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MB Sample ID: SA333287
| Local Sample ID: | 02_023 |
| Subject ID: | SU003208 |
| Subject Type: | Mammal |
| Subject Species: | Rattus norvegicus |
| Taxonomy ID: | 10116 |
| Weight Or Weight Range: | 400g |
| Gender: | Male and female |
| Animal Animal Supplier: | Charles River |
| Animal Housing: | Double Housed |
| Animal Light Cycle: | Reverse Light Cycle |
| Species Group: | Sprague Dawley |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU003208 |
| Subject Type: | Mammal |
| Subject Species: | Rattus norvegicus |
| Taxonomy ID: | 10116 |
| Weight Or Weight Range: | 400g |
| Gender: | Male and female |
| Animal Animal Supplier: | Charles River |
| Animal Housing: | Double Housed |
| Animal Light Cycle: | Reverse Light Cycle |
| Species Group: | Sprague Dawley |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| 02_023 | SA333287 | FL039571 | Norm. Area 02_23.raw (F66) | Sample source |
| 02_023 | SA333287 | FL039571 | 3X | Injury severity |
| 02_023 | SA333287 | FL039571 | M | Sex |
| 02_023 | SA333287 | FL039571 | Batch 2 | Batches |
Collection:
| Collection ID: | CO003201 |
| Collection Summary: | Brain samples were harvested and collected following transcardial perfusion with phosphate buffer (0.1 M, pH 7.4) 24 hr post-TBI. The perfused whole brains were rapidly removed, and flash frozen in an isopentane-methanol ice slurry. Pieces of parietal cortices (5 mm x 2 mm) were dissected from partially thawed brains by removing the subcortical structures including the majority of white matter and stored at -80° C in microcentrifuge tubes. The cortices were then transferred to liquid nitrogen and manually pulverized with a pestle and mortar submerged in liquid nitrogen and aliquoted in ~10-30 mg tissue samples. |
| Sample Type: | Brain |
Treatment:
| Treatment ID: | TR003217 |
| Treatment Summary: | Experimental batch 1 contained female (n = 16) and male (n = 10) to either sham procedure (n = 10), 1X, single mild traumatic brain injury (mTBI) (n = 8), and 3X, repetitive mTBI (n = 8) groups. Experimental batch 2 contained female (n = 11) and male (n = 17) to either sham procedure (n = 8), smTBI(n = 9), and rmTBI (n = 11) groups. |
Sample Preparation:
| Sampleprep ID: | SP003214 |
| Sampleprep Summary: | Experimental batch 1 and 2 aliquoted tissue samples were thawed simultane-ously on ice prior to addition of solvent (IPA and Splash II Lipidomix in (1:3 v/v)) to sep-arate lipids and small non-polar metabolites. LC-MS grade water was used to prepare sample blanks, and pooled quality control (QC) samples were prepared from 5 µL ali-quoted supernatant of all samples in the study. The brain and solvent (1:4 w/v), and beads were placed in a Tissuelyser II for 8 min and centrifuged at 16000 g for 7 min. The supernatant was collected for LC-MS. Pooled quality control samples were formed from combining 6 µL aliquots of all brain sample extracts. Sample blanks were prepared with the same procedure except instead of a brain sample, 50 µL of LC-MS grade water was used. |
Combined analysis:
| Analysis ID | AN005062 | AN005063 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Thermo Vanquish | Thermo Vanquish |
| Column | Thermo Accucore C30 (50 x 2.1mm,2.1um) | Thermo Accucore C30 (50 x 2.1mm,2.1um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo ID-X Orbitrap Tribrid | Thermo ID-X Orbitrap Tribrid |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | m/z | m/z |
Chromatography:
| Chromatography ID: | CH003822 |
| Chromatography Summary: | MS |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Thermo Accucore C30 (50 x 2.1mm,2.1um) |
| Column Temperature: | 50 |
| Flow Gradient: | 0 minutes 80% A; 1 minute 40% A; 5 minutes 30% A; 5.5 minutes 15% A; 8 minutes 10% A; held 8.2 minutes to 10.5 minutes 0% A; 10.7 minutes 80% A; and held until 12 minutes |
| Flow Rate: | 0.40 mL/min |
| Solvent A: | 40% water/60% acetonitrile; 10 mM ammonium formate; 0.1% formic acid |
| Solvent B: | 10% acetonitrile/90% isopropanol; with 10 mM ammonium formate; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH003823 |
| Chromatography Summary: | MS |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Thermo Accucore C30 (50 x 2.1mm,2.1um) |
| Column Temperature: | 50 |
| Flow Gradient: | 0 minutes 80% A; 1 minute 40% A; 5 minutes 30% A; 5.5 minutes 15% A; 8 minutes 10% A; held 8.2 minutes to 10.5 minutes 0% A; 10.7 minutes 80% A; and held until 12 minutes |
| Flow Rate: | 0.40 mL/min |
| Solvent A: | 40% water/60% acetonitrile; 10 mM ammonium formate; 0.1% formic acid |
| Solvent B: | 10% acetonitrile/90% isopropanol; with 10 mM ammonium formate; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS004800 |
| Analysis ID: | AN005062 |
| Instrument Name: | Thermo ID-X Orbitrap Tribrid |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | LCMS Pos |
| Ion Mode: | POSITIVE |
| MS ID: | MS004801 |
| Analysis ID: | AN005063 |
| Instrument Name: | Thermo ID-X Orbitrap Tribrid |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | LCMS Neg |
| Ion Mode: | NEGATIVE |
