{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002310","ANALYSIS_ID":"AN003773","VERSION":"1","CREATED_ON":"September 12, 2022, 2:09 am"},

"PROJECT":{"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"},

"STUDY":{"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","EMAIL":"laura.lorenzorebenaque@uchceu.com","PHONE":"615056012"},

"SUBJECT":{"SUBJECT_TYPE":"Bird","SUBJECT_SPECIES":"Gallus gallus","TAXONOMY_ID":"9031"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"J1",
"Factors":{"Group":"Control","Moment":"Week 4"},
"Additional sample data":{"RAW_FILE_NAME":"J1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"J2",
"Factors":{"Group":"Control","Moment":"Week 4"},
"Additional sample data":{"RAW_FILE_NAME":"J2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"J3",
"Factors":{"Group":"Control","Moment":"Week 4"},
"Additional sample data":{"RAW_FILE_NAME":"J3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"J4",
"Factors":{"Group":"Control","Moment":"Week 4"},
"Additional sample data":{"RAW_FILE_NAME":"J4.raw"}
},
{
"Subject ID":"-",
"Sample ID":"K1",
"Factors":{"Group":"Water","Moment":"Week 4"},
"Additional sample data":{"RAW_FILE_NAME":"K1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"K2",
"Factors":{"Group":"Water","Moment":"Week 4"},
"Additional sample data":{"RAW_FILE_NAME":"K2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"K3",
"Factors":{"Group":"Water","Moment":"Week 4"},
"Additional sample data":{"RAW_FILE_NAME":"K3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"K4",
"Factors":{"Group":"Water","Moment":"Week 4"},
"Additional sample data":{"RAW_FILE_NAME":"K4.raw"}
},
{
"Subject ID":"-",
"Sample ID":"L1",
"Factors":{"Group":"Feed","Moment":"Week 4"},
"Additional sample data":{"RAW_FILE_NAME":"L1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"L2",
"Factors":{"Group":"Feed","Moment":"Week 4"},
"Additional sample data":{"RAW_FILE_NAME":"L2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"L3",
"Factors":{"Group":"Feed","Moment":"Week 4"},
"Additional sample data":{"RAW_FILE_NAME":"L3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"L4",
"Factors":{"Group":"Feed","Moment":"Week 4"},
"Additional sample data":{"RAW_FILE_NAME":"L4.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M2",
"Factors":{"Group":"Control","Moment":"Week 5"},
"Additional sample data":{"RAW_FILE_NAME":"M2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M3",
"Factors":{"Group":"Control","Moment":"Week 5"},
"Additional sample data":{"RAW_FILE_NAME":"M3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M4",
"Factors":{"Group":"Control","Moment":"Week 5"},
"Additional sample data":{"RAW_FILE_NAME":"M4.raw"}
},
{
"Subject ID":"-",
"Sample ID":"M5",
"Factors":{"Group":"Control","Moment":"Week 5"},
"Additional sample data":{"RAW_FILE_NAME":"M5.raw"}
},
{
"Subject ID":"-",
"Sample ID":"N1",
"Factors":{"Group":"Water","Moment":"Week 5"},
"Additional sample data":{"RAW_FILE_NAME":"N1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"N2",
"Factors":{"Group":"Water","Moment":"Week 5"},
"Additional sample data":{"RAW_FILE_NAME":"N2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"N3",
"Factors":{"Group":"Water","Moment":"Week 5"},
"Additional sample data":{"RAW_FILE_NAME":"N3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"O1",
"Factors":{"Group":"Feed","Moment":"Week 5"},
"Additional sample data":{"RAW_FILE_NAME":"O1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"O2",
"Factors":{"Group":"Feed","Moment":"Week 5"},
"Additional sample data":{"RAW_FILE_NAME":"O2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"O3",
"Factors":{"Group":"Feed","Moment":"Week 5"},
"Additional sample data":{"RAW_FILE_NAME":"O3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"O4",
"Factors":{"Group":"Feed","Moment":"Week 5"},
"Additional sample data":{"RAW_FILE_NAME":"O4.raw"}
},
{
"Subject ID":"-",
"Sample ID":"P1",
"Factors":{"Group":"Control","Moment":"Week 6"},
"Additional sample data":{"RAW_FILE_NAME":"P1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"P2",
"Factors":{"Group":"Control","Moment":"Week 6"},
"Additional sample data":{"RAW_FILE_NAME":"P2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"P3",
"Factors":{"Group":"Control","Moment":"Week 6"},
"Additional sample data":{"RAW_FILE_NAME":"P3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"P4",
"Factors":{"Group":"Control","Moment":"Week 6"},
"Additional sample data":{"RAW_FILE_NAME":"P4.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Q1",
"Factors":{"Group":"Water","Moment":"Week 6"},
"Additional sample data":{"RAW_FILE_NAME":"Q1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Q2",
"Factors":{"Group":"Water","Moment":"Week 6"},
"Additional sample data":{"RAW_FILE_NAME":"Q2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Q3",
"Factors":{"Group":"Water","Moment":"Week 6"},
"Additional sample data":{"RAW_FILE_NAME":"Q3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Q4",
"Factors":{"Group":"Water","Moment":"Week 6"},
"Additional sample data":{"RAW_FILE_NAME":"Q4.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Q5",
"Factors":{"Group":"Water","Moment":"Week 6"},
"Additional sample data":{"RAW_FILE_NAME":"Q5.raw"}
},
{
"Subject ID":"-",
"Sample ID":"R1",
"Factors":{"Group":"Feed","Moment":"Week 6"},
"Additional sample data":{"RAW_FILE_NAME":"R1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"R2",
"Factors":{"Group":"Feed","Moment":"Week 6"},
"Additional sample data":{"RAW_FILE_NAME":"R2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"R3",
"Factors":{"Group":"Feed","Moment":"Week 6"},
"Additional sample data":{"RAW_FILE_NAME":"R3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"R4",
"Factors":{"Group":"Feed","Moment":"Week 6"},
"Additional sample data":{"RAW_FILE_NAME":"R4.raw"}
},
{
"Subject ID":"-",
"Sample ID":"R5",
"Factors":{"Group":"Feed","Moment":"Week 6"},
"Additional sample data":{"RAW_FILE_NAME":"R5.raw"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Cecal sample were collected and immediately snap frozen for metabolomics analysis at the end of experiment","SAMPLE_TYPE":"Cecum"},

"TREATMENT":{"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."},

"SAMPLEPREP":{"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."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Dionex Ultimate 3000","COLUMN_NAME":"Phenomenex Luna (100x2.1, 2.5um)"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"POSITIVE","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).","MS_RESULTS_FILE":"ST002310_AN003773_Results.txt UNITS:m/z ratio Has m/z:Yes Has RT:Yes RT units:Minutes"}

}