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MB Sample ID: SA014871
| Local Sample ID: | 2.dist.56 |
| Subject ID: | SU000352 |
| Subject Type: | Animal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Species Group: | Mammal |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU000352 |
| Subject Type: | Animal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Species Group: | Mammal |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| 2.dist.56 | SA014871 | FL003344 | uninfected distal | Location |
Collection:
| Collection ID: | CO000346 |
| Collection Summary: | C57B6J mice were infected via oral gavage with Giardia intestinalis, then sacrificed 7 days later. Intestinal samples containing Giardia were excised and flash frozen in liquid nitrogen. |
| Collection Protocol Filename: | StudyDesign-JohnPham-12814.pdf |
| Sample Type: | Small intestine tissue |
Treatment:
| Treatment ID: | TR000366 |
| Treatment Summary: | 3 segments originating from the proximal small intestine of uninfected mice 3 segments originating from the distal small intestine of uninfected mice 4 segments originating from the proximal small intestine of Giardiainfected mice 4 segments originating from the distal small intestine of Giardiainfected mice |
| Treatment Protocol Filename: | StudyDesign-JohnPham-12814.pdf |
Sample Preparation:
| Sampleprep ID: | SP000360 |
| Sampleprep Summary: | 1. Weigh 50 mg tissue sample in to a 25 ml conical polypropylene centrifuge tube. 2. Add 2.5mL extraction solvent to the tissue sample and homogenize for 45 seconds ensuring that sample resembles a powder. In between samples, clean the homogenizer in solutions of methanol, acetone, water, and the extraction solvent. 3. Centrifuge the samples at 2500 rpm. for 5 minutes. Aliquot 2 X 500µl supernatant, one for analysis and one for a backup sample. Store backup aliquot in the -20°C freezer. 4. Evaporate one 500µl aliquot of the sample in the Labconco Centrivap cold trap concentrator to complete dryness 5. The dried aliquot is then re-suspended with 500l 50% acetonitrile (degassed as given) 6. Centrifuge for 2 min at 14000 rcf using the centrifuge Eppendorf 5415. 7. Remove supernatant to a new Eppendorff tube. 8. Evaporate the supernatant to dryness in the the Labconco Centrivap cold trap concentrator. 9. Submit to derivatization. |
| Sampleprep Protocol Filename: | SOP_Extraction_of_Mammalian_Tissue_Samples.pdf |
Combined analysis:
| Analysis ID | AN000531 | AN000532 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Unspecified | Unspecified |
| Column | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) |
| MS Type | ESI | ESI |
| MS instrument type | QTOF | QTOF |
| MS instrument name | Agilent 6530 QTOF | Agilent 6550 QTOF |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | Peak height | Peak height |
Chromatography:
| Chromatography ID: | CH000370 |
| Chromatography Summary: | UPLC |
| Methods Filename: | Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics_05-29-2014.pdf |
| Instrument Name: | Unspecified |
| Column Name: | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) |
| Column Pressure: | 450-850 bar |
| Column Temperature: | 65 C |
| Flow Gradient: | 15% B to 99% B |
| Flow Rate: | 0.6 mL/min |
| Internal Standard: | See data dictionary |
| Retention Time: | See data dictionary |
| Sample Injection: | 1.67 uL |
| Solvent A: | 60% acetonitrile/40% water; 10mM formic acid; 10mM ammonium formate |
| Solvent B: | 90% isopropanol/10% acetonitrile; 10mM formic acid; 10mM ammonium formate |
| Analytical Time: | 13 min |
| Capillary Voltage: | 3500 |
| Time Program: | 15 min |
| Weak Wash Solvent Name: | Isopropanol |
| Weak Wash Volume: | 5 seconds |
| Strong Wash Solvent Name: | Isopropanol |
| Target Sample Temperature: | Autosampler temp 4 C |
| Randomization Order: | Excel |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS000467 |
| Analysis ID: | AN000531 |
| Instrument Name: | Agilent 6530 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | POSITIVE |
| Capillary Voltage: | 3500 |
| Collision Gas: | Nitrogen |
| Dry Gas Flow: | 8 l/min |
| Dry Gas Temp: | 325 |
| Fragment Voltage: | 120 |
| Fragmentation Method: | Auto MS/MS |
| Ion Source Temperature: | 325 |
| Ion Spray Voltage: | 1000 |
| Ionization: | Pos |
| Precursor Type: | Intact Molecule |
| Reagent Gas: | Nitrogen |
| Source Temperature: | 325 C |
| Desolvation Gas Flow: | 11 l/min |
| Desolvation Temperature: | 350 C |
| Nebulizer: | 35 psig |
| Octpole Voltage: | 750 |
| Resolution Setting: | Extended Dynamic Range |
| Scan Range Moverz: | 60-1700 Da |
| Scanning Cycle: | 2 Hz |
| Scanning Range: | 60-1700 Da |
| Skimmer Voltage: | 65 |
| MS ID: | MS000468 |
| Analysis ID: | AN000532 |
| Instrument Name: | Agilent 6550 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | NEGATIVE |
| Capillary Voltage: | 3500 |
| Collision Gas: | Nitrogen |
| Dry Gas Flow: | 8 l/min |
| Dry Gas Temp: | 325 |
| Fragment Voltage: | 120 |
| Fragmentation Method: | Auto MS/MS |
| Ion Source Temperature: | 325 |
| Ion Spray Voltage: | 1000 |
| Ionization: | Pos |
| Precursor Type: | Intact Molecule |
| Reagent Gas: | Nitrogen |
| Source Temperature: | 325 C |
| Desolvation Gas Flow: | 11 l/min |
| Desolvation Temperature: | 350 C |
| Nebulizer: | 35 psig |
| Octpole Voltage: | 750 |
| Resolution Setting: | Extended Dynamic Range |
| Scan Range Moverz: | 60-1700 Da |
| Scanning Cycle: | 2 Hz |
| Scanning Range: | 60-1700 Da |
| Skimmer Voltage: | 65 |
