Summary of Study ST001280

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR000865. The data can be accessed directly via it's Project DOI: 10.21228/M8W40B This work is supported by NIH grant, U2C- DK119886.


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Study IDST001280
Study TitleMacrophage-Mediated Clofazimine Sequestration is Accompanied by a Shift in Host Energy Metabolism
Study Type4 timepoints for urine collection, whole blood collected at sacrifice (8 weeks)
Study SummaryExamined the effects of long-term dosing with CFZ of mice, metabolic data on CFZ and sham mice was collected at 0, 2, 4, and 8 weeks, at 8 weeks mice were sacrificed and WB was collected from 6 CFZ treated mice and 7 sham mice
University of Michigan
DepartmentClinical Pharmacy
LaboratoryNMR Metabolomics Laboratory, University of Michigan
Last NameStringer
First NameKathleen
AddressCollege of Pharmacy, 428 Church St, Ann Arbor, MI, 48109
Submit Date2019-11-05
Num Groups2
Total Subjects13, 48 urine Samples, 13 WB Samples
Num Males13
Raw Data File Type(s)fid
Analysis Type DetailNMR
Release Date2020-01-13
Release Version1
Kathleen Stringer Kathleen Stringer application/zip

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Project ID:PR000865
Project DOI:doi: 10.21228/M8W40B
Project Title:Macrophage-Mediated Clofazamine Sequestration is Accompanied by a Shift in Host Energy Metabolism
Project Summary:Examined the effects of long-term dosing with CFZ of mice, metabolic data on CFZ and sham mice was collected at 0, 2, 4, and 8 weeks, at 8 weeks mice were sacrificed and WB was collected from 6 CFZ treated mice and 7 sham mice
Institute:University of Michigan
Department:Clinical Pharmacy, Center for Bioinformatics and Computational Medicine
Laboratory:NMR Metabolomics Laboratory, University of Michigan
Last Name:Stringer
First Name:Kathleen
Address:College of Pharmacy, 428 Church St, Ann Arbor, MI, 48109
Phone:734- 647-4775
Funding Source:NIGMS


Subject ID:SU001352
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:C57Bl6
Age Or Age Range:5wks-13wks
Animal Animal Supplier:Jackson Laboratory (Bar Harbor, ME)
Animal Light Cycle:12hr light 12hr dark
Animal Feed:LabDiet 5001 (PMI International, Inc, St. Louis, MO) ad libitum
Animal Water:ad libitum


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

mb_sample_id local_sample_id Condition Timepoint (weeks)
SA093442Cage9_Wk0CFZ -
SA093443Cage7_Wk0CFZ -
SA093444Cage10_Wk0CFZ -
SA093445Cage11_Wk0CFZ -
SA093446Cage12_Wk0CFZ -
SA093447Cage8_Wk0CFZ -
SA093448Cage9_Wk2CFZ 2
SA093449Cage12_Wk2CFZ 2
SA093450Cage11_Wk2CFZ 2
SA093451Cage10_Wk2CFZ 2
SA093452Cage8_Wk2CFZ 2
SA093453Cage7_Wk2CFZ 2
SA093454Cage8_Wk4CFZ 4
SA093455Cage7_Wk4CFZ 4
SA093456Cage9_Wk4CFZ 4
SA093457Cage10_Wk4CFZ 4
SA093458Cage12_Wk4CFZ 4
SA093459Cage11_Wk4CFZ 4
SA093460Cage11_Wk8CFZ 8
SA093461Cage10_Wk8CFZ 8
SA093462Cage9_Wk8CFZ 8
SA093463Cage7_Wk8CFZ 8
SA093464Cage8_Wk8CFZ 8
SA093465Cage12_Wk8CFZ 8
SA093466Cage1_Wk0Placebo -
SA093467Cage5_Wk0Placebo -
SA093468Cage2_Wk0Placebo -
SA093469Cage4_Wk0Placebo -
SA093470Cage6_Wk0Placebo -
SA093471Cage3_Wk0Placebo -
SA093472Cage4_Wk2placebo 2
SA093473Cage3_Wk2placebo 2
SA093474Cage5_Wk2placebo 2
SA093475Cage6_Wk2placebo 2
SA093476Cage2_Wk2placebo 2
SA093477Cage1_Wk2placebo 2
SA093478Cage1_Wk4placebo 4
SA093479Cage5_Wk4placebo 4
SA093480Cage4_Wk4placebo 4
SA093481Cage3_Wk4placebo 4
SA093482Cage2_Wk4placebo 4
SA093483Cage6_Wk4placebo 4
SA093484Cage1_Wk8placebo 8
SA093485Cage4_Wk8placebo 8
SA093486Cage5_Wk8placebo 8
SA093487Cage6_Wk8placebo 8
SA093488Cage2_Wk8placebo 8
SA093489Cage3_Wk8placebo 8
Showing results 1 to 48 of 48


Collection ID:CO001346
Collection Summary:Urine: 18 hour collection from metabolic cages. At the end of each collection urine volume was measured and centrifuged (2000xg, 10 mins, °C). Internal standard was added equivalent to 10% of sample volume, aliquots were transferred into screw-top cryotubes and stored at -80°C. WB: cardiac puncture after anesthesia. Collected by cardiac puncture and transferred to a microcentrifuge tube containing sodium heparin in an ice water bath. Stored @ -80°C within 10 minutes of collection
Collection Protocol Filename:MouseUrineCollection,Processing_MetabolicCages.V1.5.pdf
Collection Protocol Comments:Urine Collected 4 times over 8 weeks, each collection over 18 hours
Sample Type:Urine
Collection Method:From Metabolic cages
Collection Frequency:2 weeks
Collection Duration:18hr
Storage Conditions:-80℃
Collection Vials:Sterile 2mL microcentrifuge tubes
Storage Vials:Sterile 2mL microcentrifuge tubes
Collection Tube Temp:Room temp


Treatment ID:TR001367
Treatment Summary:For treated mice: CFZ dissolved in sesame oil, added to chow, as 0.03% to powdered feed mix, chow provided ad libitum
Treatment Compound:Clofazamine (C8895; Sigma-Aldrich, St. Louis, MO)
Treatment Route:CFZ dissolved in sesame oil, added to chow, chow provided ad libitum
Treatment Dose:0.03% CFZ to powdered feed mix
Treatment Doseduration:8 weeks
Treatment Vehicle:sesame oil (Shirakiku, Japan)
Animal Acclimation Duration:1 week
Animal Endp Euthanasia:exsanguination while deeply anethetied with an intraperitoneal injection of ketamine (100mg/kg) and xlazine (10mg/kg)

Sample Preparation:

Sampleprep ID:SP001360
Sampleprep Summary:Urine: centrifugation (2000xg, 10mins, 4°C) before NMR
Processing Method:centrifugation
Processing Storage Conditions:4℃
Sample Spiking:DSS-IS2 (Chenomx, Inc)


Analysis ID:AN002121
Laboratory Name:NMR Metabolomics Laboratory
Analysis Type:NMR
Acquisition Date:1/29/2014, 5/15/14, 5/19/14, 5/20/14, 5/21/14, 5/22/14, 5/23/14, 10/23/14, 11/11/14, 11/24/14
Operator Name:Larisa Yeomans
Detector Type:1D-1H
Num Factors:8
Num Metabolites:34


NMR ID:NM000153
Analysis ID:AN002121
Instrument Name:Varian 500 MHz
Instrument Type:FT-NMR
NMR Experiment Type:1D-1H
NMR Comments:Arrayed for water saturation frequency and 90deg. pulse width for each sample
Spectrometer Frequency:500 MHz
NMR Probe:ONE-Probe
NMR Solvent:D2O
NMR Tube Size:5mm
Shimming Method:Auto shim (gradient shimming), manual when necessary.
Pulse Sequence:1D-NOESY
Water Suppression:saturation at 80 Hz induced field strength
Pulse Width:5.5ms
Offset Frequency:around -178Hz
Chemical Shift Ref Cpd:DSS-d6 IS-2 (Chenomx)
Number Of Scans:32