Summary of Study ST002310
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 PR001481. The data can be accessed directly via it's Project DOI: 10.21228/M8941F 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.
Study ID | ST002310 |
Study Title | Cecal Microbiome in Phage treated broilers |
Study Summary | The objective of this study was to assess the impact of Salmonella bacteriophage treatment on microbiome in the ceca and serum of the broilers during the rearing period |
Institute | La Agenzia nazionale per le nuove tecnologie, l'energia e lo sviluppo económico sostenibile |
Last Name | Lorenzo Rebenaque |
First Name | Laura |
Address | Ed. Seminario. S/n |
laura.lorenzorebenaque@uchceu.com | |
Phone | 615056012 |
Submit Date | 2022-09-12 |
Raw Data Available | Yes |
Raw Data File Type(s) | raw(Thermo) |
Analysis Type Detail | LC-MS |
Release Date | 2022-10-18 |
Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
Project ID: | PR001481 |
Project DOI: | doi: 10.21228/M8941F |
Project Title: | Cecal Microbiome in Phage treated broilers |
Project Summary: | The objective of this study was to assess the impact of Salmonella bacteriophage treatment on microbiome in the ceca and serum of the broilers during the rearing period |
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: | SU002396 |
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 |
---|---|---|---|
SA226980 | J1 | Control | Week 4 |
SA226981 | J4 | Control | Week 4 |
SA226982 | J3 | Control | Week 4 |
SA226983 | J2 | Control | Week 4 |
SA226984 | M3 | Control | Week 5 |
SA226985 | M5 | Control | Week 5 |
SA226986 | M2 | Control | Week 5 |
SA226987 | M4 | Control | Week 5 |
SA226988 | P2 | Control | Week 6 |
SA226989 | P1 | Control | Week 6 |
SA226990 | P4 | Control | Week 6 |
SA226991 | P3 | Control | Week 6 |
SA226992 | L2 | Feed | Week 4 |
SA226993 | L1 | Feed | Week 4 |
SA226994 | L3 | Feed | Week 4 |
SA226995 | L4 | Feed | Week 4 |
SA226996 | O2 | Feed | Week 5 |
SA226997 | O4 | Feed | Week 5 |
SA226998 | O3 | Feed | Week 5 |
SA226999 | O1 | Feed | Week 5 |
SA227000 | R3 | Feed | Week 6 |
SA227001 | R2 | Feed | Week 6 |
SA227002 | R4 | Feed | Week 6 |
SA227003 | R1 | Feed | Week 6 |
SA227004 | R5 | Feed | Week 6 |
SA227005 | K2 | Water | Week 4 |
SA227006 | K3 | Water | Week 4 |
SA227007 | K4 | Water | Week 4 |
SA227008 | K1 | Water | Week 4 |
SA227009 | N3 | Water | Week 5 |
SA227010 | N2 | Water | Week 5 |
SA227011 | N1 | Water | Week 5 |
SA227012 | Q1 | Water | Week 6 |
SA227013 | Q2 | Water | Week 6 |
SA227014 | Q4 | Water | Week 6 |
SA227015 | Q3 | Water | Week 6 |
SA227016 | Q5 | Water | Week 6 |
Showing results 1 to 37 of 37 |
Collection:
Collection ID: | CO002389 |
Collection Summary: | Cecal sample were collected and immediately snap frozen for metabolomics analysis at the end of experiment |
Sample Type: | Cecum |
Treatment:
Treatment ID: | TR002408 |
Treatment Summary: | The water group received a 108 PFU/mL phage concentration via drinking water, the feed group received a 108 PFU/g phage concentration via feed (encapsulated), and the control group did not receive a phage. Caecal samples were obtained 1 day after delivery of the phage. |
Sample Preparation:
Sampleprep ID: | SP002402 |
Sampleprep Summary: | Cecal contents 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 | AN003773 | AN003774 |
---|---|---|
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: | CH002791 |
Instrument Name: | Thermo Dionex Ultimate 3000 |
Column Name: | Phenomenex Luna (100 x 2.1mm,2.5um) |
Chromatography Type: | Reversed phase |
MS:
MS ID: | MS003516 |
Analysis ID: | AN003773 |
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: | MS003517 |
Analysis ID: | AN003774 |
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 |