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MB Sample ID: SA164106
| Local Sample ID: | brain_Neg_CN_9A2D_F |
| Subject ID: | SU001835 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | C57BL/6 |
| Age Or Age Range: | 7-8 week old |
| Gender: | Male and female |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU001835 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | C57BL/6 |
| Age Or Age Range: | 7-8 week old |
| Gender: | Male and female |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| brain_Neg_CN_9A2D_F | SA164106 | FL019544 | Conventionally-raised (CONV-R) | Experimental factor |
Collection:
| Collection ID: | CO001828 |
| Collection Summary: | Prior to sacrifice and sample harvest, all mice were observed under their original housing conditions for one week; animals were not considered if they exhibited significant signs of serious injury or morbidity (e.g. malocclusion or fight wounds). Upon euthanization in CO2 chambers, feces, bulk brain, and heart blood sera were harvested, snap-frozen, and stored in -80 ºC freezer before analysis. |
| Sample Type: | Brain |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR001848 |
| Treatment Summary: | Steady states only: C57BL/6 mouse littermates of ~7 weeks old raised under GF and conventional conditions were age-matched upon selection for sacrifice and analyses, resulting in a final total of 24 mice, including 12 GF mice and 12 SPF CONV-R mice with 6 males and 6 females included in each. The animals were raised under the following conditions: 22ºC, 40-70% humidity, and a daily 12:12 hour light-dark cycle. For dietary administration, we consistently fed all mice the same purified (and sterile) standard rodent diets and provided tap water ad libitum. |
Sample Preparation:
| Sampleprep ID: | SP001841 |
| Sampleprep Summary: | Fecal matter, blood sera, and brain tissues (of the cerebral cortical region) were aliquoted and extracted for metabolome analyses. To maximize coverage and throughput, extraction procedures were kept as simple and non-selective as can be. |
| Sampleprep Protocol Filename: | Protocol_sample_extraction.docx |
Combined analysis:
| Analysis ID | AN002864 | AN002865 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Thermo Vanquish | Thermo Vanquish |
| Column | Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um) | Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | Peak intensity (area) | Peak intensity (area) |
Chromatography:
| Chromatography ID: | CH002120 |
| Chromatography Summary: | UHPLC reverse phase C18 chromatography |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um) |
| Column Temperature: | 40 |
| Flow Gradient: | 2% B, 0-1 min; 2% to 15% B, 1-3 min; 15% to 50% B, 3-6 min; 50% to 98% B, 6-7.5 min; 98% B, 7.5-11.5 min; 98% to 2% B, 11.5-11.6 min; 2% B, 11.6-15 min |
| Flow Rate: | 0.4 mL/min |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS002657 |
| Analysis ID: | AN002864 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | fullscan XCMS Online for data processing |
| Ion Mode: | POSITIVE |
| MS ID: | MS002658 |
| Analysis ID: | AN002865 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | fullscan XCMS Online for data processing |
| Ion Mode: | NEGATIVE |
