Summary of Study ST000967

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 IDST000967
Study TitleMetabolomics Involved in Early-Life Single Pulse Antibiotic Exposures - Serum (part II)
Study TypeTimecourse treatment Vs control
Study SummaryThe mice serum 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 ERCMRC GCMS Core
Last NameSumner
First NameSusan
Address500 Laureate Way, Kannapolis, NC 28081
Emailsusan_sumner@unc.edu
Phone704-250-5066
Submit Date2018-04-20
Num Groups10
Total Subjects86
Num Males30
Num Females56
Study Commentsgroups include FRDA samples, Control samples, FRDA pools, Control pools, and Total pools
Raw Data AvailableYes
Raw Data File Type(s)cdf
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

Select appropriate tab below to view additional metadata details:


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:SU001006
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 Group
SA057763BS_58Control15
SA057764BS_50Control15
SA057765BS_56Control15
SA057766BS_57Control15
SA057767BS_51Control15
SA057768BS_55Control15
SA057769BS_52Control15
SA057770BS_54Control15
SA057771BS_69Control23
SA057772BS_70Control23
SA057773BS_71Control23
SA057774BS_68Control23
SA057775BS_48Control23
SA057776BS_43Control23
SA057777BS_45Control23
SA057778BS_44Control23
SA057779BS_47Control23
SA057780BS_24Control42
SA057781BS_23Control42
SA057782BS_72Control42
SA057783BS_78Control42
SA057784BS_22Control42
SA057785BS_77Control42
SA057786BS_73Control42
SA057787BS_9Control42
SA057788BS_7Control42
SA057789BS_21Control42
SA057790BS_8Control42
SA057791BS_17Control42
SA057792BS_10Control42
SA057793BS_18Control42
SA057794BS_19Control42
SA057795BS_20Control42
SA057796BS_66Control70
SA057797BS_67Control70
SA057798BS_35PAT15
SA057799BS_33PAT15
SA057800BS_42PAT15
SA057801BS_36PAT15
SA057802BS_28PAT15
SA057803BS_32PAT15
SA057804BS_29PAT15
SA057805BS_31PAT15
SA057806BS_30PAT15
SA057807BS_65PAT23
SA057808BS_39PAT23
SA057809BS_40PAT23
SA057810BS_37PAT23
SA057811BS_25PAT23
SA057812BS_26PAT23
SA057813BS_27PAT23
SA057814BS_63PAT42
SA057815BS_15PAT42
SA057816BS_64PAT42
SA057817BS_75PAT42
SA057818BS_14PAT42
SA057819BS_76PAT42
SA057820BS_74PAT42
SA057821BS_16PAT42
SA057822BS_3PAT42
SA057823BS_2PAT42
SA057824BS_13PAT42
SA057825BS_1PAT42
SA057826BS_4PAT42
SA057827BS_5PAT42
SA057828BS_12PAT42
SA057829BS_11PAT42
SA057830BS_6PAT42
SA057831BS_62PAT70
SA057832BS_60PAT70
SA057833BS_61PAT70
SA057834BSP_5Total Pool
SA057835BSP_4Total Pool
SA057836BSP_6Total Pool
SA057837BSP_8Total Pool
SA057838BSP_3Total Pool
SA057839BSP_9Total Pool
SA057840BSP_11Total Pool
SA057841BSP_12Total Pool
SA057842BSP_10Total Pool
SA057843BSP_14Total Pool
SA057844BSP_15Total Pool
SA057845BSP_17Total Pool
SA057846BSP_16Total Pool
SA057847BSP_2Total Pool
Showing results 1 to 85 of 85

Collection:

Collection ID:CO001000
Collection Summary:Serum was collected via standard operating procedures.
Sample Type:Blood (serum)
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001020
Treatment Summary:PAT15= NOD mice received antibiotics and sacrifced at age of day at 15; Control-15=NOD mice received no antibiotics and sacrifced at age of day at 15; PAT23= NOD mice received antibiotics and sacrifced at age of day at 23; Control-23=NOD mice received no antibiotics and sacrifced at age of day at 23; PAT42= NOD mice received antibiotics and sacrifced at age of day at 42; Control-42=NOD mice received no antibiotics and sacrifced at age of day at 42; PAT70= NOD mice received antibiotics and sacrifced at age of day at 70; Control-70=NOD mice received no antibiotics and sacrifced 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
Treatment Protocol Comments: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:SP001013
Sampleprep Summary:Extraction, Solvent Removal, Resuspension, Solvent Removal, Two-step Derivatization and Addition of FAME Markers
Processing Method:Aliquots of 30 µL serum were mixed with 1000 µL of degassed 3:3:2 Acetonitrile:Isopropanol:Water solution in a 2 mL snap cap tube. Samples were vortexed, shaken for 5 minutes then centrifuged at 4⁰C for 2 minutes at 14000rcf. The supernatant was recovered and split into two fractions. Fraction 1 (450 µL) was archived and fraction 2 (450 µL) was subjected to complete sample processing. Processing continued as follows. Samples were completely dried by vacuum centrifuge and reconstituted with 450 µL 1:1 acetonitrile:water solution. Samples were centrifuged for 2 minutes at 14000rcf and transferred to new snap cap tubes followed by complete evaporation at room temperature by vacuum centrifuge.
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 AN001581
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:CH001110
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 Temperature:250⁰C
Flow Gradient:constant flow
Flow Rate:1 mL/min
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
Randomization Order:Yes
Chromatography Type:GC

MS:

MS ID:MS001459
Analysis ID:AN001581
Instrument Name:Leco Pegasus 4D GCxGC TOF
Instrument Type:GC x GC-TOF
MS Type:EI
Ion Mode:POSITIVE
Collision Gas:Medium
Helium Flow:1 ml/min
Ion Source Temperature:250⁰C
Ionization Energy:70eV
Source Temperature:250⁰C
Dataformat:netcdf
Probe Tip:1200
Scan Range Moverz:50-750
Scanning:20 spectra/sec
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