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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 |