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MB Sample ID: SA057569
| Local Sample ID: | BL_81 |
| Subject ID: | SU001001 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001001 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| BL_81 | SA057569 | FL010365 | Control-42 | Factor 1 |
Collection:
| Collection ID: | CO000995 |
| Collection Summary: | livers were collected via standard operating procedures. |
| Sample Type: | Liver |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR001015 |
| Treatment Summary: | PAT15= NOD mice received antibiotics and sacrificed at age of day at 15; Control-15=NOD mice received no antibiotics and sacrificed at age of day at 15; PAT23= NOD mice received antibiotics and sacrificed at age of day at 23; Control-23=NOD mice received no antibiotics and sacrificed at age of day at 23; PAT42= NOD mice received antibiotics and sacrificed at age of day at 42; Control-42=NOD mice received no antibiotics and sacrificed at age of day at 42; PAT70= NOD mice received antibiotics and sacrificed at age of day at 70; Control-70=NOD mice received no antibiotics and sacrificed 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 Comments Treatment (Abiotic, Biotic, Intervention) 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: | SP001008 |
| Sampleprep Summary: | Extraction, Solvent Removal, Resuspension, Solvent Removal, Two-step Derivatization and Addition of FAME Markers |
| Processing Method: | Liver tissue were frozen on dry ice and weighed at approximate 100 mg to a MagNa Lyser tube with 10 to 15 ceramic beads inside. The ice-cold homogenization buffer (50% acetonitrile) was added with the mass/volume ratio at 1 mg tissue per 5 µL buffer. The homogenization was carried on at 4,500 rpm for two 30 sec pulses by the MagNA Lyser. The homogenized mixture was centrifuged at 14,000 rpm for 5 min at -4 °C for the supernatant. Aliquots of 100 µL homogenized supernatant of the study sample (equal to 20 mg tissue) were mixed with 1000 µL of cold degassed 3:3:2 ACN:ISP:H20 solution in a 2 mL snap cap tube. Samples are vortex and shaken for 5 min, and then centrifuged at 4 °C for 2 min at 14000 rcf. The supernatant was split into (2)-450 µL fractions, one fraction was archived in -80°C the second fraction was subject t complete sample processing. Transfer supernatant to a new vial. Evaporate supernatant to complete dryness at room temp. |
| 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 | AN001576 |
|---|---|
| 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: | CH001105 |
| 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 Pressure: | 14.05psi |
| Column Temperature: | Initial Oven Temp 100⁰C, hold 60 sec. Ramp rate 20⁰C/min to 330⁰C, hold 5 min. |
| Flow Gradient: | constant flow |
| Flow Rate: | 1 mL/min |
| Injection Temperature: | 250⁰C |
| 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 |
| Chromatography Type: | GC |
MS:
| MS ID: | MS001454 |
| Analysis ID: | AN001576 |
| Instrument Name: | Leco Pegasus 4D GCxGC TOF |
| Instrument Type: | GC x GC-TOF |
| MS Type: | EI |
| Ion Mode: | POSITIVE |
| Helium Flow: | 1 mL/min |
| Ion Source Temperature: | 250⁰C |
| Ionization Energy: | 70eV |
| Source Temperature: | 250⁰C |
| Dataformat: | netcdf |
| Resolution Setting: | 1200 |
| Scan Range Moverz: | 50-750 |
| Scanning: | 20 spectra/sec |
