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MB Sample ID: SA014980
Local Sample ID: | 21003 |
Subject ID: | SU000355 |
Subject Type: | Animal |
Subject Species: | Bos taurus |
Taxonomy ID: | 9913 |
Species Group: | Mammal |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU000355 |
Subject Type: | Animal |
Subject Species: | Bos taurus |
Taxonomy ID: | 9913 |
Species Group: | Mammal |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
21003 | SA014980 | FL003355 | 3 | Main factor (1 to 5) |
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 |