Summary of Study ST001282
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 PR000867. The data can be accessed directly via it's Project DOI: 10.21228/M8MM6Z 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.
| Study ID | ST001282 |
| Study Title | Role of Hi1a in mitochondrial metabolic rewiring in M1 Macrophages |
| Study Summary | Study of Metabolome of WT and Hi1a KO Bone Marrow Derived Macrophages in resting state or activated for 18h with LPS+IFN gamma |
| Institute | National Cancer Institute |
| Last Name | Palmieri |
| First Name | Erika M |
| Address | 1050 Boyles street, Frederick MD 21702 |
| erikamariana.palmieri@nih.gov | |
| Phone | 3018461946 |
| Submit Date | 2019-11-22 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | cdf |
| Analysis Type Detail | GC-MS |
| Release Date | 2019-11-27 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000867 |
| Project DOI: | doi: 10.21228/M8MM6Z |
| Project Title: | Nitric Oxide is responsible of mitochondrial metabolic rewiring in murine M1 macrophages |
| Project Type: | Metabolomics |
| Project Summary: | Study of metabolome of WT, Nos2 KO and Hi1a KO Bone Marrow Derived Macrophages in resting state or activated with LPS or combination of LPS+IFN gamma |
| Institute: | National Cancer Institute |
| Laboratory: | Laboratory of Cancer Immunometabolism |
| Last Name: | Palmieri |
| First Name: | Erika |
| Address: | 1050 Boyles street, Frederick MD 21702 |
| Email: | erikamariana.palmieri@nih.gov |
| Phone: | 3018461946 |
| Publications: | Nitric Oxide Orchestrates Metabolic Rewiring in M1 Macrophages by Targeting Aconitase 2 and Pyruvate Dehydrogenase |
| Contributors: | Erika M. Palmieri, Marieli Gonzalez-Cotto, Walter A. Baseler, Luke C. Davies, Bart Ghesquiere, Nunziata Maio, Christopher M. Rice,Tracey A. Rouault, Teresa Cassel, Richard M. Higashi, Andrew N. Lane, Teresa W.-M. Fan, David A. Wink and Daniel |
Subject:
| Subject ID: | SU001354 |
| Subject Type: | Cultured cells |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Factors:
Subject type: Cultured cells; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Hours | LPS (ng/mL) | IFNgamma ng/mL) |
|---|---|---|---|---|
| SA093505 | EMP_11 WT-LPSIFN | 18 | 100 | 50 |
| SA093506 | EMP_12 WT-LPSIFN | 18 | 100 | 50 |
| SA093507 | EMP_10 WT-LPSIFN | 18 | 100 | 50 |
| SA093508 | EMP_13 KO-LPSIFN | 18 | 100 | 50 |
| SA093509 | EMP_14 KO-LPSIFN | 18 | 100 | 50 |
| SA093510 | EMP_15 KO-LPSIFN | 18 | 100 | 50 |
| SA093511 | EMP_16 KO-LPSIFN | 18 | 100 | 50 |
| SA093512 | EMP_09 WT-LPSIFN | 18 | 100 | 50 |
| SA093497 | EMP_04 WT-CTRL | 18 | - | - |
| SA093498 | EMP_05 KO-CTRL | 18 | - | - |
| SA093499 | EMP_03 WT-CTRL | 18 | - | - |
| SA093500 | EMP_02 WT-CTRL | 18 | - | - |
| SA093501 | EMP_06 KO-CTRL | 18 | - | - |
| SA093502 | EMP_08 KO-CTRL | 18 | - | - |
| SA093503 | EMP_07 KO-CTRL | 18 | - | - |
| SA093504 | EMP_01 WT-CTRL | 18 | - | - |
| Showing results 1 to 16 of 16 |
Collection:
| Collection ID: | CO001348 |
| Collection Summary: | WT and Hif1a-/- BMDM (~107 cells per sample) were treated with vehicle (PBS) or 100ng/mL of LPS + 50ng/mL for 18 hours. Cells were then washed, gently scraped, pelleted, snap frozen in liquid nitrogen and sent to West Coast Metabolomic Center at the University of California, Davis (Davis, CA) for metabolomic analyses. |
| Sample Type: | Macrophages |
Treatment:
| Treatment ID: | TR001369 |
| Treatment Summary: | As mentioned in the sample information. |
Sample Preparation:
| Sampleprep ID: | SP001362 |
| Sampleprep Summary: | WT and Hif1a-/- BMDM (~107 cells per sample) were treated with vehicle (PBS) or 100ng/mL of LPS + 50ng/mL for 18 hours. Cells were then washed, gently scraped, pelleted, snap frozen in liquid nitrogen and sent to West Coast Metabolomic Center at the University of California, Davis (Davis, CA) for metabolomic analyses. |
Combined analysis:
| Analysis ID | AN002126 |
|---|---|
| Analysis type | MS |
| Chromatography type | GC |
| Chromatography system | Agilent 6890N |
| Column | Restek Rtx-5Sil (30m x 0.25mm,0.25um) |
| MS Type | EI |
| MS instrument type | GC-TOF |
| MS instrument name | Leco Pegasus III GC TOF |
| Ion Mode | POSITIVE |
| Units | normalized peak height |
Chromatography:
| Chromatography ID: | CH001558 |
| Instrument Name: | Agilent 6890N |
| Column Name: | Restek Rtx-5Sil (30m x 0.25mm,0.25um) |
| Chromatography Type: | GC |
MS:
| MS ID: | MS001980 |
| Analysis ID: | AN002126 |
| Instrument Name: | Leco Pegasus III GC TOF |
| Instrument Type: | GC-TOF |
| MS Type: | EI |
| MS Comments: | Raw GC-TOF MS data files were preprocessed directly after data acquisition and stored as ChromaTOF-specific peg files, as generic txt result files and additionally as generic ANDI MS cdf files. ChromaTOF version 4.0 was used for data preprocessing without smoothing, 3 s peak width, baseline subtraction just above the noise level, and automatic mass spectral deconvolution and peak detection at signal/noise (s/n) levels of 5:1 throughout the chromatogram. Results in .txt format were exported to a data server with absolute spectra intensities and further processed by a filtering algorithm implemented in the metabolomics BinBase database. The BinBase algorithm (rtx5) used the following settings: validity of chromatogram (107 counts/s), unbiased retention index marker detection (MS similarity > 800, validity of intensity range for high m/z |
| Ion Mode: | POSITIVE |
