Summary of Study ST001234

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 PR000827. The data can be accessed directly via it's Project DOI: 10.21228/M8SD6F This work is supported by NIH grant, U2C- DK119886.

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This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST001234
Study TitleThe effect of weaning stress, sex and temperament on fecal microbiota and metabolites in Brahman calves.
Study SummaryThe objective of this study was to conduct a cross-sectional study to 1) investigate the effect of weaning on the fecal microbiota as well as serum metabolites in Bos indicus (Brahman) calves, and 2) compare the fecal microbiota as well as serum metabolites between males (bulls) and females (heifers) as well as between calm and temperamental animals at weaning (d0) and 4 days post weaning (d4). Equal numbers of animals were present in each category (5 calm female, 5 temperamental female, 5 calm male, and 5 temperamental male animals).
Institute
Texas A&M University
DepartmentVeterinary Pathobiology
Last NameLawhon
First NameSara
AddressMS4467
Emailslawhon@tamu.edu
Phone979-218-7156
Submit Date2019-08-06
Raw Data AvailableYes
Raw Data File Type(s)cdf
Analysis Type DetailGC-MS
Release Date2024-08-06
Release Version1
Sara Lawhon Sara Lawhon
https://dx.doi.org/10.21228/M8SD6F
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000827
Project DOI:doi: 10.21228/M8SD6F
Project Title:The effect of weaning stress, sex and temperament on fecal microbiota and serum metabolites in Brahman calves.
Project Summary:The objective of this study was to conduct a cross-sectional study to 1) investigate the effect of weaning on the fecal microbiota and serum metabolites in Bos indicus (Brahman) calves, and 2) compare the fecal microbiota and serum metabolites between males (bulls) and females (heifers) as well as between calm and temperamental animals at weaning (d0) and 4 days post weaning (d4). Equal numbers of animals were present in each category (5 calm female, 5 temperamental female, 5 calm male, and 5 temperamental male animals).
Institute:Texas A&M University
Last Name:Lawhon
First Name:Sara
Address:MS4467, College of Veterinary Medicine, College Station, TX 77843-4467
Email:slawhon@tamu.edu
Phone:979-218-7156
Funding Source:USDA Formula Animal Health 1433 Program TEXO9584 Funds

Subject:

Subject ID:SU001302
Subject Type:Mammal
Subject Species:Bos indicus
Taxonomy ID:9915

Factors:

Subject type: Mammal; Subject species: Bos indicus (Factor headings shown in green)

mb_sample_id local_sample_id Temperament Sex Experiment Day
SA088168160322cOEsa17_1Calm Female -
SA088169160322cOEsa35_1Calm Female -
SA088170160322cOEsa16_1Calm Female -
SA088171160322cOEsa09_1Calm Female -
SA088172160322cOEsa27_1Calm Female -
SA088173160322cOEsa20_1Calm Female 4
SA088174160322cOEsa10_1Calm Female 4
SA088175160322cOEsa03_1Calm Female 4
SA088176160322cOEsa37_1Calm Female 4
SA088177160322cOEsa40_1Calm Female 4
SA088178160322cOEsa23_1Calm Male -
SA088179160322cOEsa25_1Calm Male -
SA088180160322cOEsa04_1Calm Male -
SA088181160322cOEsa28_1Calm Male -
SA088182160322cOEsa19_1Calm Male -
SA088183160322cOEsa42_2Calm Male 4
SA088184160322cOEsa36_1Calm Male 4
SA088185160322cOEsa11_1Calm Male 4
SA088186160322cOEsa13_1Calm Male 4
SA088187160322cOEsa07_1Calm Male 4
SA088188160322cOEsa46_2Temperamental Female -
SA088189160322cOEsa34_1Temperamental Female -
SA088190160322cOEsa01_1Temperamental Female -
SA088191160322cOEsa38_1Temperamental Female -
SA088192160322cOEsa12_1Temperamental Female -
SA088193160322cOEsa06_1Temperamental Female 4
SA088194160322cOEsa02_1Temperamental Female 4
SA088195160322cOEsa18_1Temperamental Female 4
SA088196160322cOEsa15_1Temperamental Female 4
SA088197160322cOEsa08_1Temperamental Female 4
SA088198160322cOEsa24_1Temperamental Male -
SA088199160322cOEsa45_2Temperamental Male -
SA088200160322cOEsa26_1Temperamental Male -
SA088201160322cOEsa14_1Temperamental Male -
SA088202160322cOEsa29_1Temperamental Male -
SA088203160322cOEsa30_1Temperamental Male 4
SA088204160322cOEsa21_1Temperamental Male 4
SA088205160322cOEsa44_2Temperamental Male 4
SA088206160322cOEsa33_1Temperamental Male 4
SA088207160322cOEsa05_1Temperamental Male 4
Showing results 1 to 40 of 40

Collection:

Collection ID:CO001296
Collection Summary:Blood was collected via jugular venipuncture into vacutainer tubes without an anti-clotting reagent. Samples were allowed to coagulate on ice followed by centrifugation at 1600 x g for 30 min. Serum was aspirated and stored at -20 ⁰C.
Sample Type:Blood (serum)
Storage Conditions:-20℃

Treatment:

Treatment ID:TR001317
Treatment Summary:Calves were weaned and blood samples collected at the time of weaning and four days after weaning. No other treatments were performed. No drugs were employed.

Sample Preparation:

Sampleprep ID:SP001310
Sampleprep Summary:Blood serum was extracted following the protocols published in Fiehn et al. PLoS ONE (2010) e15234. A 30 ul aliquot of each sample was extracted with 1 ml of degassed acetonitrile : isopropanol : water (3:3:2, v/v/v) at -20C, centrifuged and decanted with subsequent evaporation of the solvent to complete dryness. A clean-up step with acetonitrile/water (1:1) was used to remove membrane lipids and triglycerides. The cleaned extract was aliquoted into two equal portions and the supernatant was dried again. Internal standards C08-C30 FAMEs were added and the samples were derivatized by methoxyamine hydrochloride in pyridine and subsequently by N-methyl-N-trimethylsilyltrifluoroacetamide for trimethylsilylation of acidic protons.
Processing Storage Conditions:-20℃
Extraction Method:A 30 ul aliquot of each sample was extracted with 1 ml of degassed acetonitrile : isopropanol : water (3:3:2, v/v/v) at -20C, centrifuged and decanted with subsequent evaporation of the solvent to complete dryness.
Extract Cleanup:A clean-up step with acetonitrile/water (1:1) was used to remove membrane lipids and triglycerides.
Extract Storage:-20℃
Sample Derivatization:Samples were derivatized by methoxyamine hydrochloride in pyridine and subsequently by N-methyl-N-trimethylsilyltrifluoroacetamide for trimethylsilylation of acidic protons.
Sample Spiking:Internal standards C08-C30 FAMEs were added.

Combined analysis:

Analysis ID AN002052
Analysis type MS
Chromatography type GC
Chromatography system none
Column none
MS Type EI
MS instrument type GC-TOF
MS instrument name Leco Pegasus IV TOF
Ion Mode POSITIVE
Units Peak height

Chromatography:

Chromatography ID:CH001491
Chromatography Summary:See method file.
Methods Filename:GC TOF method.doc
Instrument Name:none
Column Name:none
Column Temperature:50-275°C
Flow Rate:1 mL min-1
Injection Temperature:50°C ramped to 250°C by 12°C s-1
Chromatography Type:GC

MS:

MS ID:MS001904
Analysis ID:AN002052
Instrument Name:Leco Pegasus IV TOF
Instrument Type:GC-TOF
MS Type:EI
MS Comments:See attached file.
Ion Mode:POSITIVE
Acquisition Parameters File:Acquisition rate is 17 spectra
second, with a scan mass range of 85-500 Da.
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