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.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000835 |
| Study Title | Deubiquitinase inhibitor compound C6 effect on cellular metabolism |
| Study Type | MS analysis |
| Study Summary | 6.0 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 |
| Department | Biomedical Research Core Facilities |
| Laboratory | Metabolomics core |
| Last Name | Kachman |
| First Name | Maureen |
| Address | 6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714 |
| mkachman@med.umich.edu | |
| Phone | (734) 232-8175 |
| Submit Date | 2017-08-02 |
| Num Groups | 7 |
| Total Subjects | 1 |
| Study Comments | I 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 Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | LC-MS |
| Release Date | 2018-02-07 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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: | Mammals |
Factors:
Subject type: MOUSE; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample type | Treatment | Type |
|---|---|---|---|---|
| SA046609 | S00026317 | Cell Line | DUB inhibitor | RAW |
| SA046610 | S00026318 | Cell Line | DUB inhibitor | RAW |
| SA046611 | S00026319 | Cell Line | DUB inhibitor | RAW |
| SA046612 | S00026315 | Cell Line | DUB inhibitor | RAW |
| SA046613 | S00026316 | Cell Line | DUB inhibitor | RAW |
| SA046614 | S00026311 | Cell Line | Vehicle | RAW |
| SA046615 | S00026310 | Cell Line | Vehicle | RAW |
| SA046616 | S00026312 | Cell Line | Vehicle | RAW |
| SA046617 | S00026313 | Cell Line | Vehicle | RAW |
| SA046618 | S00026314 | Cell Line | Vehicle | RAW |
| SA046619 | S00026320 | Macrophages | Control-Other_Cells | Primary BL6 BMM |
| SA046620 | S00026321 | Macrophages | 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) |
| Solvent A: | 100% water; 5 mM ammonium acetate, pH 9.9 |
| Solvent B: | 100% acetonitrile |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS001228 |
| Analysis ID: | AN001336 |
| Instrument Name: | Agilent 6520B QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | NEGATIVE |
| Analysis Protocol File: | A043-TCA-Plus-20170713.pdf |
| MS ID: | MS001229 |
| Analysis ID: | AN001337 |
| Instrument Name: | Agilent 6520B QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | NEGATIVE |
| Analysis Protocol File: | A043-TCA-Plus-20170713.pdf |
