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.

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Study IDST001282
Study TitleRole of Hi1a in mitochondrial metabolic rewiring in M1 Macrophages
Study SummaryStudy 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 NamePalmieri
First NameErika M
Address1050 Boyles street, Frederick MD 21702
Emailerikamariana.palmieri@nih.gov
Phone3018461946
Submit Date2019-11-22
Raw Data AvailableYes
Raw Data File Type(s).peg
Analysis Type DetailGC-MS
Release Date2019-11-27
Release Version1
Erika M Palmieri Erika M Palmieri
https://dx.doi.org/10.21228/M8MM6Z
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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)
SA093505EMP_11 WT-LPSIFN18 100 50
SA093506EMP_12 WT-LPSIFN18 100 50
SA093507EMP_10 WT-LPSIFN18 100 50
SA093508EMP_13 KO-LPSIFN18 100 50
SA093509EMP_14 KO-LPSIFN18 100 50
SA093510EMP_15 KO-LPSIFN18 100 50
SA093511EMP_16 KO-LPSIFN18 100 50
SA093512EMP_09 WT-LPSIFN18 100 50
SA093497EMP_04 WT-CTRL18 - -
SA093498EMP_05 KO-CTRL18 - -
SA093499EMP_03 WT-CTRL18 - -
SA093500EMP_02 WT-CTRL18 - -
SA093501EMP_06 KO-CTRL18 - -
SA093502EMP_08 KO-CTRL18 - -
SA093503EMP_07 KO-CTRL18 - -
SA093504EMP_01 WT-CTRL18 - -
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 MS (30 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 MS (30 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
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