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

Study ID	ST001218
Study Title	Wild type versus TRACK Mice on regular chow and Vitamin A deprived diet
Study Type	MS-based metabolite profiling
Study Summary	Kidney 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
Department	Pharmacology
Laboratory	Gudas/Gross
Last Name	Chen
First Name	Quiying
Address	1300 York Ave
Email	qic2005@med.cornell.edu
Phone	212-746-6250
Submit Date	2019-07-10
Num Groups	4
Total Subjects	16
Num Males	16
Raw Data Available	Yes
Raw Data File Type(s)	d
Analysis Type Detail	LC-MS
Release Date	2021-03-01
Release Version	1

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
Species Group:	Mammals

Factors:

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

mb_sample_id	local_sample_id	Treatment
SA086143	p_track3	Control-chow
SA086144	p_track2	Control-chow
SA086145	track1	Control-chow
SA086146	p_track4	Control-chow
SA086147	P_wt2	Control-chow
SA086148	P_wt4	Control-chow
SA086149	P_wt3	Control-chow
SA086150	wt4	Control-chow
SA086151	P_wt1	Control-chow
SA086152	p_track1	Control-chow
SA086153	track3	Control-chow
SA086154	wt2	Control-chow
SA086155	wt3	Control-chow
SA086156	track4	Control-chow
SA086157	track2	Control-chow
SA086158	wt1	Control-chow
SA086159	p_rqc1	N/A
SA086160	p_rqc2	N/A
SA086161	p_rqc3	N/A
SA086162	qc5	N/A
SA086163	qc4	N/A
SA086164	p_rqc5	N/A
SA086165	p_rqc6	N/A
SA086166	rqc1	N/A
SA086167	p_rqc4	N/A
SA086168	qc1	N/A
SA086169	qc3	N/A
SA086170	qc2	N/A
SA086171	p_WT-VAd1	Vitamin A deficent -chow
SA086172	p_WT-VAd3	Vitamin A deficent -chow
SA086173	p_WT-VAd4	Vitamin A deficent -chow
SA086174	p_WT-VAd2	Vitamin A deficent -chow
SA086175	P_track-VAd2	Vitamin A deficent -chow
SA086176	WT-VAd4	Vitamin A deficent -chow
SA086177	WT-VAd3	Vitamin A deficent -chow
SA086178	WT-VAd2	Vitamin A deficent -chow
SA086179	WT-VAd1	Vitamin A deficent -chow
SA086180	track-VAd4	Vitamin A deficent -chow
SA086181	track-VAd3	Vitamin A deficent -chow
SA086182	track-VAd2	Vitamin A deficent -chow
SA086183	P_track-VAd4	Vitamin A deficent -chow
SA086184	P_track-VAd3	Vitamin A deficent -chow
SA086185	P_track-VAd1	Vitamin A deficent -chow
SA086186	track-VAd1	Vitamin A deficent -chow

Showing results 1 to 44 of 44

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

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

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

Analysis:

Analysis ID:	AN002031
Analysis Type:	MS
Chromatography ID:	CH001472
Num Factors:	3
Num Metabolites:	310
Rt Units:	Minutes
Units:	Peak Area