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MB Sample ID: SA326022
| Local Sample ID: | 9992_Diagnosis_Con |
| Subject ID: | SU003107 |
| Subject Type: | Mammal |
| Subject Species: | Bos taurus |
| Taxonomy ID: | 9913 |
| Gender: | Female |
| Animal Housing: | Free-stalls |
| Animal Feed: | TMR |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU003107 |
| Subject Type: | Mammal |
| Subject Species: | Bos taurus |
| Taxonomy ID: | 9913 |
| Gender: | Female |
| Animal Housing: | Free-stalls |
| Animal Feed: | TMR |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| 9992_Diagnosis_Con | SA326022 | FL038761 | Con | Group |
| 9992_Diagnosis_Con | SA326022 | FL038761 | Diagnosis | Time |
| 9992_Diagnosis_Con | SA326022 | FL038761 | Mult | Parity |
Collection:
| Collection ID: | CO003100 |
| Collection Summary: | All cows had uterine fluid collected at calving (first 24h after calving), and at diagnosis (day of metritis diagnosis). Briefly, cows’ cervix was stabilized by rectal palpation, the vulva was rinsed with alcohol 70% and dried with paper towels. Subsequently, a single-use plastic round-tip pipette (UterFlush pipettes, Van Beek) was introduced into the vagina at a 45° angle and manipulated through the cervix. A total of 50 mL of sterile saline solution (0.9% sodium chloride irrigation, Baxter) was infused into the uterine lumen using a 60-mL syringe (Covidien) attached to the end of the pipette. Uterine contents were homogenized, retrieved into the same 60-mL syringe, and transferred to a sterile 15-mL conical tube (VWR). After collection, tubes were placed on ice and transported to the laboratory within 2 hours. Once in the laboratory, uterine fluid samples were aliquoted into 2-mL microcentrifuge tubes (Eppendorf) and stored at -80 oC until essayed. One frozen uterine fluid aliquot was submitted to the University of California’s West Coast Metabolomics Center in Davis, CA for metabolome analysis. |
| Sample Type: | Uterine fluid |
Treatment:
| Treatment ID: | TR003116 |
| Treatment Summary: | This was a case-control study, hence, there were not treatments applied. Cows were self-assigned to the groups. Cows that developed metritis were paired with healthy cows by days in milk. |
Sample Preparation:
| Sampleprep ID: | SP003113 |
| Sampleprep Summary: | Uterine fluid samples were aliquoted into 2-mL microcentrifuge tubes (Eppendorf) and stored at -80 oC until essayed. |
Combined analysis:
| Analysis ID | AN004918 |
|---|---|
| Analysis type | MS |
| Chromatography type | GC |
| Chromatography system | Leco Pegasus IV GC |
| Column | Restek Rtx-5Sil MS (30m x 0.25mm, 0.25um) |
| MS Type | EI |
| MS instrument type | GC-TOF |
| MS instrument name | Leco Pegasus IV TOF |
| Ion Mode | POSITIVE |
| Units | peak heights |
Chromatography:
| Chromatography ID: | CH003713 |
| Instrument Name: | Leco Pegasus IV GC |
| Column Name: | Restek Rtx-5Sil MS (30m x 0.25mm, 0.25um) |
| Column Temperature: | 50-330 |
| Flow Gradient: | . |
| Flow Rate: | 1 mL min-1 |
| Solvent A: | . |
| Solvent B: | . |
| Chromatography Type: | GC |
MS:
| MS ID: | MS004661 |
| Analysis ID: | AN004918 |
| Instrument Name: | Leco Pegasus IV TOF |
| Instrument Type: | GC-TOF |
| MS Type: | EI |
| MS Comments: | Data are acquired using the following chromatographic parameters, with more details to be found in Fiehn O. et al. Plant J. 53 (2008) 691–704. Column: Restek corporation Rtx-5Sil MS (30 m length x 0.25 mm internal diameter with 0.25 μm film made of 95% dimethyl/5%diphenylpolysiloxane) Mobile phase: Helium Column temperature: 50-330°C Flow- rate: 1 mL min-1 Injection volume: 0.5 μL Injection: 25 splitless time into a multi-baffled glass liner Injection temperature: 50°C ramped to 250°C by 12°C s-1 Oven temperature program: 50°C for 1 min, then ramped at 20°C min-1 to 330°C, held constant for 5 min. The analytical GC column is protected by a 10 m long empty guard column which is cut by 20 cm intervals whenever the reference mixture QC samples indicate problems caused by column contaminations. We have validated that at this sequence of column cuts, no detrimental effects are detected with respect to peak shapes, absolute or relative metabolite retention times or reproducibility of quantifications. This chromatography method yields excellent retention and separation of primary metabolite classes (amino acids, hydroxyl acids, carbohydrates, sugar acids, sterols, aromatics, nucleosides, amines and miscellaneous compounds) with narrow peak widths of 2–3 s and very good within-series retention time reproducibility of better than 0.2 s absolute deviation of retention times. We use automatic liner exchanges after each set of 10 injections which we could show to reduce sample carryover for highly lipophilic compounds such as free fatty acids. Mass spectrometry parameters are used as follows: a Leco Pegasus IV mass spectrometer is used with unit mass resolution at 17 spectra s-1 from 80-500 Da at - 70 eV ionization energy and 1800 V detector voltage with a 230°C transfer line and a 250°C ion source. |
| Ion Mode: | POSITIVE |
