Summary of Study ST000335

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 PR000267. The data can be accessed directly via it's Project DOI: 10.21228/M88K54 This work is supported by NIH grant, U2C- DK119886.

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Study IDST000335
Study TitleMetabolomics of bovine uterine fluid at the onset of conceptus elongation
Study TypeProspective cohort study
Study SummaryThe 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
DepartmentSECIM
LaboratoryLaboratory of Reproduction and Nutrition of Dairy Cows
Last NameRibeiro
First NameEduardo
Address2250 Shealy Drive, Bldg. 499, Room 228, Gainesville, FL 32611-0910
Emailribeiro.es@ufl.edu
Phone3522227333
Submit Date2016-01-17
Num Groups5
Total Subjects30
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2017-01-17
Release Version1
Eduardo Ribeiro Eduardo Ribeiro
https://dx.doi.org/10.21228/M88K54
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000267
Project DOI:doi: 10.21228/M88K54
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

Subject:

Subject ID:SU000355
Subject Type:Animal
Subject Species:Bos taurus
Taxonomy ID:9913
Species Group:Mammals

Factors:

Subject type: Animal; Subject species: Bos taurus (Factor headings shown in green)

mb_sample_id local_sample_id Main factor (1 to 5)
SA01495826488-
SA0149591721-
SA0149606754-
SA0149616570-
SA01496226416-
SA0149636609-
SA014964210681
SA01496561651
SA01496663141
SA014967279171
SA014968199941
SA014969198301
SA01497061542
SA01497114152
SA01497262992
SA014973273272
SA01497461252
SA014975118042
SA014976260683
SA014977262893
SA014978261283
SA01497997983
SA014980210033
SA01498167973
SA01498268205
SA014983227325
SA014984198255
SA014985115235
SA014986279055
SA01498751355
Showing results 1 to 30 of 30

Collection:

Collection ID:CO000349
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.
Sample Type:Uterus

Treatment:

Treatment ID:TR000369
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.

Sample Preparation:

Sampleprep ID:SP000363
Sampleprep Summary:None
Sampleprep Protocol Filename:Metabolomics_LCMSProtocol_plasma.pdf
Appendix A - Internal Standard Prep GLCMS.pdf

Combined analysis:

Analysis ID AN000540 AN000541
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Thermo Scientific-Dionex Ultimate 3000 Thermo Scientific-Dionex Ultimate 3000
Column ACE Excel 2 C18-PFP (100 x 2.1mm, 2um) ACE Excel 2 C18-PFP (100 x 2.1mm, 2um)
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 peak area peak area

Chromatography:

Chromatography ID:CH000378
Chromatography Summary:None
Methods Filename:Metabolomics_LCMSProtocol_plasma.pdf
Instrument Name:Thermo Scientific-Dionex Ultimate 3000
Column Name:ACE Excel 2 C18-PFP (100 x 2.1mm, 2um)
Flow Rate:0.350mL/min-0.600mL/min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile
Chromatography Type:Reversed phase

MS:

MS ID:MS000476
Analysis ID:AN000540
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:POSITIVE
  
MS ID:MS000477
Analysis ID:AN000541
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
Ion Mode:NEGATIVE
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