Summary of Study ST002556
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 PR001648. The data can be accessed directly via it's Project DOI: 10.21228/M8PF0K This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
Study ID | ST002556 |
Study Title | Blood metabolomics and impacted cellular mechanisms during transition into lactation in dairy cows that develop metritis |
Study Type | Case-Control Study |
Study Summary | The objective of this study was to identify metabolites associated with metritis and use them for identification of cellular mechanisms affected during transition into lactation. Holstein cows (n = 104) had blood collected in the prepartum period (d-14 ± 6), at calving (d0), and at the day of metritis diagnosis (d7 ± 2). Cows with reddish or brownish, watery, and fetid discharge were diagnosed with metritis (n = 52). Cows with metritis were paired with herdmates without metritis (n = 52) based on DIM. The metabolome of plasma samples was evaluated using untargeted gas chromatography time-of-flight mass spectrometry. Univariate analyses included t-tests and fold change analyses. Metabolites with false discovery rate (FDR) adjusted P ≤ 0.10 on t-tests were used for partial least squares – discriminant analysis PLS-DA coupled with permutational analysis using 2,000 permutations. Metabolites with FDR adjusted P ≤ 0.10 on t-tests were also used for enriched pathway analyses and identification of cellular processes. Cows that developed metritis had affected cellular processes associated with lower amino acid metabolism in the prepartum period, greater lipolysis, cell death, and oxidative stress at calving and at metritis diagnosis, and greater leukocyte activation at calving, but lower immune cell activation at metritis diagnosis. In summary, cows that developed metritis had plasma metabolomic changes associated with greater lipolysis, oxidative stress, and a dysregulated immune response which may predispose cows to metritis development. |
Institute | University of Florida |
Department | College of Veterinary Medicine |
Laboratory | Large Animal Clinical Sciences |
Last Name | segundocasaro |
First Name | Segundo |
Address | 117 Deriso Hall, 2015 SW 16th Ave. |
segundocasaro@ufl.edu | |
Phone | 3522844016 |
Submit Date | 2023-04-11 |
Num Groups | 2 |
Total Subjects | 104 |
Num Females | 104 |
Analysis Type Detail | GC-MS |
Release Date | 2023-04-28 |
Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
Project ID: | PR001648 |
Project DOI: | doi: 10.21228/M8PF0K |
Project Title: | Blood metabolomics and impacted cellular mechanisms during transition into lactation in dairy cows that develop metritis |
Project Type: | Case-Control Study |
Project Summary: | The objective of this study was to identify metabolites associated with metritis and use them for identification of cellular mechanisms affected during transition into lactation. Holstein cows (n = 104) had blood collected in the prepartum period (d-14 ± 6), at calving (d0), and at the day of metritis diagnosis (d7 ± 2). Cows with reddish or brownish, watery, and fetid discharge were diagnosed with metritis (n = 52). Cows with metritis were paired with herdmates without metritis (n = 52) based on DIM. The metabolome of plasma samples was evaluated using untargeted gas chromatography time-of-flight mass spectrometry. Univariate analyses included t-tests and fold change analyses. Metabolites with false discovery rate (FDR) adjusted P ≤ 0.10 on t-tests were used for partial least squares – discriminant analysis PLS-DA coupled with permutational analysis using 2,000 permutations. Metabolites with FDR adjusted P ≤ 0.10 on t-tests were also used for enriched pathway analyses and identification of cellular processes. Cows that developed metritis had affected cellular processes associated with lower amino acid metabolism in the prepartum period, greater lipolysis, cell death, and oxidative stress at calving and at metritis diagnosis, and greater leukocyte activation at calving, but lower immune cell activation at metritis diagnosis. In summary, cows that developed metritis had plasma metabolomic changes associated with greater lipolysis, oxidative stress, and a dysregulated immune response which may predispose cows to metritis development. |
Institute: | University of Florida |
Department: | College of Veterinary Medicine |
Laboratory: | Large Animal Clinical Sciences |
Last Name: | Casaro |
First Name: | Segundo |
Address: | 117 Deriso Hall, 2015 SW 16th Ave. |
Email: | segundocasaro@ufl.edu |
Phone: | 3522844016 |
Funding Source: | USDA NIFA AFRI |
Subject:
Subject ID: | SU002657 |
Subject Type: | Mammal |
Subject Species: | Bos taurus |
Taxonomy ID: | 9913 |
Weight Or Weight Range: | 700 kg |
Gender: | Female |
Animal Housing: | Free-stalls |
Animal Feed: | TMR |
Species Group: | Mammals |
Factors:
Subject type: Mammal; Subject species: Bos taurus (Factor headings shown in green)
mb_sample_id | local_sample_id | Group | Time | Parity |
---|---|---|---|---|
SA256898 | 9794_Calving_Con | Con | Calving | Mult |
SA256899 | 9778_Calving_Con | Con | Calving | Mult |
SA256900 | 9979_Calving_Con | Con | Calving | Mult |
SA256901 | 9971_Calving_Con | Con | Calving | Mult |
SA256902 | 9802_Calving_Con | Con | Calving | Mult |
SA256903 | 9966_Calving_Con | Con | Calving | Mult |
SA256904 | 9804_Calving_Con | Con | Calving | Mult |
SA256905 | 9536_Calving_Con | Con | Calving | Mult |
SA256906 | 9985_Calving_Con | Con | Calving | Mult |
SA256907 | 9280_Calving_Con | Con | Calving | Mult |
SA256908 | 9268_Calving_Con | Con | Calving | Mult |
SA256909 | 9945_Calving_Con | Con | Calving | Mult |
SA256910 | 10001_Calving_Con | Con | Calving | Mult |
SA256911 | 9992_Calving_Con | Con | Calving | Mult |
SA256912 | 9823_Calving_Con | Con | Calving | Mult |
SA256913 | 9987_Calving_Con | Con | Calving | Mult |
SA256914 | 9509_Calving_Con | Con | Calving | Mult |
SA256915 | 10038_Calving_Con | Con | Calving | Mult |
SA256916 | 9924_Calving_Con | Con | Calving | Mult |
SA256917 | 9918_Calving_Con | Con | Calving | Mult |
SA256918 | 9917_Calving_Con | Con | Calving | Mult |
SA256919 | 9925_Calving_Con | Con | Calving | Mult |
SA256920 | 9927_Calving_Con | Con | Calving | Mult |
SA256921 | 9957_Calving_Con | Con | Calving | Mult |
SA256922 | 9944_Calving_Con | Con | Calving | Mult |
SA256923 | 9950_Calving_Con | Con | Calving | Mult |
SA256924 | 9942_Calving_Con | Con | Calving | Mult |
SA256925 | 9954_Calving_Con | Con | Calving | Mult |
SA256926 | 9956_Calving_Con | Con | Calving | Mult |
SA256927 | 9875_Calving_Con | Con | Calving | Mult |
SA256928 | 9872_Calving_Con | Con | Calving | Mult |
SA256929 | 9904_Calving_Con | Con | Calving | Mult |
SA256930 | 9876_Calving_Con | Con | Calving | Mult |
SA256931 | 9907_Calving_Con | Con | Calving | Mult |
SA256932 | 10303_Calving_Con | Con | Calving | Prim |
SA256933 | 10264_Calving_Con | Con | Calving | Prim |
SA256934 | 10254_Calving_Con | Con | Calving | Prim |
SA256935 | 10212_Calving_Con | Con | Calving | Prim |
SA256936 | 10246_Calving_Con | Con | Calving | Prim |
SA256937 | 10262_Calving_Con | Con | Calving | Prim |
SA256938 | 10268_Calving_Con | Con | Calving | Prim |
SA256939 | 10274_Calving_Con | Con | Calving | Prim |
SA256940 | 10311_Calving_Con | Con | Calving | Prim |
SA256941 | 10261_Calving_Con | Con | Calving | Prim |
SA256942 | 10229_Calving_Con | Con | Calving | Prim |
SA256943 | 10290_Calving_Con | Con | Calving | Prim |
SA256944 | 10245_Calving_Con | Con | Calving | Prim |
SA256945 | 10194_Calving_Con | Con | Calving | Prim |
SA256946 | 10171_Calving_Con | Con | Calving | Prim |
SA256947 | 10165_Calving_Con | Con | Calving | Prim |
SA256948 | 10199_Calving_Con | Con | Calving | Prim |
SA256949 | 10189_Calving_Con | Con | Calving | Prim |
SA256950 | 9985_Diagnosis_Con | Con | Diagnosis | Mult |
SA256951 | 9904_Diagnosis_Con | Con | Diagnosis | Mult |
SA256952 | 9907_Diagnosis_Con | Con | Diagnosis | Mult |
SA256953 | 9918_Diagnosis_Con | Con | Diagnosis | Mult |
SA256954 | 9954_Diagnosis_Con | Con | Diagnosis | Mult |
SA256955 | 9917_Diagnosis_Con | Con | Diagnosis | Mult |
SA256956 | 9872_Diagnosis_Con | Con | Diagnosis | Mult |
SA256957 | 9876_Diagnosis_Con | Con | Diagnosis | Mult |
SA256958 | 9804_Diagnosis_Con | Con | Diagnosis | Mult |
SA256959 | 9794_Diagnosis_Con | Con | Diagnosis | Mult |
SA256960 | 9778_Diagnosis_Con | Con | Diagnosis | Mult |
SA256961 | 9536_Diagnosis_Con | Con | Diagnosis | Mult |
SA256962 | 9802_Diagnosis_Con | Con | Diagnosis | Mult |
SA256963 | 9268_Diagnosis_Con | Con | Diagnosis | Mult |
SA256964 | 9509_Diagnosis_Con | Con | Diagnosis | Mult |
SA256965 | 9823_Diagnosis_Con | Con | Diagnosis | Mult |
SA256966 | 9280_Diagnosis_Con | Con | Diagnosis | Mult |
SA256967 | 9875_Diagnosis_Con | Con | Diagnosis | Mult |
SA256968 | 9925_Diagnosis_Con | Con | Diagnosis | Mult |
SA256969 | 9979_Diagnosis_Con | Con | Diagnosis | Mult |
SA256970 | 9971_Diagnosis_Con | Con | Diagnosis | Mult |
SA256971 | 9987_Diagnosis_Con | Con | Diagnosis | Mult |
SA256972 | 10038_Diagnosis_Con | Con | Diagnosis | Mult |
SA256973 | 9992_Diagnosis_Con | Con | Diagnosis | Mult |
SA256974 | 9924_Diagnosis_Con | Con | Diagnosis | Mult |
SA256975 | 10001_Diagnosis_Con | Con | Diagnosis | Mult |
SA256976 | 9966_Diagnosis_Con | Con | Diagnosis | Mult |
SA256977 | 9944_Diagnosis_Con | Con | Diagnosis | Mult |
SA256978 | 9942_Diagnosis_Con | Con | Diagnosis | Mult |
SA256979 | 9927_Diagnosis_Con | Con | Diagnosis | Mult |
SA256980 | 9957_Diagnosis_Con | Con | Diagnosis | Mult |
SA256981 | 9945_Diagnosis_Con | Con | Diagnosis | Mult |
SA256982 | 9956_Diagnosis_Con | Con | Diagnosis | Mult |
SA256983 | 9950_Diagnosis_Con | Con | Diagnosis | Mult |
SA256984 | 10254_Diagnosis_Con | Con | Diagnosis | Prim |
SA256985 | 10194_Diagnosis_Con | Con | Diagnosis | Prim |
SA256986 | 10171_Diagnosis_Con | Con | Diagnosis | Prim |
SA256987 | 10189_Diagnosis_Con | Con | Diagnosis | Prim |
SA256988 | 10261_Diagnosis_Con | Con | Diagnosis | Prim |
SA256989 | 10165_Diagnosis_Con | Con | Diagnosis | Prim |
SA256990 | 10199_Diagnosis_Con | Con | Diagnosis | Prim |
SA256991 | 10212_Diagnosis_Con | Con | Diagnosis | Prim |
SA256992 | 10245_Diagnosis_Con | Con | Diagnosis | Prim |
SA256993 | 10262_Diagnosis_Con | Con | Diagnosis | Prim |
SA256994 | 10229_Diagnosis_Con | Con | Diagnosis | Prim |
SA256995 | 10274_Diagnosis_Con | Con | Diagnosis | Prim |
SA256996 | 10303_Diagnosis_Con | Con | Diagnosis | Prim |
SA256997 | 10311_Diagnosis_Con | Con | Diagnosis | Prim |
Collection:
Collection ID: | CO002650 |
Collection Summary: | All cows had blood collected in the prepartum period (-14 DRP), calving (first 24h after calving), and at diagnosis (day of metritis diagnosis). Blood was sampled from the jugular vein using a 20-gauge x 2.54-cm needle and 10-mL evacuated tube containing lithium heparin (Vacutainer, Becton, Dickinson and Company, Franklin Lakes, NJ, USA). After collection, the blood tubes were placed on ice and transported to the laboratory within 2 hours. Once in the laboratory, the blood tubes were centrifuged at 4000 g, 4 °C, for 10 min, and the plasma was stored at -80 oC for further characterization of the plasma metabolome. The frozen plasma was submitted to the University of California’s West Coast Metabolomics Center in Davis, CA for metabolome analysis. Samples were analyzed by blinded technicians using untargeted gas chromatography with time-of-flight mass spectrometry (GC-TOF-MS) in a single batch. |
Sample Type: | Blood (plasma) |
Treatment:
Treatment ID: | TR002669 |
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: | SP002663 |
Sampleprep Summary: | After collection, the blood tubes were placed on ice and transported to the laboratory within 2 hours. Once in the laboratory, the blood tubes were centrifuged at 4000 g, 4 °C, for 10 min, and the plasma was stored at -80 oC for further characterization of the plasma metabolome. The frozen plasma was submitted to the University of California’s West Coast Metabolomics Center in Davis, CA for metabolome analysis |
Combined analysis:
Analysis ID | AN004211 |
---|---|
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: | CH003122 |
Chromatography Summary: | 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. |
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: | MS003958 |
Analysis ID: | AN004211 |
Instrument Name: | Leco Pegasus IV TOF |
Instrument Type: | GC-TOF |
MS Type: | EI |
MS Comments: | See data acquisition, processing, and reporting in "Methods.pdf" file |
Ion Mode: | POSITIVE |
Analysis Protocol File: | Methods_SC.pdf |