Summary of Study ST001218

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000817. The data can be accessed directly via it's Project DOI: 10.21228/M82X16 This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

Perform statistical analysis  |  Show all samples  |  Show named metabolites  |  Download named metabolite data  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files (Contains raw data)
Study IDST001218
Study TitleWild type versus TRACK Mice on regular chow and Vitamin A deprived diet
Study TypeMS-based metabolite profiling
Study SummaryKidney cortex tissue of wild type and TRACK (transgenic cancer of the kidney) mice fed on a regular chow or vitamin A deprived diet were analyzed
Institute
Weill Cornell Medicine
DepartmentPharmacology
LaboratoryGudas/Gross
Last NameChen
First NameQuiying
Address1300 York Ave
Emailqic2005@med.cornell.edu
Phone212-746-6250
Submit Date2019-07-10
Num Groups4
Total Subjects16
Num Males16
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2021-03-01
Release Version1
Quiying Chen Quiying Chen
https://dx.doi.org/10.21228/M82X16
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000817
Project DOI:doi: 10.21228/M82X16
Project Title:Wild type versus TRACK Mice on regular chow and Vitamin A deprived diet
Project Type:MS-based metabolite profiling
Project Summary:Kidney cortex tissue from wild type mice and transgenic TRACK (TRAnsgenic Cancer of the Kidney) mice fed on a regular chow or vitamin A deprived diet were analyzed
Institute:Weill Cornell Medicine
Department:Pharmacology
Laboratory:Gudas/Gross laboratory
Last Name:Chen
First Name:Quiying
Address:1300 York Ave
Email:qic2005@med.cornell.edu
Phone:212-746-6250
Contributors:Johannes van der Mijn, Quiying Chen, Francesca Khani, Steven S. Gross, David M. Nanus, Lorraine J. Gudas

Subject:

Subject ID:SU001285
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:C57BL/6
Age Or Age Range:24 weeks
Weight Or Weight Range:20-30 gram
Gender:Male
Animal Housing:Research Animal Resource Center of Weill Cornell Medicine
Animal Feed:regular chow (#88406, Harlan, Madison, WI) or VA-deficient diet (#88407, Harlan)
Animal Water:regular water

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Treatment
SA086143p_track3Control-chow
SA086144p_track2Control-chow
SA086145track1Control-chow
SA086146p_track4Control-chow
SA086147P_wt2Control-chow
SA086148P_wt4Control-chow
SA086149P_wt3Control-chow
SA086150wt4Control-chow
SA086151P_wt1Control-chow
SA086152p_track1Control-chow
SA086153track3Control-chow
SA086154wt2Control-chow
SA086155wt3Control-chow
SA086156track4Control-chow
SA086157track2Control-chow
SA086158wt1Control-chow
SA086159p_rqc1N/A
SA086160p_rqc2N/A
SA086161p_rqc3N/A
SA086162qc5N/A
SA086163qc4N/A
SA086164p_rqc5N/A
SA086165p_rqc6N/A
SA086166rqc1N/A
SA086167p_rqc4N/A
SA086168qc1N/A
SA086169qc3N/A
SA086170qc2N/A
SA086171p_WT-VAd1Vitamin A deficent -chow
SA086172p_WT-VAd3Vitamin A deficent -chow
SA086173p_WT-VAd4Vitamin A deficent -chow
SA086174p_WT-VAd2Vitamin A deficent -chow
SA086175P_track-VAd2Vitamin A deficent -chow
SA086176WT-VAd4Vitamin A deficent -chow
SA086177WT-VAd3Vitamin A deficent -chow
SA086178WT-VAd2Vitamin A deficent -chow
SA086179WT-VAd1Vitamin A deficent -chow
SA086180track-VAd4Vitamin A deficent -chow
SA086181track-VAd3Vitamin A deficent -chow
SA086182track-VAd2Vitamin A deficent -chow
SA086183P_track-VAd4Vitamin A deficent -chow
SA086184P_track-VAd3Vitamin A deficent -chow
SA086185P_track-VAd1Vitamin A deficent -chow
SA086186track-VAd1Vitamin A deficent -chow
Showing results 1 to 44 of 44

Collection:

Collection ID:CO001279
Collection Summary:Pieces of organ tissue were snap-frozen in liquid nitrogen
Sample Type:Kidney

Treatment:

Treatment ID:TR001300
Treatment Summary:After weaning for 2 weeks all mice were randomized to a Vitamin A (VA) sufficient regular chow (#88406, Harlan, Madison, WI) or VA-deficient diet (#88407, Harlan). Mice were sacrificed by cervical dislocation after 24 weeks to harvest the organs.
Treatment:vitamin A deficient diet (#88407, Harlan)
Treatment Compound:chow diet
Treatment Route:oral
Treatment Dose:ad libitum
Treatment Doseduration:24 weeks
Treatment Vehicle:none
Animal Vet Treatments:none
Animal Fasting:Mice were fasted overnight prior to sacrifice

Sample Preparation:

Sampleprep ID:SP001293
Sampleprep Summary:After washes in cold PBS, samples were lysed by three cycles of bead-beating in 80% -70 ᵒC methanol: water using a tissue lyser cell disrupter. Proteins were removed from the extraction mixture by centrifugation to yield the metabolites for analysis. The metabolites were dried in a speed-vac, and stored at -80 ᵒC. Prior to measurement, the metabolites were solubilized in 0.2 M NaOH and subsequently analyzed by LC/MS and LC MS/MS

Combined analysis:

Analysis ID AN002031
Analysis type MS
Chromatography type Normal phase
Chromatography system Agilent 6550
Column Cogent Diamond Hydride HPLCs,MicroSolv Technology Corporation
MS Type ESI
MS instrument type QTOF
MS instrument name Agilent 6550 QTOF
Ion Mode UNSPECIFIED
Units Peak Area

Chromatography:

Chromatography ID:CH001472
Chromatography Summary:Aqueous Normal Phase
Instrument Name:Agilent 6550
Column Name:Cogent Diamond Hydride HPLCs,MicroSolv Technology Corporation
Column Temperature:25
Flow Gradient:linear
Flow Rate:0.4ml/min
Solvent A:50% isopropanol/50% water
Solvent B:90% acetonitrile/10% water
Chromatography Type:Normal phase

MS:

MS ID:MS001884
Analysis ID:AN002031
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:MS only molecular feature extraction Agilent MassProfinder 8.0
Ion Mode:UNSPECIFIED
  logo