{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000335","ANALYSIS_ID":"AN000541","VERSION":"1","CREATED_ON":"January 21, 2016, 10:27 am"},

"PROJECT":{"PROJECT_TITLE":"Metabolomics of bovine uterine fluid at the onset of conceptus elongation","PROJECT_TYPE":"Research","PROJECT_SUMMARY":"Research The objective is to investigate changes in metabolomics of uterine lumen content of lactating dairy cows associated with the onset of conceptus (embryo and associated membranes) elongation. Lactating dairy cows had estrous cycles synchronized and were subjected to induced ovulation and timed artificial insemination (AI). The day of AI was considered study d 0. On d 15, uteri were flushed by transcervical catheterization and infusion of 20 mL of phosphate buffered solution with 0.1% of polyvinyl acetate. Recovered conceptuses were classified based on morphology/length as ovoid (OV; 1-4 mm), tubular (TUB; 5-19 mm) and filamentous (FIL; 20-85 mm). The first 20 mL infused in the uterus were recovered, placed in conical tubes and centrifuged at 2,000 × g at 4ᵒC. The supernatant was collect, aliquoted and stored at -80ᵒC for later analyses of fluid composition, including measurement of IFN-τ concentration. Cows with no conceptus recovered and no detection of IFN-τ in uterine flushing were considered as nonpregnant (NPREG). The experimental design was then considered a prospective cohort study with 4 independent groups (NPREG, OV, TUB, and FIL). The additional 5th group represents a specific physiological condition of cows within the study and it will be compared to TUB and FIL groups combined, working as a pilot study for future research.","INSTITUTE":"University of Florida","DEPARTMENT":"Department of Animal Sciences","LABORATORY":"Laboratory of Reproduction and Nutrition of Dairy Cows","LAST_NAME":"Santos","FIRST_NAME":"José Eduardo","ADDRESS":"2250 Shealy Drive, Bldg. 499, Room 204, Gainesville, FL 32611-0910","EMAIL":"jepsantos@ufl.edu","PHONE":"3522227333","FUNDING_SOURCE":"Internal"},

"STUDY":{"STUDY_TITLE":"Metabolomics of bovine uterine fluid at the onset of conceptus elongation","STUDY_TYPE":"Prospective cohort study","STUDY_SUMMARY":"The objective is to investigate changes in metabolomics of uterine lumen content of lactating dairy cows associated with the onset of conceptus (embryo and associated membranes) elongation. Lactating dairy cows had estrous cycles synchronized and were subjected to induced ovulation and timed artificial insemination (AI). The day of AI was considered study d 0. On d 15, uteri were flushed by transcervical catheterization and infusion of 20 mL of phosphate buffered solution with 0.1% of polyvinyl acetate. Recovered conceptuses were classified based on morphology/length as ovoid (OV; 1-4 mm), tubular (TUB; 5-19 mm) and filamentous (FIL; 20-85 mm). The first 20 mL infused in the uterus were recovered, placed in conical tubes and centrifuged at 2,000 × g at 4ᵒC. The supernatant was collect, aliquoted and stored at -80ᵒC for later analyses of fluid composition, including measurement of IFN-τ concentration. Cows with no conceptus recovered and no detection of IFN-τ in uterine flushing were considered as nonpregnant (NPREG). The experimental design was then considered a prospective cohort study with 4 independent groups (NPREG, OV, TUB, and FIL). The additional 5th group represents a specific physiological condition of cows within the study and it will be compared to TUB and FIL groups combined, working as a pilot study for future research.","INSTITUTE":"University of Florida","DEPARTMENT":"SECIM","LABORATORY":"Laboratory of Reproduction and Nutrition of Dairy Cows","LAST_NAME":"Ribeiro","FIRST_NAME":"Eduardo","ADDRESS":"2250 Shealy Drive, Bldg. 499, Room 228, Gainesville, FL 32611-0910","EMAIL":"ribeiro.es@ufl.edu","PHONE":"3522227333","NUM_GROUPS":"5","TOTAL_SUBJECTS":"30"},

"SUBJECT":{"SUBJECT_TYPE":"Animal","SUBJECT_SPECIES":"Bos Taurus","TAXONOMY_ID":"9913"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"26488",
"Factors":{"Main factor (1 to 5)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"27917",
"Factors":{"Main factor (1 to 5)":"1"}
},
{
"Subject ID":"-",
"Sample ID":"6820",
"Factors":{"Main factor (1 to 5)":"5"}
},
{
"Subject ID":"-",
"Sample ID":"6125",
"Factors":{"Main factor (1 to 5)":"2"}
},
{
"Subject ID":"-",
"Sample ID":"21003",
"Factors":{"Main factor (1 to 5)":"3"}
},
{
"Subject ID":"-",
"Sample ID":"6314",
"Factors":{"Main factor (1 to 5)":"1"}
},
{
"Subject ID":"-",
"Sample ID":"6570",
"Factors":{"Main factor (1 to 5)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"5135",
"Factors":{"Main factor (1 to 5)":"5"}
},
{
"Subject ID":"-",
"Sample ID":"26128",
"Factors":{"Main factor (1 to 5)":"3"}
},
{
"Subject ID":"-",
"Sample ID":"27327",
"Factors":{"Main factor (1 to 5)":"2"}
},
{
"Subject ID":"-",
"Sample ID":"1721",
"Factors":{"Main factor (1 to 5)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"21068",
"Factors":{"Main factor (1 to 5)":"1"}
},
{
"Subject ID":"-",
"Sample ID":"11523",
"Factors":{"Main factor (1 to 5)":"5"}
},
{
"Subject ID":"-",
"Sample ID":"11804",
"Factors":{"Main factor (1 to 5)":"2"}
},
{
"Subject ID":"-",
"Sample ID":"26068",
"Factors":{"Main factor (1 to 5)":"3"}
},
{
"Subject ID":"-",
"Sample ID":"6299",
"Factors":{"Main factor (1 to 5)":"2"}
},
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"Subject ID":"-",
"Sample ID":"26416",
"Factors":{"Main factor (1 to 5)":"-"}
},
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"Subject ID":"-",
"Sample ID":"19830",
"Factors":{"Main factor (1 to 5)":"1"}
},
{
"Subject ID":"-",
"Sample ID":"19825",
"Factors":{"Main factor (1 to 5)":"5"}
},
{
"Subject ID":"-",
"Sample ID":"6797",
"Factors":{"Main factor (1 to 5)":"3"}
},
{
"Subject ID":"-",
"Sample ID":"6754",
"Factors":{"Main factor (1 to 5)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"1415",
"Factors":{"Main factor (1 to 5)":"2"}
},
{
"Subject ID":"-",
"Sample ID":"19994",
"Factors":{"Main factor (1 to 5)":"1"}
},
{
"Subject ID":"-",
"Sample ID":"22732",
"Factors":{"Main factor (1 to 5)":"5"}
},
{
"Subject ID":"-",
"Sample ID":"26289",
"Factors":{"Main factor (1 to 5)":"3"}
},
{
"Subject ID":"-",
"Sample ID":"27905",
"Factors":{"Main factor (1 to 5)":"5"}
},
{
"Subject ID":"-",
"Sample ID":"6609",
"Factors":{"Main factor (1 to 5)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"6154",
"Factors":{"Main factor (1 to 5)":"2"}
},
{
"Subject ID":"-",
"Sample ID":"6165",
"Factors":{"Main factor (1 to 5)":"1"}
},
{
"Subject ID":"-",
"Sample ID":"9798",
"Factors":{"Main factor (1 to 5)":"3"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"On day 15 after insemination, the uterine horn ipsilateral to the corpus luteum was flushed by transcervical catheterization and infusion of 20 mL of phosphate buffered solution with 0.1% of polyvinyl acetate. The solution was infused using a 60 mL dosing plastic syringe connected in a 20 to 24 French silicone coated latex Foley catheter. The fluid infused was recovery into the same syringe used for infusion and then examined in a petri dish under stereoscope for location of conceptus tissue. The uterine fluid recovered was placed in conical tubes in ice and later centrifuged at 2,000 × g at 4ᵒC. The supernatant was collect, aliquoted and stored at -80ᵒC for later analyses of fluid composition."},

"TREATMENT":{"TREATMENT_SUMMARY":"No treatments were administered on the subjects. The factors of interest are pregnant status (pregnant vs. nonpregnant) and stage of conceptus development (ovoid vs. tubular vs. filamentous), which was evaluated base on the shape and length of the conceptus. Thus, cows were classified as nonpregnant (no conceptus recovered), pregnant with an ovoid conceptus (1-4 mm), pregnant with a tubular conceptus (5-19 mm), or pregnant with a filamentous conceptus (20-80 mm). The fifth group is part of a preliminary study comparing a different reproductive physiology condition prior enrollment. Cows in the fifth group are all pregnant with a filamentous conceptus. Interferon-tau, a type-I interferon secreted by exclusively by trophectoderm cells of ruminants conceptuses, was measured in all uterine flushing. Nonpregnant status was confirmed only for those that had no signal of interferon-tau in the uterine flushing. Samples were arranged in 6 blocks of 5 samples each. Within each block, all 5 groups are represented. For each group, samples were selected randomly from the population in the study. All investigators, except for the study administrator, and collaborators should be blind to factors of interest."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"None","SAMPLEPREP_PROTOCOL_FILENAME":"Metabolomics_LCMSProtocol_plasma.pdf;Appendix A - Internal Standard Prep GLCMS.pdf"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"None","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Scientific-Dionex Ultimate 3000","COLUMN_NAME":"ACE Excel 2 C18-PFP (100 x 2.1mm, 2um)","METHODS_FILENAME":"Metabolomics_LCMSProtocol_plasma.pdf"},

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

"MS":{"MS_COMMENTS":"-","INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"NEGATIVE"},

"MS_METABOLITE_DATA":{
"Units":"peak area",

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}

}