Summary of study ST000962

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 PR000660. The data can be accessed directly via it's Project DOI: 10.21228/M8C39R This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

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 IDST000962
Study TitleMetabolomics Involved in Early-Life Single Pulse Antibiotic Exposures - Liver (part I)
Study TypeTimecourse treatment Vs control
Study SummaryThe mice liver samples were extracted and analyzed using broad spectrum GCMS for the identification of compounds distinguishing the groups.
Institute
University of North Carolina
DepartmentNIH Eastern Regional Comprehensive Metabolomics Resource Core (RTI RCMRC)
LaboratoryUNC NRI ERCMRC GCMS Core
Last NameSumner
First NameSusan
Address500 Laureate Way Kannapolis NC 28081
Emailsusan_sumner@unc.edu
Phone1-919-622-4456
Submit Date2018-04-13
Num Groups10
Total Subjects86
Num Males30
Num Females56
Analysis Type DetailGC-MS
Release Date2018-08-02
Release Version1
Susan Sumner Susan Sumner
https://dx.doi.org/10.21228/M8C39R
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000660
Project DOI:doi: 10.21228/M8C39R
Project Title:Metabolomics Involved in Early-Life Single Pulse Antibiotic Exposures
Project Type:Timecourse treatment Vs control
Project Summary:The mice liver samples were extracted and analyzed using broad spectrum GCMS for the identification of compounds distinguishing the groups.
Institute:University of North Carolina
Department:NIH Eastern Regional Comprehensive Metabolomics Resource Core (RTI RCMRC)
Laboratory:UNC NRI ERCMRC GCMS Core
Last Name:Sumner
First Name:Susan
Address:500 Laureate Way Kannapolis NC 28081
Email:susan_sumner@unc.edu
Phone:1-919-622-4456

Subject:

Subject ID:SU001001
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Factor 1
SA057543BL_51Control-15
SA057544BL_53Control-15
SA057545BL_54Control-15
SA057546BL_50Control-15
SA057547BL_52Control-15
SA057548BL_46Control-15
SA057549BL_49Control-15
SA057550BL_47Control-15
SA057551BL_45Control-15
SA057552BL_48Control-15
SA057553BL_76Control-23
SA057554BL_44Control-23
SA057555BL_77Control-23
SA057556BL_78Control-23
SA057557BL_79Control-23
SA057558BL_43Control-23
SA057559BL_41Control-23
SA057560BL_37Control-23
SA057561BL_42Control-23
SA057562BL_39Control-23
SA057563BL_38Control-23
SA057564BL_40Control-23
SA057565BL_74Control-42
SA057566BL_73Control-42
SA057567BL_72Control-42
SA057568BL_75Control-42
SA057569BL_81Control-42
SA057570BL_7Control-42
SA057571BL_80Control-42
SA057572BL_8Control-42
SA057573BL_17Control-42
SA057574BL_18Control-42
SA057575BL_10Control-42
SA057576BL_24Control-42
SA057577BL_19Control-42
SA057578BL_20Control-42
SA057579BL_23Control-42
SA057580BL_22Control-42
SA057581BL_21Control-42
SA057582BL_71Control-70
SA057583BL_70Control-70
SA057584BL_68Control-70
SA057585BL_69Control-70
SA057586Graphical IDGroup
SA057587BL_33PAT15
SA057588BL_36PAT15
SA057589BL_32PAT15
SA057590BL_35PAT15
SA057591BL_34PAT15
SA057592BL_27PAT15
SA057593BL_31PAT15
SA057594BL_28PAT15
SA057595BL_30PAT15
SA057596BL_29PAT15
SA057597BL_67PAT23
SA057598BL_65PAT23
SA057599BL_66PAT23
SA057600BL_64PAT23
SA057601BL_25PAT23
SA057602BL_26PAT23
SA057603BL_63PAT23
SA057604BL_5PAT42
SA057605BL_4PAT42
SA057606BL_59PAT42
SA057607BL_61PAT42
SA057608BL_3PAT42
SA057609BL_60PAT42
SA057610BL_6PAT42
SA057611BL_62PAT42
SA057612BL_11PAT42
SA057613BL_2PAT42
SA057614BL_1PAT42
SA057615BL_12PAT42
SA057616BL_13PAT42
SA057617BL_16PAT42
SA057618BL_15PAT42
SA057619BL_14PAT42
SA057620BL_58PAT70
SA057621BL_55PAT70
SA057622BL_57PAT70
SA057623BL_56PAT70
SA057624BL_9Resoration-Control
SA057625BL_86Resoration-Control
SA057626BL_85Resoration-Control
SA057627BL_84Resoration-PAT
SA057628BL_82Resoration-PAT
SA057629BL_83Resoration-PAT
SA057630BLP_4Total Pool
SA057631BLP_3Total Pool
SA057632BLP_5Total Pool
SA057633BLP_6Total Pool
SA057634BLP_9Total Pool
SA057635BLP_8Total Pool
SA057636BLP_2Total Pool
SA057637BLP_18Total Pool
SA057638BLP_11Total Pool
SA057639BLP_10Total Pool
SA057640BLP_12Total Pool
SA057641BLP_14Total Pool
SA057642BLP_16Total Pool
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Collection:

Collection ID:CO000995
Collection Summary:livers were collected via standard operating procedures.
Sample Type:Liver
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001015
Treatment Summary:PAT15= NOD mice received antibiotics and sacrificed at age of day at 15; Control-15=NOD mice received no antibiotics and sacrificed at age of day at 15; PAT23= NOD mice received antibiotics and sacrificed at age of day at 23; Control-23=NOD mice received no antibiotics and sacrificed at age of day at 23; PAT42= NOD mice received antibiotics and sacrificed at age of day at 42; Control-42=NOD mice received no antibiotics and sacrificed at age of day at 42; PAT70= NOD mice received antibiotics and sacrificed at age of day at 70; Control-70=NOD mice received no antibiotics and sacrificed at age of day at 70; Restoration-PAT= C57 mice received poo from NOD mice given antibiotics Restoration-Control= C57 mice received poo from NOD mice given no antibiotics Comments Treatment (Abiotic, Biotic, Intervention) treated with antibiotics at 5 to 10 days vehicle treated with antibiotics at 5 to 10 days vehicle treated with antibiotics at 5 to 10 days vehicle treated with antibiotics at 5 to 10 days vehicle Treated with poo from NOD mice given antibiotics. Treated with poo from NOD mice given vehicle.

Sample Preparation:

Sampleprep ID:SP001008
Sampleprep Summary:Extraction, Solvent Removal, Resuspension, Solvent Removal, Two-step Derivatization and Addition of FAME Markers
Processing Method:Liver tissue were frozen on dry ice and weighed at approximate 100 mg to a MagNa Lyser tube with 10 to 15 ceramic beads inside. The ice-cold homogenization buffer (50% acetonitrile) was added with the mass/volume ratio at 1 mg tissue per 5 µL buffer. The homogenization was carried on at 4,500 rpm for two 30 sec pulses by the MagNA Lyser. The homogenized mixture was centrifuged at 14,000 rpm for 5 min at -4 °C for the supernatant. Aliquots of 100 µL homogenized supernatant of the study sample (equal to 20 mg tissue) were mixed with 1000 µL of cold degassed 3:3:2 ACN:ISP:H20 solution in a 2 mL snap cap tube. Samples are vortex and shaken for 5 min, and then centrifuged at 4 °C for 2 min at 14000 rcf. The supernatant was split into (2)-450 µL fractions, one fraction was archived in -80°C the second fraction was subject t complete sample processing. Transfer supernatant to a new vial. Evaporate supernatant to complete dryness at room temp.
Processing Storage Conditions:On ice
Extraction Method:(step 1) 3:3:2 Acetonitrile:Isopropanol:H2O, (step 2) 1:1 Acetonitrile:H2O
Extract Storage:-80℃
Sample Resuspension:Samples resuspended in 200 µL of 1:1 ACN:H2O. Evaporated to dryness w/speed vac.
Sample Derivatization:Formation of methoximes by adding 10µL of 40mg/mL MeOx in pyridine to each sample. Placed onto Thermomixer for 90 min at 30⁰C. Then FAME retention index markers and MSTFA added to each sample for derivatization step. Samples returned to Thermomixer for 45 min at 70⁰C.
Sample Spiking:Fatty acid methyl esters (FAME)

Combined analysis:

Analysis ID AN001576
Analysis type MS
Chromatography type GC
Chromatography system Leco Pegasus 4D GC
Column Restek Rtx-5Sil MS (30 x 0.25mm, 0.25um)
MS Type EI
MS instrument type GC x GC-TOF
MS instrument name Leco Pegasus 4D GCxGC TOF
Ion Mode POSITIVE
Units m/z

Chromatography:

Chromatography ID:CH001105
Chromatography Summary:GCMS analysis is based on the Oliver Fiehn method
Instrument Name:Leco Pegasus 4D GC
Column Name:Restek Rtx-5Sil MS (30 x 0.25mm, 0.25um)
Column Pressure:14.05psi
Column Temperature:Initial Oven Temp 100⁰C, hold 60 sec. Ramp rate 20⁰C/min to 330⁰C, hold 5 min.
Flow Gradient:constant flow
Flow Rate:1 mL/min
Injection Temperature:250⁰C
Retention Index:FAME retention index markers C8-C30
Sample Injection:1.0 µL
Analytical Time:20 min
Oven Temperature:Initial Oven Temp100⁰C, hold 60 sec. Ramp rate 20⁰C/min to 330⁰C, hold 5 min.
Transferline Temperature:280⁰C
Chromatography Type:GC

MS:

MS ID:MS001454
Analysis ID:AN001576
Instrument Name:Leco Pegasus 4D GCxGC TOF
Instrument Type:GC x GC-TOF
MS Type:EI
Ion Mode:POSITIVE
Helium Flow:1 mL/min
Ion Source Temperature:250⁰C
Ionization Energy:70eV
Source Temperature:250⁰C
Dataformat:netcdf
Resolution Setting:1200
Scan Range Moverz:50-750
Scanning:20 spectra/sec
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