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MB Sample ID: SA093510

Local Sample ID:EMP_15 KO-LPSIFN
Subject ID:SU001354
Subject Type:Cultured cells
Subject Species:Mus musculus
Taxonomy ID:10090

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Subject:

Subject ID:SU001354
Subject Type:Cultured cells
Subject Species:Mus musculus
Taxonomy ID:10090

Factors:

Local Sample IDMB Sample IDFactor Level IDLevel ValueFactor Name
EMP_15 KO-LPSIFNSA093510FL01338418Hours
EMP_15 KO-LPSIFNSA093510FL013384100LPS (ng/mL)
EMP_15 KO-LPSIFNSA093510FL01338450IFNgamma ng/mL)

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
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