Summary of Study ST001850

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 PR001167. The data can be accessed directly via it's Project DOI: 10.21228/M8VM4C This work is supported by NIH grant, U2C- DK119886.

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This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST001850
Study TitleUnbiased LC-MS-based metabolomics analysis for both whole cell and mitochondria metabolites to gain an insight into the role of Tug1/PGC1 axis on metabolite profiles in podocytes
Study Summaryunbiased LC-MS-based metabolomics analysis for both whole cell and mitochondria metabolites to gain an insight into the role of Tug1/PGC1 axis on metabolite profiles in podocytes
Institute
University of Texas MD Anderson Cancer Center
Last NameDanesh
First NameFarhad
Address1515 Holcombe Blvd, Houston ,TX77030
Emailfdanesh@mdanderson.org
Phone7135634498
Submit Date2021-06-25
Num Groups3
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2021-06-29
Release Version1
Farhad Danesh Farhad Danesh
https://dx.doi.org/10.21228/M8VM4C
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001167
Project DOI:doi: 10.21228/M8VM4C
Project Title:NonTargeted LC-MS-based metabolomics analysis for both whole cell and mitochondria metabolites to gain an insight into the role of Tug1/PGC1 axis on metabolite profiles in podocytes
Project Type:Biomarker
Project Summary:We found that double mutant Tug1-KD/Pgc1-OE rescued the effects of Tug1-KD on basal, maximal, and spare capacity respiration rates in podocytes. Therefore we employed an unbiased LCMS based metabolomics analysis or both whole cell and mitochondria metabolites to gain an insight into the role of Tug1/PGC1 on metabolite profiles in podocytes.
Institute:University of Texas MD Anderson Cancer Center
Department:Nephrology
Last Name:Danesh
First Name:Farhad
Address:1515 Holcombe Blvd, Houston, TX77030
Email:fdanesh@mdanderson.org
Phone:7135634498

Subject:

Subject ID:SU001927
Subject Type:Cultured cells
Subject Species:Mus musculus
Taxonomy ID:10090

Factors:

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

mb_sample_id local_sample_id Treatment
SA172704Tugl-KD_PGCOE_2_HilicPGCOE
SA172705Tugl-KD_PGCOE_3_HilicPGCOE
SA172706Tugl-KD_PGCOE_1_HilicPGCOE
SA172707Tugl-KD_PGCOE_1_ICPGCOE
SA172708Tugl-KD_PGCOE_3_ICPGCOE
SA172709Tugl-KD_PGCOE_2_ICPGCOE
SA172710PLKO_2_ICPLKO
SA172711PLKO_3_ICPLKO
SA172712PLKO_1_ICPLKO
SA172713PLKO_1_HilicPLKO
SA172714PLKO_3_HilicPLKO
SA172715PLKO_2_HilicPLKO
SA172716Tugl-KD_1_HilicTug1-KD
SA172717Tugl-KD_2_HilicTug1-KD
SA172718Tugl-KD_3_ICTug1-KD
SA172719Tugl-KD_3_HilicTug1-KD
SA172720Tugl-KD_1_ICTug1-KD
SA172721Tugl-KD_2_ICTug1-KD
Showing results 1 to 18 of 18

Collection:

Collection ID:CO001920
Collection Summary:Briefly, podocytes were cultured on BD BioCoat Collagen I plates (BD Biosciences, San Jose, CA) at 33°C in RPMI 1640 complete media with 20 U/ml mouse recombinant IFN-g (Thermo Fisher, Carlsbad, CA). To induce differentiation, we cultured podocytes in DMEM (5.5mM glucose and 5% FBS) at 37°C without IFN-g for 10-12 days. To rescue the expression of PGC1-a in stable Tug1-knockdown CRISPR clone (Tug1-KD)(Long et al., 2016), CMV enhancer/promoter-driven mouse Pgc1-a cDNA (Addgene, Watertown, MA) was inserted into vector Zeo-pT-MCS-GFP-T2A-Puro(Long et al., 2020), a modified PiggyBac transposon system, selected with 1ug/ml puromycin and sorted by GFP, to generate Tug1-KD/Pgc1-OE. We isolated kidney podocytes by positive selection with biotin-labelled Kirrel3 and Podocalyxin antibodies (2.5 μg/antibody/mouse, R&D Systems, Minneapolis, MN) followed by Streptavidin M-280 Dynabeads as previously described (Badal et al., 2016).
Sample Type:Epithelial cells

Treatment:

Treatment ID:TR001939
Treatment Summary:we cultured podocytes in DMEM (5.5mM glucose and 5% FBS) at 37°C without IFN-g for 10-12 days. To rescue the expression of PGC1-a in stable Tug1-knockdown CRISPR clone (Tug1-KD)(Long et al., 2016), CMV enhancer/promoter-driven mouse Pgc1-a cDNA (Addgene, Watertown, MA) was inserted into vector Zeo-pT-MCS-GFP-T2A-Puro(Long et al., 2020), a modified PiggyBac transposon system, selected with 1ug/ml puromycin and sorted by GFP, to generate Tug1-KD/Pgc1-OE.

Sample Preparation:

Sampleprep ID:SP001933
Sampleprep Summary:Metabolites from cell samples (in triplicates) grown on 10cm dishes were extracted with ice-cold 80% methanol. After centrifugation, extracts in supernatants were dried by evaporation under nitrogen.
Processing Storage Conditions:On ice
Extract Storage:-80℃

Combined analysis:

Analysis ID AN002997 AN002998
Analysis type MS MS
Chromatography type Ion exchange HILIC
Chromatography system Thermo Dionex ICS-5000+ Thermo Vanquish
Column Dionex IonPac AS11 Waters XBridge Amide (100 x 4.6mm, 3.5um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Fusion Orbitrap Thermo Fusion Orbitrap
Ion Mode NEGATIVE POSITIVE
Units AUC/ngDNA AUC/ngDNA

Chromatography:

Chromatography ID:CH002222
Chromatography Summary:ion chromatography (IC)-MS
Instrument Name:Thermo Dionex ICS-5000+
Column Name:Dionex IonPac AS11
Chromatography Type:Ion exchange
  
Chromatography ID:CH002223
Chromatography Summary:liquid chromatography (LC)-MS
Instrument Name:Thermo Vanquish
Column Name:Waters XBridge Amide (100 x 4.6mm, 3.5um)
Chromatography Type:HILIC

MS:

MS ID:MS002786
Analysis ID:AN002997
Instrument Name:Thermo Fusion Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Data were acquired using a Thermo Orbitrap Fusion Tribrid Mass Spectrometer under ESI negative ionization mode. Raw data files were imported to Thermo Trace Finder software for final analysis. The relative abundance of each metabolite was normalized by DNA concentrations.
Ion Mode:NEGATIVE
  
MS ID:MS002787
Analysis ID:AN002998
Instrument Name:Thermo Fusion Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Data were acquired using a Thermo Orbitrap Fusion Tribrid Mass Spectrometer under ESI positive ionization mode at a resolution of 240,000.Raw data files were imported to Thermo Trace Finder software for final analysis. The relative abundance of each metabolite was normalized by DNA concentrations.
Ion Mode:POSITIVE
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