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MB Sample ID: SA093506
| Local Sample ID: | EMP_12 WT-LPSIFN |
| Subject ID: | SU001354 |
| Subject Type: | Cultured cells |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001354 |
| Subject Type: | Cultured cells |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| EMP_12 WT-LPSIFN | SA093506 | FL013384 | 18 | Hours |
| EMP_12 WT-LPSIFN | SA093506 | FL013384 | 100 | LPS (ng/mL) |
| EMP_12 WT-LPSIFN | SA093506 | FL013384 | 50 | IFNgamma 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 |
