strains has faced a long-standing bottleneck: how to efficiently transform DNA. Here we report IMPRINT, a generalized, rapid and scalable approach to overcome DNA restriction, a prominent barrier to transformation. IMPRINT utilizes cell-free systems to express DNA methyltransferases from the bacterial host’s restriction-modification systems. The expressed methyltransferases then methylate DNA in vitro to match the host DNA’s methylation pattern, circumventing restriction and enhancing transformation. Unlike established approaches, IMPRINT can be completed in under one day, readily accommodates all methyltransferase types, and avoids methylation-induced cytotoxicity. With IMPRINT, we efficiently multiplex DNA methylation and maximize plasmid transformation in gram-negative and gram-positive bacteria. We also developed a high-throughput pipeline that identifies the most consequential methyltransferases in one transformation. Overall, IMPRINT can vastly enhance DNA transformation, enabling use of increasingly sophisticated genetic manipulation tools across the bacterial world.

2024-04-07 | GSE240651 | GEO

Comparative genomic hybridization of Bordetella bronchiseptica strains 253 and RB50 to investigate the cya adenylate cyclase toxin (ACT) operon

Project description:Bordetella bronchiseptica is a gram-negative respiratory pathogen that causes a diverse spectrum of respiratory disease in a wide-range of hosts. We sought to determine if strains of B. bronchiseptica differed in virulence using the mouse model of infection. Mean lethal doses (LD50) of different B. bronchiseptica strains varied widely in the murine model. B. bronchiseptica strain 253 had a LD50 that was 10-fold lower than the prototypical and fully sequenced B. bronchiseptica strain RB50. Using whole genomic transcriptome analysis covering 100% of B. bronchisetpctica strain RB50ÃÂs predicted open reading frames (ORFs), 253 was identified as lacking expression of adenylate cyclase toxin (ACT). Using whole genomic comparative genomic hybridization analysis and whole genome sequencing, we determined that the cya operon, which is required for ACT production, was absent from the 253 genome.

2007-10-01 | E-MEXP-1205 | biostudies-arrayexpress

carbapenem-resistant gram-negative bacterial isolates

Project description:Characterization of carbapenem-resistant Gram-negative bacterial isolates from Nigeria by whole genome sequencing

| PRJNA701275 | ENA

Expression data from bone marrow neutrophils with or without LPS stimulation in wild type and miR-125a deficient mice

Project description:Neutrophil activation plays a critical role in the inflammatory response to gram-negative bacterial infections. Lipopolysaccharide (LPS) from gram-negative bacterial has been shown to be a major mediator of neutrophil activation to produce pro-inflammatory cytokines, chemokines and ROS which are important to tissue damage in LPS induced septic shock. We used microarrays to detail the global gene expression of neutrophils from miR-125a+/+ and miR-125a-/- mice after LPS stimulation.

2014-12-02 | GSE63739 | GEO

Gram negative bacteria

Project description:Gram negative bacteria Genome sequencing

| PRJNA594823 | ENA