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MB Sample ID: SA057811
| Local Sample ID: | BS_25 |
| Subject ID: | SU001006 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001006 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| BS_25 | SA057811 | FL010395 | PAT23 | Group |
Collection:
| Collection ID: | CO001000 |
| Collection Summary: | Serum was collected via standard operating procedures. |
| Sample Type: | Blood (serum) |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR001020 |
| Treatment Summary: | PAT15= NOD mice received antibiotics and sacrifced at age of day at 15; Control-15=NOD mice received no antibiotics and sacrifced at age of day at 15; PAT23= NOD mice received antibiotics and sacrifced at age of day at 23; Control-23=NOD mice received no antibiotics and sacrifced at age of day at 23; PAT42= NOD mice received antibiotics and sacrifced at age of day at 42; Control-42=NOD mice received no antibiotics and sacrifced at age of day at 42; PAT70= NOD mice received antibiotics and sacrifced at age of day at 70; Control-70=NOD mice received no antibiotics and sacrifced at age of day at 70; Restoration-PAT= C57 mice received poo from NOD mice given antibiotics Restoration-Control= C57 mice received poo from NOD mice given no antibiotics |
| Treatment Protocol Comments: | treated with antibiotics at 5 to 10 days; vehicle; treated with antibiotics at 5 to 10 days; vehicle; treated with antibiotics at 5 to 10 days; vehicle; treated with antibiotics at 5 to 10 days; vehicle; Treated with poo from NOD mice given antibiotics; Treated with poo from NOD mice given vehicle |
Sample Preparation:
| Sampleprep ID: | SP001013 |
| Sampleprep Summary: | Extraction, Solvent Removal, Resuspension, Solvent Removal, Two-step Derivatization and Addition of FAME Markers |
| Processing Method: | Aliquots of 30 µL serum were mixed with 1000 µL of degassed 3:3:2 Acetonitrile:Isopropanol:Water solution in a 2 mL snap cap tube. Samples were vortexed, shaken for 5 minutes then centrifuged at 4⁰C for 2 minutes at 14000rcf. The supernatant was recovered and split into two fractions. Fraction 1 (450 µL) was archived and fraction 2 (450 µL) was subjected to complete sample processing. Processing continued as follows. Samples were completely dried by vacuum centrifuge and reconstituted with 450 µL 1:1 acetonitrile:water solution. Samples were centrifuged for 2 minutes at 14000rcf and transferred to new snap cap tubes followed by complete evaporation at room temperature by vacuum centrifuge. |
| Processing Storage Conditions: | On ice |
| Extraction Method: | (step 1) 3:3:2 Acetonitrile:Isopropanol:H2O, (step 2) 1:1 Acetonitrile:H2O |
| Extract Storage: | -80℃ |
| Sample Resuspension: | Samples resuspended in 200 µL of 1:1 ACN:H2O. Evaporated to dryness w/speed vac. |
| Sample Derivatization: | Formation of methoximes by adding 10µL of 40mg/mL MeOx in pyridine to each sample. Placed onto Thermomixer for 90 min at 30⁰C. Then FAME retention index markers and MSTFA added to each sample for derivatization step. Samples returned to Thermomixer for 45 min at 70⁰C. |
| Sample Spiking: | Fatty acid methyl esters (FAME) |
Combined analysis:
| Analysis ID | AN001581 |
|---|---|
| Analysis type | MS |
| Chromatography type | GC |
| Chromatography system | Leco Pegasus 4D GC |
| Column | Restek Rtx-5Sil (30m x 0.25mm,0.25um) |
| MS Type | EI |
| MS instrument type | GC x GC-TOF |
| MS instrument name | Leco Pegasus 4D GCxGC TOF |
| Ion Mode | POSITIVE |
| Units | m/z |
Chromatography:
| Chromatography ID: | CH001110 |
| Chromatography Summary: | GCMS analysis is based on the Oliver Fiehn method |
| Instrument Name: | Leco Pegasus 4D GC |
| Column Name: | Restek Rtx-5Sil (30m x 0.25mm,0.25um) |
| Column Temperature: | 250⁰C |
| Flow Gradient: | constant flow |
| Flow Rate: | 1 mL/min |
| Retention Index: | FAME retention index markers C8-C30 |
| Sample Injection: | 1.0 µL |
| Analytical Time: | 20 min |
| Oven Temperature: | Initial Oven Temp100⁰C, hold 60 sec. Ramp rate 20⁰C/min to 330⁰C, hold 5 min. |
| Transferline Temperature: | 280⁰C |
| Randomization Order: | Yes |
| Chromatography Type: | GC |
MS:
| MS ID: | MS001459 |
| Analysis ID: | AN001581 |
| Instrument Name: | Leco Pegasus 4D GCxGC TOF |
| Instrument Type: | GC x GC-TOF |
| MS Type: | EI |
| Ion Mode: | POSITIVE |
| Collision Gas: | Medium |
| Helium Flow: | 1 ml/min |
| Ion Source Temperature: | 250⁰C |
| Ionization Energy: | 70eV |
| Source Temperature: | 250⁰C |
| Dataformat: | netcdf |
| Probe Tip: | 1200 |
| Scan Range Moverz: | 50-750 |
| Scanning: | 20 spectra/sec |
