Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative - Escherichia coli

ABSTRACT: The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies. The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. This submission pertains to Escherichia coli strains B36, MS14384, MS14385, MS14386 and MS14387.

INSTRUMENT(S): TripleTOF 6600

ORGANISM(S): Escherichia Coli

TISSUE(S): Permanent Cell Line Cell, Cell Culture

SUBMITTER: Dana Pascovici

LAB HEAD: Mabel Lum, Bioplatforms Australia (project manager)

PROVIDER: PXD016840 | Pride | 2021-07-05

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Similar Datasets

Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative - Streptococcus pyogenes

Project description:The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies. The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. This submission pertains to Streptococcus pyogenes strains 5448, SP444, HKU419, PS003 and PS006.

2021-07-05 | PXD016913 | Pride

Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative - Klebsiella pneumoniae complex

Project description:The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies. The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. This submission pertains to Klebsiella pneumoniae complex strains AJ055, AJ218, AJ292, KPC2, 03-311-0071 and 04153260899A.

2021-07-05 | PXD016672 | Pride

Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative - Streptococcus pneumoniae

Project description:The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies. The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. This submission pertains to Streptococcus pneumoniae strains 4496, 947, 4559, 180-2 and 180-15.

2021-07-05 | PXD017606 | Pride

Bioplatforms Australia: Antibiotic Resistant Sepsis Pathogens Framework Initiative - Staphylococcus aureus

Project description:The Antibiotic Resistant Sepsis Pathogens Framework Initiative aims to develop a framework dataset of 5 sepsis pathogens (5 strains each) using an integrated application of genomic, transcriptomic, metabolomic and proteomic technologies. The pathogens included in this initiative are: Escherichia coli, Klebsiella pneumoniae complex, Staphylococcus aureus, Streptococcus pyogenes, and Streptococcus pneumoniae. This submission pertains to Staphylococcus aureus strains BPH2760, BPH2819, BPH2900, BPH2947 and BPH2986.

2021-07-05 | PXD016504 | Pride

SWATH-based quantitative proteomics data derived from whole grain of Malaysian local pigmented and non-pigmented rice varieties

Project description:Information about protein expression in rice grain across both pigmented and non-pigmented rice varieties is still relatively scarce. The data provided here represent proteomic data obtained from selected 6 Malaysian local rice varieties with varying pigmentations (black, red and white). The selected pigmented rice varieties such as black (BALI and Pulut hitam 9) and red rice (MRQ100 and MRM16) have shown high antioxidant activities and non-pigmented rice (MRQ76 and MR297) contain amino acid and micronutrient contents. This project aimed to obtain global protein expression profile as well as differential protein expression between the selected pigmented and non-pigmented rice varieties particularly proteins with their functions responsible for nutritional (i.e. antioxidant, folate and low glycaemic index) and quality (i.e. aromatic) traits. Integration of this proteomics dataset with other available in-house omics data could facilitate the identification of significant functional markers related to nutritional and quality traits. Total proteins were prepared from dehusked matured seeds harvested from three different rice plants of each variety (3 protein samples per variety). The proteins were trypsin digested before subjected to SWATH-MS proteomics analysis. Proteins were identified by matching tandem mass (MS/MS) spectra from both 1D and 2D IDA to Oryza sativa japonica and indica rice databases available at UniProt by using ProteinPilot software (v4.2) (AB Sciex). Quantification of proteins was carried out by determining protein peak areas extracted from SWATH analysis data sets using PeakView (v2.1) (AB Sciex) software. Differentially expressed protein between varieties were identified using T-test analysis with a set threshold for fold change ± 1.5 and p‐value < 0.05.

2020-04-27 | PXD018338 | Pride

Generation of host-directed and virus-specific antivirals using targeted protein degradation promoted by small molecules and viral RNA mimics

Project description:Targeted protein degradation (TPD), as exemplified by proteolysis-targeting chimera (PROTAC), is a prominent paradigm in drug discovery. In this study, we applied conventional and novel PROTAC approaches to develop broad-spectrum antivirals (targeting key host factors for many different viruses) and virus-specific antivirals (targeting unique viral proteins). With respect to host-directed antivirals, we identified a small molecule degrader, FM-74-103, with pan-antiviral activities, as shown by inhibiting both RNA and DNA viruses. FM-74-103 elicits the selective degradation of human GSPT1, a translation termination factor, which further shuts down translation initiation. With respect to virus-specific antivirals, we developed viral RNA oligonucleotide-based bifunctional molecules (Destroyers). We provided proof-ofprinciple that RNA mimics of viral promoter sequences can be used as molecular glues to recruit viral polymerase (vPOL) and target it for degradation. Collectively, this study shows that TPD can be exploited to rationally design and develop the next generations of antivirals.

2023-06-15 | PXD042352 | Pride

Integrated transcriptomic and proteomic analyses revealed the participation of endogenous protease inhibitors in the regulation of protease gene expression in Helicoverpa armigera

Project description:Insects adapt to plant protease inhibitors (PIs) present in their diet by differentially regulating multiple digestive proteases. However, mechanisms regulating protease gene expression in insects are largely enigmatic. Ingestion of Capsicum annuum protease inhibitor-7 (CanPI-7) arrests growth and development of Helicoverpa armigera (Lepidoptera: noctuidae). Using de novo RNA sequencing and proteomic analysis, we examined the response of H. armigera larvae fed on recombinant C. annuum PI (CanPI) at different time intervals. Here, we present evidence supporting a dynamic transition in H. armigera protease expression upon CanPI feeding with general down-regulation of protease genes at early time points (0.5 to 6 h) and significant up-regulation of specific trypsin, chymotrypsin and aminopeptidase genes at later time points (12 to 48 h).

2018-04-25 | PXD008376 | Pride

Proteome Dynamics Reveals Pro-inflammatory Remodeling of Plasma Proteome in a Mouse Model of NAFLD

Project description:Nonalcoholic fatty liver disease (NAFLD) is associated with an increased risk of cardiovascular disease (CVD). Liver is the major source of the circulatory proteins and alterations in plasma proteome have been implicated in atherosclerosis. We used a recently developed 2H2O-metabolic labeling method in combination with the label-free quantification to evaluate the effect of a Western diet (WD) on the dynamics of plasma proteins in LDL receptor-deficient (LDLR-/-) mice, a model of NAFLD and atherosclerosis. There were no significant changes in the expression level of total proteins due to the WD with a bulk protein mean half-life of 18.0±15.1 hours in control and 16.7±11.1 hours in WD groups. WD led to pro-inflammatory distribution of circulatory proteins analyzed in apoB-depleted plasma attributed to their increased production. The fractional catabolic rates of fast-turnover proteins with stress-response, lipid metabolism and transport functions were significantly increased with WD (P<0.05). The pathway analyses revealed that alterations in plasma proteome dynamics were related to the suppression of hepatic PPARα, which was confirmed based on reduced gene and protein expression of PPARα on WD. These changes were associated with ~4 fold increase (P<0.0001) in pro-inflammatory property of apoB-depleted plasma. In conclusion, the proteome dynamics method reveals pro-inflammatory remodeling of plasma proteome relevant to liver disease. As in vivo metrics of liver function, this approach can be used to test therapies in NAFLD and other diseases

2016-06-06 | PXD004270 | Pride

Evolution of enhanced innate immune evasion by the SARS-CoV-2 B.1.1.7 UK variant

Project description:Here we use unbiased abundance proteomics and phosphoproteomics to assess global changes to host and viral proteins in Calu-3 cells at 10 and 24 hours post infection with either the B.1.1.7 UK variant or early-lineage SARS-CoV-2 viruses VIC and IC19.

2022-01-20 | PXD026302 | Pride

Proteomic profiling of NCI60 cell lines from Cancer Cell Line Encyclopedia

Project description:This ArrayExpress record contains meta-data and results of quantitative analysis of cell lines from the NCI-60 panel using pressure cycling technology (PCT) and SWATH-mass spectrometry. Each cell line was analyzed in duplicate. Raw data files are available at the EMBL-EBI protemics data archive (PRIDE) at accession PXD003539 (http://www.ebi.ac.uk/pride/archive/projects/PXD003539). Since the record here does not include the raw data files and hence there is no need to explicitly link individual replicate to a raw file, each sample is only listed once in the ArrayExpress samples table for clarity.

2017-01-27 | E-PROT-2 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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