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 all metabolite data  |  Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data (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
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™ HPLC columns, 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™ HPLC columns, MicroSolv Technology Corporation
Column Temperature:25
Flow Gradient:linear
Flow Rate:0.4ml/min
Solvent A:50% IPA
Solvent B:90%ACN
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