Summary of study ST000835

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 PR000595. The data can be accessed directly via it's Project DOI: 10.21228/M8RQ4G This work is supported by NIH grant, U2C- DK119886.

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Study IDST000835
Study TitleDeubiquitinase inhibitor compound C6 effect on cellular metabolism
Study TypeMS analysis
Study Summary6.0 X 10^6 cells were plated in 10 cm Tissue Culture dishes and allowed to recover overnight at 37 degrees and 5% CO2. In the am, supernatant was removed, and 12 mL of fresh medium with either 2.5 micromolar Compound C6 or a v/v match of DMSO (vehicle control) was added to the cells. Cells were incubated at 37 degrees in 5% CO2 for 30 minutes. Cells were washed 3X with cold DPBS++ and 10 mL of medium was added to the cells with either 1.0 micromolar Compound C6 or v/v match of DMSO. Cells were incubated at 37 degrees and 5% CO2 for 7.0 hours. Cells were washed with 10 mL of 150 mM Ammonium Acetate, swirled, washed again with 5 mL, and immediately quenched with liquid nitrogen. Cells were then frozen at -80 degrees.
Institute
University of Michigan
DepartmentBiomedical Research Core Facilities
LaboratoryMetabolomics core
Last NameKachman
First NameMaureen
Address6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Emailmkachman@med.umich.edu
Phone(734) 232-8175
Submit Date2017-08-02
Num Groups7
Total Subjects1
Study CommentsI request that the metabolites of the TCA+ assay that are to be assessed quantitatively please be sure to include ATP, ADP, AMP, NAD, NADH, NADP, NADPH, E4P, S7P, 6PG, G3P, H6P, and Lactate in particular. Also, I would request that both reduced and oxidized Glutathione as well as Fructose 1,6-bisphosphate be included in the non-quantitative data.
Raw Data AvailableYes
Raw Data File Type(s).d
Analysis Type DetailLC-MS
Release Date2018-02-07
Release Version1
Maureen Kachman Maureen Kachman
https://dx.doi.org/10.21228/M8RQ4G
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000595
Project DOI:doi: 10.21228/M8RQ4G
Project Title:Purine and TCA Measurements in SS Hypertension
Project Type:MS analysis
Project Summary:Based on RNA-seq ontological and Bayesian analyses, both purine levels and TCA-cycle intermediates have been nominated as being regulated by pressure in the SS rat. This project seeks to verify the previous RNA-seq prediction.
Institute:Medical College of Wisconsin
Department:Physiology
Laboratory:Cowley Lab
Last Name:Cowley
First Name:Allen
Address:Milwaukee, WI
Email:cowley@mcw.edu
Phone:414-955-8277

Subject:

Subject ID:SU000862
Subject Type:MOUSE
Subject Species:Mus musculus
Taxonomy ID:10090
Species Group:Mammal

Factors:

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

mb_sample_id local_sample_id Sample type Treatment Type
SA046609S00026317Cell Line DUB inhibitor RAW
SA046610S00026318Cell Line DUB inhibitor RAW
SA046611S00026319Cell Line DUB inhibitor RAW
SA046612S00026315Cell Line DUB inhibitor RAW
SA046613S00026316Cell Line DUB inhibitor RAW
SA046614S00026311Cell Line Vehicle RAW
SA046615S00026310Cell Line Vehicle RAW
SA046616S00026312Cell Line Vehicle RAW
SA046617S00026313Cell Line Vehicle RAW
SA046618S00026314Cell Line Vehicle RAW
SA046619S00026320Macrophages Control-Other_Cells Primary BL6 BMM
SA046620S00026321Macrophages Control-Other_Cells Primary BL6 BMM
Showing results 1 to 12 of 12

Collection:

Collection ID:CO000856
Collection Summary:-
Sample Type:Cultured cells

Treatment:

Treatment ID:TR000876
Treatment Summary:-

Sample Preparation:

Sampleprep ID:SP000869
Sampleprep Summary:-
Sampleprep Protocol Filename:A043-TCA-Plus-20170713.pdf

Combined analysis:

Analysis ID AN001336 AN001337
Analysis type MS MS
Chromatography type HILIC HILIC
Chromatography system Agilent Agilent
Column Phenomenex Luna NH2 (150 x 1mm, 3um) Phenomenex Luna NH2 (150 x 1mm, 3um)
MS Type ESI ESI
MS instrument type QTOF QTOF
MS instrument name Agilent 6520B QTOF Agilent 6520B QTOF
Ion Mode NEGATIVE NEGATIVE
Units ISTD response ratio pmol/ug protein

Chromatography:

Chromatography ID:CH000934
Instrument Name:Agilent
Column Name:Phenomenex Luna NH2 (150 x 1mm, 3um)
Chromatography Type:HILIC

MS:

MS ID:MS001228
Analysis ID:AN001336
Instrument Name:Agilent 6520B QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:NEGATIVE
  
MS ID:MS001229
Analysis ID:AN001337
Instrument Name:Agilent 6520B QTOF
Instrument Type:QTOF
MS Type:ESI
Ion Mode:NEGATIVE
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