Metabolomics Workbench : NIH Data Repository

MB Sample ID: SA014836

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Subject:

Factors:

Local Sample ID	MB Sample ID	Factor Level ID	Level Value	Factor Name
P45	SA014836	FL003338	Zn-sufficient	Treatment

Collection:

Collection ID:	CO000344
Collection Summary:	At sacrifice, esophagi were isolated. Esophageal epithelium was prepared by using a blade to remove the submucosal and muscularis layers, snapfrozen in liquid nitrogen, and stored at –80 °C.
Collection Protocol Filename:	StudyDesign-LouiseFong-102314.pdf
Sample Type:	Tissue

Treatment:

Treatment ID:	TR000364
Treatment Summary:	Three dietary Zn modulated groups: Zn deficient, Zn replenished,and control Zn sufficient Male weanling rats were fed a Zn deficient diet ad libitum (n = 16) or pairfed a control Zn sufficient diet (n = 8). After 6 weeks Zn deficient rats evidenced increased cell proliferation in the esophagus. Eight Zn deficient rats were switched immediately to the Zn sufficient diet to form the Zn replenished group. At 72 hours after replenishment, all animals (Zn deficient, Zn replenished, and Zn sufficient;n = 8/group) were killed. Note: Zn sufficient is the control group for each tissue (plasma, esophagus, or prostate)
Treatment Protocol Filename:	StudyDesign-LouiseFong-102314.pdf

Sample Preparation:

Sampleprep ID:	SP000358
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:

Chromatography:

Chromatography ID:	CH000368
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: