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.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
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.
| Study ID | ST001850 |
| Study Title | Unbiased 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 Summary | unbiased 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 Name | Danesh |
| First Name | Farhad |
| Address | 1515 Holcombe Blvd, Houston ,TX77030 |
| fdanesh@mdanderson.org | |
| Phone | 7135634498 |
| Submit Date | 2021-06-25 |
| Num Groups | 3 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2021-06-29 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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 |
|---|---|---|
| SA172704 | Tugl-KD_PGCOE_2_Hilic | PGCOE |
| SA172705 | Tugl-KD_PGCOE_3_Hilic | PGCOE |
| SA172706 | Tugl-KD_PGCOE_1_Hilic | PGCOE |
| SA172707 | Tugl-KD_PGCOE_1_IC | PGCOE |
| SA172708 | Tugl-KD_PGCOE_3_IC | PGCOE |
| SA172709 | Tugl-KD_PGCOE_2_IC | PGCOE |
| SA172710 | PLKO_2_IC | PLKO |
| SA172711 | PLKO_3_IC | PLKO |
| SA172712 | PLKO_1_IC | PLKO |
| SA172713 | PLKO_1_Hilic | PLKO |
| SA172714 | PLKO_3_Hilic | PLKO |
| SA172715 | PLKO_2_Hilic | PLKO |
| SA172716 | Tugl-KD_1_Hilic | Tug1-KD |
| SA172717 | Tugl-KD_2_Hilic | Tug1-KD |
| SA172718 | Tugl-KD_3_IC | Tug1-KD |
| SA172719 | Tugl-KD_3_Hilic | Tug1-KD |
| SA172720 | Tugl-KD_1_IC | Tug1-KD |
| SA172721 | Tugl-KD_2_IC | Tug1-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 |
