Ontology highlight
ABSTRACT:
PROVIDER: PRJNA771344 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16465657.fastq.gz | Fastqsanger.gz | |||
| SRR16465657_1.fastq.gz | Fastqsanger.gz | |||
| SRR16465657_2.fastq.gz | Fastqsanger.gz | |||
| SRR16465658.fastq.gz | Fastqsanger.gz | |||
| SRR16465658_1.fastq.gz | Fastqsanger.gz |
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Project description:We report the use of Next Generation RNA Sequencing for confirming or improving initial identification of small regulatory RNA in Staphylococcus aureus to prodive a list of the most probable RNA molecules transcribed as independent units. Extraction of RNAs in exponential phase of growth in Newman and N315 strains
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Project description:In this study, we have combined RNA-seq, Ribo-seq and shotgun proteomic analyses to identify and validate the expression of novel small proteins in Staphylococcus aureus.
2025-09-22 | PXD061402 | Pride
Project description:Staphylococcus Aureus N315-T100-1 assembly
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Project description:Becker2005 - Genome-scale metabolic network
of Staphylococcus aureus (iSB619)
This model is described in the article:
Genome-scale reconstruction
of the metabolic network in Staphylococcus aureus N315: an
initial draft to the two-dimensional annotation.
Becker SA, Palsson BØ.
BMC Microbiol. 2005; 5: 8
Abstract:
BACKGROUND: Several strains of bacteria have sequenced and
annotated genomes, which have been used in conjunction with
biochemical and physiological data to reconstruct genome-scale
metabolic networks. Such reconstruction amounts to a
two-dimensional annotation of the genome. These networks have
been analyzed with a constraint-based formalism and a variety
of biologically meaningful results have emerged. Staphylococcus
aureus is a pathogenic bacterium that has evolved resistance to
many antibiotics, representing a significant health care
concern. We present the first manually curated elementally and
charge balanced genome-scale reconstruction and model of S.
aureus' metabolic networks and compute some of its properties.
RESULTS: We reconstructed a genome-scale metabolic network of
S. aureus strain N315. This reconstruction, termed iSB619,
consists of 619 genes that catalyze 640 metabolic reactions.
For 91% of the reactions, open reading frames are explicitly
linked to proteins and to the reaction. All but three of the
metabolic reactions are both charge and elementally balanced.
The reaction list is the most complete to date for this
pathogen. When the capabilities of the reconstructed network
were analyzed in the context of maximal growth, we formed
hypotheses regarding growth requirements, the efficiency of
growth on different carbon sources, and potential drug targets.
These hypotheses can be tested experimentally and the data
gathered can be used to improve subsequent versions of the
reconstruction. CONCLUSION: iSB619 represents comprehensive
biochemically and genetically structured information about the
metabolism of S. aureus to date. The reconstructed metabolic
network can be used to predict cellular phenotypes and thus
advance our understanding of a troublesome pathogen.
This model is hosted on
BioModels Database
and identified by:
MODEL1507180070.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2024-10-15 | MODEL1507180070 | BioModels
Project description:Heinemann2005 - Genome-scale reconstruction
of Staphylococcus aureus (iMH551)
This model is described in the article:
In silico genome-scale
reconstruction and validation of the Staphylococcus aureus
metabolic network.
Heinemann M, Kümmel A,
Ruinatscha R, Panke S.
Biotechnol. Bioeng. 2005 Dec; 92(7):
850-864
Abstract:
A genome-scale metabolic model of the Gram-positive,
facultative anaerobic opportunistic pathogen Staphylococcus
aureus N315 was constructed based on current genomic data,
literature, and physiological information. The model comprises
774 metabolic processes representing approximately 23% of all
protein-coding regions. The model was extensively validated
against experimental observations and it correctly predicted
main physiological properties of the wild-type strain, such as
aerobic and anaerobic respiration and fermentation. Due to the
frequent involvement of S. aureus in hospital-acquired
bacterial infections combined with its increasing antibiotic
resistance, we also investigated the clinically relevant
phenotype of small colony variants and found that the model
predictions agreed with recent findings of proteome analyses.
This indicates that the model is useful in assisting future
experiments to elucidate the interrelationship of bacterial
metabolism and resistance. To help directing future studies for
novel chemotherapeutic targets, we conducted a large-scale in
silico gene deletion study that identified 158 essential
intracellular reactions. A more detailed analysis showed that
the biosynthesis of glycans and lipids is rather rigid with
respect to circumventing gene deletions, which should make
these areas particularly interesting for antibiotic
development. The combination of this stoichiometric model with
transcriptomic and proteomic data should allow a new quality in
the analysis of clinically relevant organisms and a more
rationalized system-level search for novel drug targets.
This model is hosted on
BioModels Database
and identified by:
MODEL1507180072.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2015-07-30 | MODEL1507180072 | BioModels
Project description:Staphylococcus aureus strain:N315 Raw sequence reads
| PRJNA669534 | ENA
Project description:Staphylococcus aureus subsp. aureus MRSA N315 Dantas genome sequencing
| PRJNA288150 | ENA
Project description:Analysis of Staphylococcus aureus treated by CDCA. Staphylococcus aureus cells are evaluated with RNA-seq to understand the genes affected by this antibacterial agent. Our results provide new vision on the mode of action by CDCA.
2022-10-15 | GSE193011 | GEO
Project description:Analysis of Staphylococcus aureus treated by Tanreqing. Staphylococcus aureus cells are evaluated with RNA-seq to understand the genes affected by this antibacterial agent. Our results provide new vision on the mode of action by Tanreqing.
2021-06-07 | GSE162107 | GEO