Summary of Study ST003663

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 PR002272. The data can be accessed directly via it's Project DOI: 10.21228/M8Z54T 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 IDST003663
Study TitleMetabolic and Morphometric Analysis of Allometric and Total Liver Growth in Post-Hatch Chickens
Study SummaryThis study was designed to characterize the liver and plasma metabolome of Ross 708 broiler chickens. Liver and plasma samples were obtained at necropsy on days 4,6,8,10,12,14,16,18 and 20 post-hatch and frozen in liquid nitrogen. Samples were submitted to the University of Carlifornia Davis campus for metabolomic analysis. Analysis revealed three distinct metabolic periods, A (days 4,6,8), B (days 10,12,14) and C (days 16,18,20). Period A corresponded to metabolism driven by yolk nutrients. Period B was a transition period during which yolk resources were being exhausted, and nutrients from feed were metabolized. Period C corresponded to the metabolism of a mature liver.
Institute
University of Delaware
DepartmentAnimal and Food Sciences
LaboratoryCarl Schmidt
Last NameSchmidt
First NameCarl
Address531 S. College Ave
Emailschmidtc@udel.edu
Phone3028311334
Submit Date2024-11-30
Raw Data AvailableYes
Raw Data File Type(s)cdf
Analysis Type DetailGC-MS
Release Date2025-02-05
Release Version1
Carl Schmidt Carl Schmidt
https://dx.doi.org/10.21228/M8Z54T
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002272
Project DOI:doi: 10.21228/M8Z54T
Project Title:Liver and Plasma Metabolome of the Post-hatch Chicken liver
Project Summary:This study was designed to characterize the liver and plasma metabolome of Ross 708 broiler chickens. Days 4-20 post-hatch were chosen as this period is when the chick shifts from reliance on nutrients from yolk to reliance on nutrients from feed.
Institute:University of Delaware
Department:Animal and Food Sciences
Laboratory:Carl Schmidt
Last Name:Schmidt
First Name:Carl
Address:531 S. College Ave, Newark, DE, 19716, USA
Email:schmidtc@udel.edu
Phone:+1 302 831-1334
Funding Source:This work is supported by the Animal Health and Production and Animal Products: Animal Breeding, Genetics, and Genomics program grant no. 2017–67015-26543 from the USDA National Institute of Food and Agriculture.

Subject:

Subject ID:SU003795
Subject Type:Bird
Subject Species:Gallus gallus
Taxonomy ID:9031
Age Or Age Range:Days 4-20
Gender:Male
Species Group:Birds

Factors:

Subject type: Bird; Subject species: Gallus gallus (Factor headings shown in green)

mb_sample_id local_sample_id Sample source Necropsy day
SA4009791601_Liver_078liver Day 10
SA4009801594_Liver_073liver Day 10
SA4009811524_Liver_072liver Day 10
SA4009821523_Liver_071liver Day 10
SA4009831522_Liver_070liver Day 10
SA4009841521_Liver_069liver Day 10
SA4009851520_Liver_068liver Day 10
SA4009861519_Liver_067liver Day 10
SA4009871595_Liver_074liver Day 10
SA4009881596_Liver_075liver Day 10
SA4009891598_Liver_077liver Day 10
SA4009901597_Liver_076liver Day 10
SA4009911525_Liver_091liver Day 12
SA4009921527_Liver_093liver Day 12
SA4009931528_Liver_094liver Day 12
SA4009941529_Liver_095liver Day 12
SA4009951607_Liver_102liver Day 12
SA4009961606_Liver_101liver Day 12
SA4009971605_Liver_100liver Day 12
SA4009981604_Liver_099liver Day 12
SA4009991603_Liver_098liver Day 12
SA4010001602_Liver_097liver Day 12
SA4010011526_Liver_092liver Day 12
SA4010021530_Liver_096liver Day 12
SA4010031532_Liver_116liver Day 14
SA4010041612_Liver_124liver Day 14
SA4010051531_Liver_115liver Day 14
SA4010061613_Liver_125liver Day 14
SA4010071533_Liver_117liver Day 14
SA4010081535_Liver_118liver Day 14
SA4010091536_Liver_119liver Day 14
SA4010101608_Liver_120liver Day 14
SA4010111609_Liver_121liver Day 14
SA4010121610_Liver_122liver Day 14
SA4010131611_Liver_123liver Day 14
SA4010141538_Liver_137liver Day 16
SA4010151619_Liver_148liver Day 16
SA4010161541_Liver_140liver Day 16
SA4010171542_Liver_141liver Day 16
SA4010181543_Liver_142liver Day 16
SA4010191540_Liver_139liver Day 16
SA4010201618_Liver_147liver Day 16
SA4010211617_Liver_146liver Day 16
SA4010221616_Liver_145liver Day 16
SA4010231615_Liver_144liver Day 16
SA4010241614_Liver_143liver Day 16
SA4010251539_Liver_138liver Day 16
SA4010261627_Liver_172liver Day 18
SA4010271623_Liver_170liver Day 18
SA4010281625_Liver_171liver Day 18
SA4010291621_Liver_168liver Day 18
SA4010301620_Liver_167liver Day 18
SA4010311548_Liver_165liver Day 18
SA4010321549_Liver_166liver Day 18
SA4010331622_Liver_169liver Day 18
SA4010341547_Liver_164liver Day 18
SA4010351544_Liver_161liver Day 18
SA4010361545_Liver_162liver Day 18
SA4010371546_Liver_163liver Day 18
SA4010381553_Liver_198liver Day 20
SA4010391555_Liver_199liver Day 20
SA4010401556_Liver_200liver Day 20
SA4010411552_Liver_197liver Day 20
SA4010421557_Liver_201liver Day 20
SA4010431629_Liver_202liver Day 20
SA4010441630_Liver_203liver Day 20
SA4010451631_Liver_204liver Day 20
SA4010461632_Liver_205liver Day 20
SA4010471633_Liver_206liver Day 20
SA4010481634_Liver_207liver Day 20
SA4010491550_Liver_196liver Day 20
SA4010501501_Liver_001liver Day 4
SA4010511577_Liver_008liver Day 4
SA4010521578_Liver_009liver Day 4
SA4010531579_Liver_010liver Day 4
SA4010541580_Liver_011liver Day 4
SA4010551581_Liver_012liver Day 4
SA4010561576_Liver_007liver Day 4
SA4010571502_Liver_002liver Day 4
SA4010581503_Liver_003liver Day 4
SA4010591504_Liver_004liver Day 4
SA4010601505_Liver_005liver Day 4
SA4010611506_Liver_006liver Day 4
SA4010621582_Liver_028liver Day 6
SA4010631508_Liver_023liver Day 6
SA4010641507_Liver_022liver Day 6
SA4010651512_Liver_027liver Day 6
SA4010661509_Liver_024liver Day 6
SA4010671510_Liver_025liver Day 6
SA4010681511_Liver_026liver Day 6
SA4010691586_Liver_032liver Day 6
SA4010701585_Liver_031liver Day 6
SA4010711584_Liver_030liver Day 6
SA4010721583_Liver_029liver Day 6
SA4010731587_Liver_033liver Day 6
SA4010741590_Liver_051liver Day 8
SA4010751589_Liver_050liver Day 8
SA4010761513_Liver_043liver Day 8
SA4010771588_Liver_049liver Day 8
SA4010781591_Liver_052liver Day 8
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Collection:

Collection ID:CO003788
Collection Summary:Birds were necropsied on days 4-20, every other day. Livers were removed and samples removed from the distal tip of the left lobe. Serum was prepared following blood drawn from the brachial vein.
Sample Type:Blood (plasma); Liver
Collection Location:distal tip of left lobe of liver
Volumeoramount Collected:200mg
Storage Conditions:-80℃

Treatment:

Treatment ID:TR003804
Treatment Summary:There were no treatments, birds were grown under normal husbandry conditions.

Sample Preparation:

Sampleprep ID:SP003802
Sampleprep Summary:Primary metabolism method summary Samples extracted using Matyash extraction procedure which includes MTBE, MeOH, and H2O. The the aqueous (bottom) phase was dried down and submitted to derivatization for GC. Samples are shaken at 30C for 1.5 hours. Then 91 uL of MSTFA + FAMEs to each sample and they are shaken at 37C for 0.5 hours to finish derivatization. Samples are then vialed, capped, and injected onto the instrument. We use a 7890A GC coupled with a LECO TOF. 0.5 uL of derivatized sample is injected using a splitless method onto a RESTEK RTX-5SIL MS column with an Intergra-Guard at 275C with a helium flow of 1 mL/min. The GC oven is set to hold at 50C for 1 min then ramp to 20C/min to 330C and then hold for 5 min. The transferline is set to 280C while the EI ion source is set to 250C. The Mass spec parameters collect data from 85m/z to 500m/z at an acquisition rate of 17 spectra/sec.
Sampleprep Protocol ID:None
Sampleprep Protocol Filename:SOP-GCMS-02252019.pdf
Processing Method:None
Processing Storage Conditions:-80℃
Extraction Method:Matyash extraction procedure MTBE, MeOH, and H2O. The the aqueous (bottom) phase was dried down and submitted to derivatization for GC. Samples are shaken at 30C for 1.5 hours. Then 91 uL of MSTFA + FAMEs to each sample and they are shaken at 37C for 0.5 hours to finish derivatization. Samples are then vialed, capped, and injected onto the instrument.
Extract Storage:-80℃

Combined analysis:

Analysis ID AN006019
Analysis type MS
Chromatography type GC
Chromatography system Agilent 7890A
Column Restek Rtx-5Sil MS (30m x 0.25mm, 0.25um)
MS Type EI
MS instrument type TOF
MS instrument name Leco Pegasus IV TOF
Ion Mode POSITIVE
Units peak height

Chromatography:

Chromatography ID:CH004573
Chromatography Summary:We use a 7890A GC coupled with a LECO TOF. 0.5 uL of derivatized sample is injected using a splitless method onto a RESTEK RTX-5SIL MS column with an Intergra-Guard at 275C with a helium flow of 1 mL/min. The GC oven is set to hold at 50C for 1 min then ramp to 20C/min to 330C and then hold for 5 min. The transferline is set to 280C while the EI ion source is set to 250C.
Instrument Name:Agilent 7890A
Column Name:Restek Rtx-5Sil MS (30m x 0.25mm, 0.25um)
Column Temperature:330˚C
Flow Gradient:N/A
Flow Rate:1 mL/min
Solvent A:N/A
Solvent B:N/A
Chromatography Type:GC

MS:

MS ID:MS005730
Analysis ID:AN006019
Instrument Name:Leco Pegasus IV TOF
Instrument Type:TOF
MS Type:EI
MS Comments:The Mass spec parameters collected data from 85m/z to 500m/z at an acquisition rate of 17 spectra/sec.
Ion Mode:POSITIVE
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