NMR metabolome data of indigenous and exotic cattle serum samples

Description

NMR metabolome data was generated in serum samples of three Bos indicus cattle (Sahiwal, Gir, Tharparkar), one cross bred (Karan fries) and one exotic Bos taurus cattle (Holstein Frisian). The samples were collected at hot summer when the temperature humity index was relatively very high. The serum metabolome data was generated using 1D 1H CPMG (Carr–Purcell–Meiboom–Gill) NMR spectra at 800 MHz to identify the differences in metabolome signature in indigenous, cross bred and exotic cattle during peak summer stress

Steps to reproduce

1. For NMR profiling, the serum samples were thawed on ice. Post-thaw, each sample was processed by combining 300 µL of serum with 300 µL of 0.9% sodium phosphate saline buffer (50 mM, pH 7.4) prepared in deuterium oxide (D₂O). The resulting 600 µL mixture was transferred into standard 5 mm NMR tubes for data acquisition. To provide a precise chemical shift reference without physically contaminating the serum matrix, a coaxial insert containing TSP (sodium salt of 3-trimethylsilyl-(2,2,3,3-d4)-propionic acid) was placed into the NMR tube reservoir. 2. Proton NMR spectra were acquired utilizing an 800 MHz NMR spectrometer (Bruker Avance-III). To effectively suppress the broad signals arising from residual macromolecules and high-molecular-weight proteins in the serum, one-dimensional (1D) H Carr–Purcell–Meiboom–Gill (CPMG) spin-echo pulse protocols were employed for all spectral recordings. Raw NMR data files were initially processed using Topspin-2.1 software (Bruker NMR Data Processing Software). Following raw processing, the generated NMR spectra were imported into the PROCESSOR module of Chenomx NMR Suite. Within the Chenomx environment, the spectra underwent automated baseline correction and were precisely calibrated to the formate signal before downstream metabolite identification and quantification. Individual serum metabolites were subsequently identified and quantified by matching experimental spectral signatures (chemical shifts and spin-spin coupling patterns) to the reference simulated patterns in the Chenomx library. 3. The quantified metabolite concentration matrix was exported as a .csv file and uploaded to the statistical analysis module of MetaboAnalyst 6.0.

Institutions

• National Bureau of Animal Genetic Resources

  Chandigarh, Chandigarh

Categories

Funders

• Indian Council of Agricultural Research

  Delhi, New Delhi

  Grant ID: This study was financially supported under the National Fellow scheme (Grant Number: 27(3)/2010-HRD) of the Indian Council of Agricultural Research, New Delhi.

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