Summary of study ST001303

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 PR000884. The data can be accessed directly via it's Project DOI: 10.21228/M8DX2P 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.

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Study IDST001303
Study TitleTGF-Beta 3 heterozygous mice
Study TypeMice nephropathy in lipotoxic model
Study SummaryTransforming growth factor β (TGFβ) family comprises the main player in the development of fibrosis including three isoforms: TGFβ1, TGFβ2 and TGFβ3. TGFβ3 may play an antifibrotic role at the renal level, counteracting the role of TGFβ1, using a mouse model heterozygous for the TGFβ3 gene (TGFβ3+/-). Partial deletion of TGFβ3 causes in the mice albuminuria, loss of glomerular filtration rate, accelerated fibrosis, epithelial-to-mesenchymal transition and increment of glomerular basement membrane thickening.
Institute
University Rey Juan Carlos
DepartmentBasics Science of Health
Last NameLanzon
First NameBorja
AddressAvenida de Atenas S/N
Emailborja.lanzon@urjc.es
Phone663692554
Submit Date2019-12-19
Num Groups2
Total Subjects14
Num Males14
Raw Data AvailableYes
Raw Data File Type(s).cd, .cg
Analysis Type DetailGC/LC-MS
Release Date2020-03-03
Release Version1
Borja Lanzon Borja Lanzon
https://dx.doi.org/10.21228/M8DX2P
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR000884
Project DOI:doi: 10.21228/M8DX2P
Project Title:TGFβ3 heterozygous mice
Project Type:Mice nephropathy in lipotoxic model
Project Summary:Transforming growth factor β (TGFβ) family comprises the main player in the development of fibrosis including three isoforms: TGFβ1, TGFβ2 and TGFβ3. TGFβ3 may play an antifibrotic role at the renal level, counteracting the role of TGFβ1, using a mouse model heterozygous for the TGFβ3 gene (TGFβ3+/-). Partial deletion of TGFβ3 causes in the mice albuminuria, loss of glomerular filtration rate, accelerated fibrosis, epithelial-to-mesenchymal transition and increment of glomerular basement membrane thickening.
Institute:University Rey Juan Carlos
Department:Basics Science of Health
Last Name:Lanzon
First Name:Borja
Address:Avenida de Atenas S/N, Alcorcón, Madrid, 28922, Spain
Email:borja.lanzon@urjc.es
Phone:663692554

Subject:

Subject ID:SU001377
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:c57bl6
Age Or Age Range:16 weeks
Gender:Male

Factors:

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

mb_sample_id local_sample_id Genotype
SA09433098 HZCDHZCD
SA094331269 HZCDHZCD
SA094332127 HZCDHZCD
SA09433325 HZCDHZCD
SA094334119 HZCDHZCD
SA094335130 HZCDHZCD
SA094336267 HZCDHZCD
SA094337QC2QC
SA094338QC3QC
SA094339QC5QC
SA094340QC1QC
SA094341QC4QC
SA094342120 WTCDWTCD
SA094343251 WTCDWTCD
SA094344132 WTCDWTCD
SA09434579 WTCDWTCD
SA094346129 WTCDWTCD
SA094347128 WTCDWTCD
SA09434892 WTCDWTCD
Showing results 1 to 19 of 19

Collection:

Collection ID:CO001372
Collection Summary:Kidney samples were powdered with mortar and pestle. Method used for extraction was previously validated for tissue
Sample Type:Kidney
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001392
Treatment Summary:Kidney homogenate was prepared by adding cold (−20 °C) methanol/water (1:1, v/v), (1:10 tissue/solvent). Tissue disruption was achieved with Tissue- Lyser LT homogenizer (Qiagen, Germany) for metabolite extraction.

Sample Preparation:

Sampleprep ID:SP001385
Sampleprep Summary:100 μL of kidney tissue homogenate was vortex-mixed with 320 μL of methanol for 2 min, followed by the addition of 80 μL of MTBE for the extraction of nonpolar compounds. Then, vials were rapidly capped and placed on a shaker for 1 h at room temperature. The extracted samples were centrifuged at 4000g for 20 min at 20 °C. For GC−MS analysis, 300 μL of supernatant was evaporated to dryness (SpeedVac Concentrator System, Thermo Fisher Scientific, Waltham, MA). Methoxymation was then performed with 20 μL of O-methoxyamine hydrochloride (15 mg/mL in pyridine) and vigorously vortex-mixed for 5 min. Vials were then incubated in darkness at room temperature for 16 h. For silylation, 20 μL of BSTFA/TMCS (99:1) was added and vortex-mixed for 5 min, and capped vials were placed in the oven at 70 °C for 1 h. Finally, 100 μL of heptane containing tricosane (20 ppm) as internal standard (IS) was added to each vial prior to injection. For LC−MS analysis, 90 μL of supernatant was transferred to an ultra-high-performance liquid chromatography−mass spectrometry.
Processing Storage Conditions:On ice
Extract Storage:-80℃

Combined analysis:

Analysis ID AN002169 AN002170 AN002171
Analysis type MS MS MS
Chromatography type Reversed phase Reversed phase GC
Chromatography system Agilent 1290 Infinity II Agilent 1290 Infinity II Agilent 7890B
Column Poroshell 120 EC-C8 (100 x 2.1mm, 2.5um) Poroshell 120 EC-C8 (100 x 2.1mm, 2.5um) Agilent DB5-MS (30m x 0.25mm, 0.25um)
MS Type ESI ESI EI
MS instrument type QTOF QTOF GC QTOF
MS instrument name Agilent 6545 Agilent 6545 Agilent 7890A
Ion Mode POSITIVE NEGATIVE POSITIVE
Units Area Area Area

Chromatography:

Chromatography ID:CH001587
Chromatography Summary:LC-MS (+)
Instrument Name:Agilent 1290 Infinity II
Column Name:Poroshell 120 EC-C8 (100 x 2.1mm, 2.5um)
Chromatography Type:Reversed phase
  
Chromatography ID:CH001588
Chromatography Summary:LC-MS (-)
Instrument Name:Agilent 1290 Infinity II
Column Name:Poroshell 120 EC-C8 (100 x 2.1mm, 2.5um)
Chromatography Type:Reversed phase
  
Chromatography ID:CH001589
Chromatography Summary:GC-MS
Instrument Name:Agilent 7890B
Column Name:Agilent DB5-MS (30m x 0.25mm, 0.25um)
Chromatography Type:GC

MS:

MS ID:MS002018
Analysis ID:AN002169
Instrument Name:Agilent 6545
Instrument Type:QTOF
MS Type:ESI
MS Comments:A UHPLC system (1290 Infinity UHPLC system, Agilent Technologies, Waldbronn, Germany), consisting of two degassers, two binary pumps, and a thermostated autosampler (maintained at 4°C) coupled with 6545 QTOF MS detector, was used in positive and negative ESI modes. In brief, 1 μL of each sample was injected into a reverse-phase Zorbax Eclipse Plus C8 column, 2.1 × 150 mm; 1.8 μm (Agilent Technologies) thermostated at 60°C. The gradient used for the analysis consisted of a mobile phase A (10 mM ammonium formate in Milli-Q water) and mobile phase B (10 mM ammonium formate in methanol:isopropanol, 85:15) pumped at 0.5 mL/min. The chromatography gradient started at 82% phase B, increasing to 90% B in 17 min. The gradient then increased to 100% B by minute 18 and was maintained for 2 minutes until 20 min. The starting condition was returned to by 21.5 min, followed by an 8.5 min reequilibration time, taking the total run time to 30 min. Data were collected in full scan mode from 100 to 1200 m/z, with a scan rate of 1.02 scans/s. The capillary voltage was set to 3500 V; the drying gas flow rate was 12 L/min at 290°C and gas nebulizer 45 psi, fragmentor voltage 175 V, and octopole radio frequency voltage (OCT RF Vpp) 750 V. Two reference masses were used over the course of the whole analysis: m/z 121.0509 (protonated purine) and m/z 922.0098 (protonated hexakis, (1H,1H,3H-tetrafluoropropoxy)phosphazine (HP-921)). These masses were continuously infused into the system to provide constant mass correction. Samples were randomly analyzed throughout the run.
Ion Mode:POSITIVE
  
MS ID:MS002019
Analysis ID:AN002170
Instrument Name:Agilent 6545
Instrument Type:QTOF
MS Type:ESI
MS Comments:A UHPLC system (1290 Infinity UHPLC system, Agilent Technologies, Waldbronn, Germany), consisting of two degassers, two binary pumps, and a thermostated autosampler (maintained at 4°C) coupled with 6545 QTOF MS detector, was used in positive and negative ESI modes. In brief, 1 μL of each sample was injected into a reverse-phase Zorbax Eclipse Plus C8 column, 2.1 × 150 mm; 1.8 μm (Agilent Technologies) thermostated at 60°C. The gradient used for the analysis consisted of a mobile phase A (0.1% formic acid in Milli-Q water) and mobile phase B (0.1% formic acid in methanol:isopropanol, 85:15) pumped at 0.5 mL/min. The chromatography gradient started at 82% phase B, increasing to 90% B in 17 min. The gradient then increased to 100% B by minute 18 and was maintained for 2 minutes until 20 min. The starting condition was returned to by 21.5 min, followed by an 8.5 min reequilibration time, taking the total run time to 30 min. Data were collected in full scan mode from 100 to 1000 m/z for the negative modes, with a scan rate of 1.02 scans/s. The capillary voltage was set to 3000 V; the drying gas flow rate was 12 L/min at 290°C and gas nebulizer 45 psi, fragmentor voltage 175 V, and octopole radio frequency voltage (OCT RF Vpp) 750 V. Two reference masses were used over the course of the whole analysis: m/z 112.9856 (proton-abstracted TFA anion) and m/z 966.0007 (formate adduct of HP921) for the negative mode. These masses were continuously infused into the system to provide constant mass correction. Samples were randomly analyzed throughout the run.
Ion Mode:NEGATIVE
  
MS ID:MS002020
Analysis ID:AN002171
Instrument Name:Agilent 7890A
Instrument Type:GC QTOF
MS Type:EI
MS Comments:An Agilent GC instrument (7890A) coupled to an inert mass spectrometer with triple-Axis detector (5975C, Agilent Technologies) was used for kidney tissue fingerprinting. Briefly, 1 μL of derivatized samples were injected by an Agilent autosampler (7693). Samples were automatically injected in split mode (split ratio 1:12), into an Agilent ultra-inert deactivated glass wool split liner. Compound separation was achieved using a pre-column (10 m J&W integrated with Agilent 122-5532G) combined with a GC column DB5-MS (length, 30m; inner diameter, 0.25 mm; and 0.25 μm film of 95% dimethyl/5% diphenylpolysiloxane). The flow rate of helium carrier gas was constant at : 0.938 mL/min through the column. The lock of the retention time (RTL) relative to the internal standard (methyl stearate) peak at 19.66 minutes was performed. The column oven temperature was initially set at 60°C (maintained for 1 minute), then raised by 10°C/min until it reached 325°C, and then was held at this temperature for 10 minutes before cooling down. The injector and the transfer line temperatures were established at 250°C and 280°C, respectively. MS system: the electron impact ionization operating parameters were set as follows: filament source temperature, 230°C; electron ionization energy, 70 eV. Mass spectra were collected over a mass range of 50-600 m/z at a scan rate of 10 spectra/s. Data were acquired using the Agilent MSD ChemStation Software (Agilent Technologies). For retention index determination, a mixture of n-alkanes (C8-C28) dissolved in nhexane was run prior to the samples. Data were acquired using Agilent MSD ChemStation Software (Agilent Technologies).
Ion Mode:POSITIVE
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