Summary of Study ST002312

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001482. The data can be accessed directly via it's Project DOI: 10.21228/M8598K This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST002312
Study TitleSerum metabolome in Phage-treated Salmonella-infected broilers
Study SummaryAnalysis of the serum metabolome of Salmonella-infected broilers has been carried out after the application of encapsulated bacteriophages in the feed, during the production cycle under farm conditions
Institute
Universidad Cardenal Herrera CEU
Last NameLorenzo-Rebenaque
First NameLaura
AddressEd. Seminario. S/n, Moncada, Valencia, 46113, Spain
Emaillaura.lorenzorebenaque@uchceu.es
Phone615056012
Submit Date2022-09-13
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2022-10-18
Release Version1
Laura Lorenzo-Rebenaque Laura Lorenzo-Rebenaque
https://dx.doi.org/10.21228/M8598K
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001482
Project DOI:doi: 10.21228/M8598K
Project Title:Cecal Microbiota in Phage-treated Salmonella-infected broilers
Project Summary:Analysis of the gastrointestinal metabolome of Salmonella-infected broilers has been carried out after the application of encapsulated bacteriophages in the feed, during the production cycle under farm conditions
Institute:Universidad Cardenal Herrera CEU
Last Name:Lorenzo-Rebenaque
First Name:Laura
Address:Ed. Seminario. S/n, Moncada, Valencia, 46113, Spain
Email:laura.lorenzorebenaque@uchceu.es
Phone:615056012

Subject:

Subject ID:SU002398
Subject Type:Bird
Subject Species:Gallus gallus
Taxonomy ID:9031
Species Group:Birds

Factors:

Subject type: Bird; Subject species: Gallus gallus (Factor headings shown in green)

mb_sample_id local_sample_id Group Moment
SA22704133Phage Week 4
SA22704235Phage Week 4
SA22704336Phage Week 4
SA22704434Phage Week 4
SA22704543Phage Week 5
SA22704644Phage Week 5
SA22704742Phage Week 5
SA22704841Phage Week 5
SA22704950Phage Week 6
SA22705052Phage Week 6
SA22705151Phage Week 6
SA22705249Phage Week 6
SA22705330Salmonella Week 4
SA22705431Salmonella Week 4
SA22705532Salmonella Week 4
SA22705629Salmonella Week 4
SA22705739Salmonella Week 5
SA22705840Salmonella Week 5
SA22705938Salmonella Week 5
SA22706037Salmonella Week 5
SA22706145Salmonella Week 6
SA22706246Salmonella Week 6
SA22706347Salmonella Week 6
SA22706448Salmonella Week 6
Showing results 1 to 24 of 24

Collection:

Collection ID:CO002391
Collection Summary:serum samples were collected and immediately snap frozen for metabolomic analysis at the end of the experiment
Sample Type:Blood (serum)

Treatment:

Treatment ID:TR002410
Treatment Summary:Half of the animals (25/50) in each experimental group (control and Φ-treated groups) were challenged with Salmonella Enteritidis (105 CFU/bird) at 24 h after placing. During the first 21 days of the chicken rearing period, Φ-treated group received 0.1% encapsulated Salmonella-phage (108 PFU/g) with the starter diet feed, and the control group did not receive any phage.

Sample Preparation:

Sampleprep ID:SP002404
Sampleprep Summary:serum samples were lyophilized and homogenated. Then, 10 mg of the sample were mixed with 0.75mL of cold 75% (v/v) methanol, 0.1% (v/v) formic acid, spiked with 10μg/ml formononetin as internal standard. Then, the mix were shaked for 40’ at 20Hz using a Mixer Mill 300 (Qiagen) and centrifuged at 20,000 xg for 15 min at 4°C. The suspension (600μL) was transferred to a new 2-mL conical tube.

Combined analysis:

Analysis ID AN003777 AN003778
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000
Column Phenomenex Luna (100 x 2.1mm,2.5um) Phenomenex Luna (100 x 2.1mm,2.5um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap
Ion Mode POSITIVE NEGATIVE
Units m/z ratio m/z ratio

Chromatography:

Chromatography ID:CH002793
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Phenomenex Luna (100 x 2.1mm,2.5um)
Chromatography Type:Reversed phase

MS:

MS ID:MS003520
Analysis ID:AN003777
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:For the untargeted metabolomic analysis, Compound Discoverer software(Thermofisher Scientific) was used to identify the peaks, peak filtration, and peak alignment, and performed chromatogram alignment, peak picking, and public database (e.g., ChemSpider, KEGG, Metabolika) querying based on accurate masses(m/z).
Ion Mode:POSITIVE
  
MS ID:MS003521
Analysis ID:AN003778
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:For the untargeted metabolomic analysis, Compound Discoverer software(Thermofisher Scientific) was used to identify the peaks, peak filtration, and peak alignment, and performed chromatogram alignment, peak picking, and public database (e.g., ChemSpider, KEGG, Metabolika) querying based on accurate masses(m/z).
Ion Mode:NEGATIVE
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